2024-04-12 07:58
ftp://ftp.de.debian.org/debian/pool/main/r/relion/relion_3.1.3.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=openmp --library=boost --library=zlib  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j4
platform: Linux-6.1.0-18-amd64-x86_64-with-glibc2.36
python: 3.11.2
client-version: 1.3.56
compiler: g++ (Debian 12.2.0-14) 12.2.0
cppcheck: head 2.13.0
head-info: 686e28d (2024-04-12 06:02:30 +0200)
count: 2383 1361
elapsed-time: 55.9 119.1
head-timing-info:

old-timing-info:

head results:
relion-3.1.3/cmake/TestX86.c:6:0: error: #error This is not x86 [preprocessorErrorDirective]
relion-3.1.3/src/Healpix_2.15a/cxxutils.cc:38:0: error: #error your C++ compiler is too old. g++ version 3.0 or higher is required. [preprocessorErrorDirective]
relion-3.1.3/src/apps/Zernike_test.cpp:16:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/align_symmetry.cpp:48:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/align_symmetry.cpp:72:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEAREST_NEIGHBOUR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/align_symmetry.cpp:94:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/align_symmetry.cpp:138:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/align_symmetry.cpp:282:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:49:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ctab [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:73:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable twothird [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:88:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:129:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:140:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:149:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:229:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:263:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:273:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scheme_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:298:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:306:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:325:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:353:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:371:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable twopi [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:462:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scheme_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:536:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fact2_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:586:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scheme_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:638:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scheme_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:684:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:722:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable twopi [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:778:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npix_ [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:784:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pi [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/align_symmetry.cpp:279:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/CPlot2D.h:183:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/CPlot2D.h:197:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/CPlot2D.h:212:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/CPlot2D.h:226:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/CPlot2D.cpp:60:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/CPlot2D.cpp:252:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/align_symmetry.cpp:55:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/autopick.cpp:61:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/autopick.cpp:58:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/autopick_mpi.cpp:51:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/autopick_mpi.cpp:56:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/convert_star.cpp:36:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/convert_star.cpp:61:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_METADATA_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/convert_star.cpp:129:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/convert_star.cpp:127:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/convert_star.cpp:43:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/convert_to_tiff.cpp:35:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/convert_to_tiff.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:30:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/convert_to_tiff_mpi.cpp:41:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/ctf_mask_test.cpp:48:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/ctf_mask_test.cpp:46:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/ctf_mask_test.cpp:24:12: style: The scope of the variable 'threads' can be reduced. [variableScope]
relion-3.1.3/src/apps/ctf_mask_test.cpp:25:9: style: The scope of the variable 'rad' can be reduced. [variableScope]
relion-3.1.3/src/apps/ctf_nyquist_test.cpp:59:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/ctf_nyquist_test.cpp:57:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/ctf_nyquist_test.cpp:125:11: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/ctf_refine.cpp:36:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/ctf_refine.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/ctf_refine_mpi.cpp:33:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/ctf_refine_mpi.cpp:36:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/ctf_toolbox.cpp:50:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/ctf_toolbox.cpp:100:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/ctf_toolbox.cpp:231:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/defocus_stats.cpp:17:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_FAILURE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/ctf_toolbox.cpp:228:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/ctf_toolbox.cpp:45:6: style: class member 'ctf_toolbox_parameters::xdim' is never used. [unusedStructMember]
relion-3.1.3/src/apps/ctf_toolbox.cpp:45:12: style: class member 'ctf_toolbox_parameters::ydim' is never used. [unusedStructMember]
relion-3.1.3/src/apps/ctf_toolbox.cpp:45:18: style: class member 'ctf_toolbox_parameters::zdim' is never used. [unusedStructMember]
relion-3.1.3/src/apps/ctf_toolbox.cpp:46:11: style: class member 'ctf_toolbox_parameters::ndim' is never used. [unusedStructMember]
relion-3.1.3/src/apps/ctf_toolbox.cpp:58:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/ctf_toolbox.cpp:62:19: style: Variable 'sim_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/ctf_toolbox.cpp:76:19: style: Variable 'cst_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/display.cpp:54:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_cXAxisLabelFormat' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_cYAxisLabelFormat' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_iXAxisNumberOfLabels' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_iYAxisNumberOfLabels' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dXScale' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dYScale' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dMaxXExtent' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dMaxYExtent' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dMinXStartPoint' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dMinYStartPoint' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dMaxXEndPoint' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dMaxYEndPoint' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.cpp:79:10: warning: Member variable 'CPlot2D::m_dTickMarkLength' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/CPlot2D.h:129:10: performance: Variable 'm_strMarker' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
relion-3.1.3/src/CPlot2D.h:135:10: performance: Variable 'm_iDashedLinePattern' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
relion-3.1.3/src/CPlot2D.h:136:10: performance: Variable 'm_strDatasetTitle' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
relion-3.1.3/src/CPlot2D.h:137:10: performance: Variable 'm_strDatasetLegendFont' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
relion-3.1.3/src/CPlot2D.h:87:11: style:inconclusive: Technically the member function 'CDataPoint::GetValues' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:94:13: style:inconclusive: Technically the member function 'CDataPoint::GetX' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:100:13: style:inconclusive: Technically the member function 'CDataPoint::GetY' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:159:17: style:inconclusive: Technically the member function 'CDataSet::GetDataPoint' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:174:10: style:inconclusive: Technically the member function 'CDataSet::GetNumberOfDataPointsInSet' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:264:13: style:inconclusive: Technically the member function 'CDataSet::GetLineWidth' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:282:11: style:inconclusive: Technically the member function 'CDataSet::GetDatasetColor' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:334:18: style:inconclusive: Technically the member function 'CDataSet::GetMarkerSymbol' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:342:13: style:inconclusive: Technically the member function 'CDataSet::GetMarkerSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:351:11: style:inconclusive: Technically the member function 'CDataSet::GetDrawLine' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:360:11: style:inconclusive: Technically the member function 'CDataSet::GetDrawMarker' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:369:11: style:inconclusive: Technically the member function 'CDataSet::GetDrawMarkerFilled' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:388:18: style:inconclusive: Technically the member function 'CDataSet::GetDashedLinePattern' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:406:11: style:inconclusive: Technically the member function 'CDataSet::GetDashedLine' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:424:18: style:inconclusive: Technically the member function 'CDataSet::GetDatasetTitle' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:442:18: style:inconclusive: Technically the member function 'CDataSet::GetDatasetLegendFont' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:503:13: style:inconclusive: Technically the member function 'CPlot2D::GetXTotalSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1108:25: note: Technically the member function 'CPlot2D::GetXTotalSize' can be const.
relion-3.1.3/src/CPlot2D.h:503:13: note: Technically the member function 'CPlot2D::GetXTotalSize' can be const.
relion-3.1.3/src/CPlot2D.h:513:13: style:inconclusive: Technically the member function 'CPlot2D::GetYTotalSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1113:25: note: Technically the member function 'CPlot2D::GetYTotalSize' can be const.
relion-3.1.3/src/CPlot2D.h:513:13: note: Technically the member function 'CPlot2D::GetYTotalSize' can be const.
relion-3.1.3/src/CPlot2D.h:523:13: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1118:25: note: Technically the member function 'CPlot2D::GetXAxisSize' can be const.
relion-3.1.3/src/CPlot2D.h:523:13: note: Technically the member function 'CPlot2D::GetXAxisSize' can be const.
relion-3.1.3/src/CPlot2D.h:533:13: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1123:25: note: Technically the member function 'CPlot2D::GetYAxisSize' can be const.
relion-3.1.3/src/CPlot2D.h:533:13: note: Technically the member function 'CPlot2D::GetYAxisSize' can be const.
relion-3.1.3/src/CPlot2D.h:545:13: style:inconclusive: Technically the member function 'CPlot2D::GetBottomFrameSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1128:25: note: Technically the member function 'CPlot2D::GetBottomFrameSize' can be const.
relion-3.1.3/src/CPlot2D.h:545:13: note: Technically the member function 'CPlot2D::GetBottomFrameSize' can be const.
relion-3.1.3/src/CPlot2D.h:557:13: style:inconclusive: Technically the member function 'CPlot2D::GetRightFrameSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1133:25: note: Technically the member function 'CPlot2D::GetRightFrameSize' can be const.
relion-3.1.3/src/CPlot2D.h:557:13: note: Technically the member function 'CPlot2D::GetRightFrameSize' can be const.
relion-3.1.3/src/CPlot2D.h:569:13: style:inconclusive: Technically the member function 'CPlot2D::GetTopFrameSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1138:25: note: Technically the member function 'CPlot2D::GetTopFrameSize' can be const.
relion-3.1.3/src/CPlot2D.h:569:13: note: Technically the member function 'CPlot2D::GetTopFrameSize' can be const.
relion-3.1.3/src/CPlot2D.h:581:13: style:inconclusive: Technically the member function 'CPlot2D::GetLeftFrameSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1143:25: note: Technically the member function 'CPlot2D::GetLeftFrameSize' can be const.
relion-3.1.3/src/CPlot2D.h:581:13: note: Technically the member function 'CPlot2D::GetLeftFrameSize' can be const.
relion-3.1.3/src/CPlot2D.h:591:13: style:inconclusive: Technically the member function 'CPlot2D::GetFrameLineWidth' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1153:25: note: Technically the member function 'CPlot2D::GetFrameLineWidth' can be const.
relion-3.1.3/src/CPlot2D.h:591:13: note: Technically the member function 'CPlot2D::GetFrameLineWidth' can be const.
relion-3.1.3/src/CPlot2D.h:601:13: style:inconclusive: Technically the member function 'CPlot2D::GetGridLineWidth' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1163:25: note: Technically the member function 'CPlot2D::GetGridLineWidth' can be const.
relion-3.1.3/src/CPlot2D.h:601:13: note: Technically the member function 'CPlot2D::GetGridLineWidth' can be const.
relion-3.1.3/src/CPlot2D.h:611:11: style:inconclusive: Technically the member function 'CPlot2D::GetFrameColor' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1175:23: note: Technically the member function 'CPlot2D::GetFrameColor' can be const.
relion-3.1.3/src/CPlot2D.h:611:11: note: Technically the member function 'CPlot2D::GetFrameColor' can be const.
relion-3.1.3/src/CPlot2D.h:621:11: style:inconclusive: Technically the member function 'CPlot2D::GetGridColor' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1189:23: note: Technically the member function 'CPlot2D::GetGridColor' can be const.
relion-3.1.3/src/CPlot2D.h:621:11: note: Technically the member function 'CPlot2D::GetGridColor' can be const.
relion-3.1.3/src/CPlot2D.h:631:13: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisNumbersSpacing' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1243:25: note: Technically the member function 'CPlot2D::GetXAxisNumbersSpacing' can be const.
relion-3.1.3/src/CPlot2D.h:631:13: note: Technically the member function 'CPlot2D::GetXAxisNumbersSpacing' can be const.
relion-3.1.3/src/CPlot2D.h:641:13: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisNumbersSpacing' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1247:25: note: Technically the member function 'CPlot2D::GetYAxisNumbersSpacing' can be const.
relion-3.1.3/src/CPlot2D.h:641:13: note: Technically the member function 'CPlot2D::GetYAxisNumbersSpacing' can be const.
relion-3.1.3/src/CPlot2D.h:651:11: style:inconclusive: Technically the member function 'CPlot2D::GetDrawXAxisTickMarks' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1251:23: note: Technically the member function 'CPlot2D::GetDrawXAxisTickMarks' can be const.
relion-3.1.3/src/CPlot2D.h:651:11: note: Technically the member function 'CPlot2D::GetDrawXAxisTickMarks' can be const.
relion-3.1.3/src/CPlot2D.h:661:11: style:inconclusive: Technically the member function 'CPlot2D::GetDrawYAxisTickMarks' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1255:23: note: Technically the member function 'CPlot2D::GetDrawYAxisTickMarks' can be const.
relion-3.1.3/src/CPlot2D.h:661:11: note: Technically the member function 'CPlot2D::GetDrawYAxisTickMarks' can be const.
relion-3.1.3/src/CPlot2D.h:671:10: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisNumberOfTicks' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1260:22: note: Technically the member function 'CPlot2D::GetXAxisNumberOfTicks' can be const.
relion-3.1.3/src/CPlot2D.h:671:10: note: Technically the member function 'CPlot2D::GetXAxisNumberOfTicks' can be const.
relion-3.1.3/src/CPlot2D.h:681:10: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisNumberOfTicks' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1265:22: note: Technically the member function 'CPlot2D::GetYAxisNumberOfTicks' can be const.
relion-3.1.3/src/CPlot2D.h:681:10: note: Technically the member function 'CPlot2D::GetYAxisNumberOfTicks' can be const.
relion-3.1.3/src/CPlot2D.h:691:11: style:inconclusive: Technically the member function 'CPlot2D::GetDrawXAxisGridLines' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1270:23: note: Technically the member function 'CPlot2D::GetDrawXAxisGridLines' can be const.
relion-3.1.3/src/CPlot2D.h:691:11: note: Technically the member function 'CPlot2D::GetDrawXAxisGridLines' can be const.
relion-3.1.3/src/CPlot2D.h:701:11: style:inconclusive: Technically the member function 'CPlot2D::GetDrawYAxisGridLines' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1275:23: note: Technically the member function 'CPlot2D::GetDrawYAxisGridLines' can be const.
relion-3.1.3/src/CPlot2D.h:701:11: note: Technically the member function 'CPlot2D::GetDrawYAxisGridLines' can be const.
relion-3.1.3/src/CPlot2D.h:711:11: style:inconclusive: Technically the member function 'CPlot2D::GetDrawGridLinesDashed' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1280:23: note: Technically the member function 'CPlot2D::GetDrawGridLinesDashed' can be const.
relion-3.1.3/src/CPlot2D.h:711:11: note: Technically the member function 'CPlot2D::GetDrawGridLinesDashed' can be const.
relion-3.1.3/src/CPlot2D.h:721:18: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisLabelFont' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1290:30: note: Technically the member function 'CPlot2D::GetXAxisLabelFont' can be const.
relion-3.1.3/src/CPlot2D.h:721:18: note: Technically the member function 'CPlot2D::GetXAxisLabelFont' can be const.
relion-3.1.3/src/CPlot2D.h:731:13: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisLabelFontSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1300:25: note: Technically the member function 'CPlot2D::GetXAxisLabelFontSize' can be const.
relion-3.1.3/src/CPlot2D.h:731:13: note: Technically the member function 'CPlot2D::GetXAxisLabelFontSize' can be const.
relion-3.1.3/src/CPlot2D.h:741:18: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisLabelFont' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1310:30: note: Technically the member function 'CPlot2D::GetYAxisLabelFont' can be const.
relion-3.1.3/src/CPlot2D.h:741:18: note: Technically the member function 'CPlot2D::GetYAxisLabelFont' can be const.
relion-3.1.3/src/CPlot2D.h:751:13: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisLabelFontSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1320:25: note: Technically the member function 'CPlot2D::GetYAxisLabelFontSize' can be const.
relion-3.1.3/src/CPlot2D.h:751:13: note: Technically the member function 'CPlot2D::GetYAxisLabelFontSize' can be const.
relion-3.1.3/src/CPlot2D.h:761:18: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisTitleFont' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1330:30: note: Technically the member function 'CPlot2D::GetXAxisTitleFont' can be const.
relion-3.1.3/src/CPlot2D.h:761:18: note: Technically the member function 'CPlot2D::GetXAxisTitleFont' can be const.
relion-3.1.3/src/CPlot2D.h:771:13: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisTitleFontSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1340:25: note: Technically the member function 'CPlot2D::GetXAxisTitleFontSize' can be const.
relion-3.1.3/src/CPlot2D.h:771:13: note: Technically the member function 'CPlot2D::GetXAxisTitleFontSize' can be const.
relion-3.1.3/src/CPlot2D.h:781:18: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisTitleFont' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1350:30: note: Technically the member function 'CPlot2D::GetYAxisTitleFont' can be const.
relion-3.1.3/src/CPlot2D.h:781:18: note: Technically the member function 'CPlot2D::GetYAxisTitleFont' can be const.
relion-3.1.3/src/CPlot2D.h:791:13: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisTitleFontSize' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1360:25: note: Technically the member function 'CPlot2D::GetYAxisTitleFontSize' can be const.
relion-3.1.3/src/CPlot2D.h:791:13: note: Technically the member function 'CPlot2D::GetYAxisTitleFontSize' can be const.
relion-3.1.3/src/apps/display.cpp:51:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/CPlot2D.h:802:18: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisTitle' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1370:30: note: Technically the member function 'CPlot2D::GetXAxisTitle' can be const.
relion-3.1.3/src/CPlot2D.h:802:18: note: Technically the member function 'CPlot2D::GetXAxisTitle' can be const.
relion-3.1.3/src/CPlot2D.h:813:18: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisTitle' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1380:30: note: Technically the member function 'CPlot2D::GetYAxisTitle' can be const.
relion-3.1.3/src/CPlot2D.h:813:18: note: Technically the member function 'CPlot2D::GetYAxisTitle' can be const.
relion-3.1.3/src/CPlot2D.h:823:11: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisTitleColor' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1392:23: note: Technically the member function 'CPlot2D::GetXAxisTitleColor' can be const.
relion-3.1.3/src/CPlot2D.h:823:11: note: Technically the member function 'CPlot2D::GetXAxisTitleColor' can be const.
relion-3.1.3/src/CPlot2D.h:833:11: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisTitleColor' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1406:23: note: Technically the member function 'CPlot2D::GetYAxisTitleColor' can be const.
relion-3.1.3/src/CPlot2D.h:833:11: note: Technically the member function 'CPlot2D::GetYAxisTitleColor' can be const.
relion-3.1.3/src/CPlot2D.h:843:11: style:inconclusive: Technically the member function 'CPlot2D::GetXAxisLabelColor' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1420:23: note: Technically the member function 'CPlot2D::GetXAxisLabelColor' can be const.
relion-3.1.3/src/CPlot2D.h:843:11: note: Technically the member function 'CPlot2D::GetXAxisLabelColor' can be const.
relion-3.1.3/src/CPlot2D.h:853:11: style:inconclusive: Technically the member function 'CPlot2D::GetYAxisLabelColor' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1434:23: note: Technically the member function 'CPlot2D::GetYAxisLabelColor' can be const.
relion-3.1.3/src/CPlot2D.h:853:11: note: Technically the member function 'CPlot2D::GetYAxisLabelColor' can be const.
relion-3.1.3/src/CPlot2D.h:863:11: style:inconclusive: Technically the member function 'CPlot2D::GetDrawLegend' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1446:23: note: Technically the member function 'CPlot2D::GetDrawLegend' can be const.
relion-3.1.3/src/CPlot2D.h:863:11: note: Technically the member function 'CPlot2D::GetDrawLegend' can be const.
relion-3.1.3/src/CPlot2D.h:868:11: style:inconclusive: Technically the member function 'CPlot2D::GetFlipY' can be const. [functionConst]
relion-3.1.3/src/CPlot2D.h:1456:23: note: Technically the member function 'CPlot2D::GetFlipY' can be const.
relion-3.1.3/src/CPlot2D.h:868:11: note: Technically the member function 'CPlot2D::GetFlipY' can be const.
relion-3.1.3/src/CPlot2D.h:914:13: performance:inconclusive: Technically the member function 'CPlot2D::NiceNum' can be static (but you may consider moving to unnamed namespace). [functionStatic]
relion-3.1.3/src/CPlot2D.cpp:761:17: note: Technically the member function 'CPlot2D::NiceNum' can be static (but you may consider moving to unnamed namespace).
relion-3.1.3/src/CPlot2D.h:914:13: note: Technically the member function 'CPlot2D::NiceNum' can be static (but you may consider moving to unnamed namespace).
relion-3.1.3/src/CPlot2D.h:481:6: style: Class 'CPlot2D' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/CPlot2D.h:334:18: performance: Function 'GetMarkerSymbol()' should return member 'm_strMarker' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:388:18: performance: Function 'GetDashedLinePattern()' should return member 'm_iDashedLinePattern' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:424:18: performance: Function 'GetDatasetTitle()' should return member 'm_strDatasetTitle' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:442:18: performance: Function 'GetDatasetLegendFont()' should return member 'm_strDatasetLegendFont' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:721:18: performance: Function 'GetXAxisLabelFont()' should return member 'm_strXAxisLabelFont' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:741:18: performance: Function 'GetYAxisLabelFont()' should return member 'm_strYAxisLabelFont' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:761:18: performance: Function 'GetXAxisTitleFont()' should return member 'm_strXAxisTitleFont' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:781:18: performance: Function 'GetYAxisTitleFont()' should return member 'm_strYAxisTitleFont' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:802:18: performance: Function 'GetXAxisTitle()' should return member 'm_strXAxisTitle' by const reference. [returnByReference]
relion-3.1.3/src/CPlot2D.h:813:18: performance: Function 'GetYAxisTitle()' should return member 'm_strYAxisTitle' by const reference. [returnByReference]
relion-3.1.3/src/apps/demodulate.cpp:28:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_FAILURE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/CPlot2D.cpp:804:12: style: The scope of the variable 'labelXCoordinate' can be reduced. [variableScope]
relion-3.1.3/src/CPlot2D.cpp:804:29: style: The scope of the variable 'labelYCoordinate' can be reduced. [variableScope]
relion-3.1.3/src/CPlot2D.cpp:826:12: style: The scope of the variable 'labelXCoordinate' can be reduced. [variableScope]
relion-3.1.3/src/CPlot2D.cpp:826:29: style: The scope of the variable 'labelYCoordinate' can be reduced. [variableScope]
relion-3.1.3/src/CPlot2D.h:292:39: performance: Function parameter 'symbol' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:379:44: performance: Function parameter 'pattern' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:415:39: performance: Function parameter 'title' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:433:44: performance: Function parameter 'font' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:1063:44: performance: Function parameter 'title' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:1285:53: performance: Function parameter 'font' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:1305:53: performance: Function parameter 'font' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:1325:53: performance: Function parameter 'font' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:1345:53: performance: Function parameter 'font' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:1365:49: performance: Function parameter 'title' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.h:1375:49: performance: Function parameter 'title' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.cpp:79:30: performance: Function parameter 'title' should be passed by const reference. However it seems that 'CPlot2D' is a callback function. [passedByValueCallback]
relion-3.1.3/src/CPlot2D.h:473:8: note: Function pointer used here.
relion-3.1.3/src/CPlot2D.cpp:79:30: note: Function parameter 'title' should be passed by const reference. However it seems that 'CPlot2D' is a callback function.
relion-3.1.3/src/CPlot2D.cpp:155:48: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.cpp:483:46: performance: Function parameter 'xValues' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.cpp:483:75: performance: Function parameter 'yValues' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.cpp:508:46: performance: Function parameter 'yValues' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.cpp:528:38: performance: Function parameter 'symbol' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.cpp:716:152: performance: Function parameter 'axis' should be passed by const reference. [passedByValue]
relion-3.1.3/src/CPlot2D.cpp:473:49: style: Parameter 'xValues' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/CPlot2D.cpp:473:66: style: Parameter 'yValues' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/apps/double_bfac_fit.cpp:33:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_FAILURE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/demodulate.cpp:30:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/demodulate.cpp:85:16: style: Local variable 'command' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/demodulate.cpp:42:14: note: Shadowed declaration
relion-3.1.3/src/apps/demodulate.cpp:85:16: note: Shadow variable
relion-3.1.3/src/apps/demodulate.cpp:86:8: style: Local variable 'res' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/demodulate.cpp:43:6: note: Shadowed declaration
relion-3.1.3/src/apps/demodulate.cpp:86:8: note: Shadow variable
relion-3.1.3/src/apps/demodulate.cpp:43:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/demodulate.cpp:53:40: style: Variable 'fts' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/demodulate.cpp:86:12: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/double_bfac_fit.cpp:122:10: style: Local variable 's' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/double_bfac_fit.cpp:63:12: note: Shadowed declaration
relion-3.1.3/src/apps/double_bfac_fit.cpp:122:10: note: Shadow variable
relion-3.1.3/src/apps/double_bfac_fit.cpp:148:10: style: Local variable 's' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/double_bfac_fit.cpp:63:12: note: Shadowed declaration
relion-3.1.3/src/apps/double_bfac_fit.cpp:148:10: note: Shadow variable
relion-3.1.3/src/apps/double_bfac_fit.cpp:63:14: style: Variable 's' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/estimate_gain.cpp:80:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/external_reconstruct.cpp:63:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_OPTIMISER_EXTERNAL_RECONS_DATA_REAL [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/estimate_gain.cpp:255:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/external_reconstruct.cpp:90:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRILINEAR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/external_reconstruct.cpp:133:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/external_reconstruct.cpp:131:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/external_reconstruct.cpp:52:12: style: Local variable 'fn_star' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/external_reconstruct.cpp:37:14: note: Shadowed declaration
relion-3.1.3/src/apps/external_reconstruct.cpp:52:12: note: Shadow variable
relion-3.1.3/src/apps/external_reconstruct.cpp:42:9: style: class member 'ext_recons_parameters::verb' is never used. [unusedStructMember]
relion-3.1.3/src/apps/estimate_gain.cpp:253:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/estimate_gain.cpp:49:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:67:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:116:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEAREST_NEIGHBOUR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:188:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:294:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:720:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/flex_analyse.cpp:37:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/flex_analyse.cpp:35:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/flex_analyse_mpi.cpp:31:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/flex_analyse_mpi.cpp:46:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/find_tiltpairs.cpp:51:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/find_tiltpairs.cpp:123:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/find_tiltpairs.cpp:186:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/find_tiltpairs.cpp:379:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/find_tiltpairs.cpp:403:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/find_tiltpairs.cpp:484:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/helix_inimodel2d.cpp:38:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::nr_iter' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::nr_classes' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::angpix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::random_seed' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::mask_diameter' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::mask_radius_pix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::maxres' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::search_size' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::crossover_distance' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::height' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::max_smear' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::max_shift' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::extract_width' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::do_only_make_3d' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::symmetry' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::nr_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::ori_size' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::down_size' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::xrect' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::yrect' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::ximg' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::down_angpix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/helix_inimodel2d.h:182:2: warning: Member variable 'HelixAligner::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_inimodel2d.cpp:35:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:78:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:108:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:942:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:875:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:234:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:240:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:368:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:417:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:1099:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/find_tiltpairs.cpp:482:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/find_tiltpairs.cpp:281:15: style: Local variable 'rot' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/find_tiltpairs.cpp:35:9: note: Shadowed declaration
relion-3.1.3/src/apps/find_tiltpairs.cpp:281:15: note: Shadow variable
relion-3.1.3/src/apps/find_tiltpairs.cpp:283:16: style: Local variable 'tilt' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/find_tiltpairs.cpp:34:9: note: Shadowed declaration
relion-3.1.3/src/apps/find_tiltpairs.cpp:283:16: note: Shadow variable
relion-3.1.3/src/apps/find_tiltpairs.cpp:268:36: style: Unused variable: best_map [unusedVariable]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:354:6: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:717:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:55:30: style: class member 'reconstruct_parameters::do_reconstruct_meas' is never used. [unusedStructMember]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:75:24: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:86:20: style: Variable 'ctf_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:103:24: style: Variable 'helical_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:108:23: style: Variable 'expert_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:65:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/image_handler.cpp:154:137: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BLACKGREYREDSCALE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/import.cpp:39:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/image_handler.cpp:187:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/import.cpp:98:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/image_handler.cpp:713:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/import.cpp:330:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/image_handler.cpp:1068:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/import.cpp:327:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/import.cpp:175:11: style: Local variable 'old_optics_group_number' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/import.cpp:110:8: note: Shadowed declaration
relion-3.1.3/src/apps/import.cpp:175:11: note: Shadow variable
relion-3.1.3/src/apps/import.cpp:30:7: style: class member 'import_parameters::do_write_types' is never used. [unusedStructMember]
relion-3.1.3/src/apps/import.cpp:46:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/import.cpp:58:19: style: Variable 'mic_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/interpolation_test.cpp:7:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/interpolation_test.cpp:3:26: style: Parameter 'argv' can be declared as const array [constParameter]
relion-3.1.3/src/apps/localsym.cpp:35:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/localsym.cpp:32:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/localsym_mpi.cpp:16:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/localsym_mpi.cpp:12:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/maingui.cpp:61:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable g_RELION_VERSION [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::Xdim' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::Ydim' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::boxdim' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::nr_subunits' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::nr_asu' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::sym_Cn' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::nr_filaments_helix_with_seam' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::do_center_of_mass_each_PDB_molecule' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::nr_outfiles' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::nr_tubes' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::is_3d_tomo' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::do_bimodal_searches' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::do_cut_into_segments' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::ignore_helical_symmetry' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::do_helical_symmetry_local_refinement' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::do_polar_reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::binning_factor' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::random_seed' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:222:2: warning: Member variable 'helix_bilder_parameters::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/helix_toolbox.cpp:366:7: performance:inconclusive: Technically the member function 'helix_bilder_parameters::displayEmptyLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
relion-3.1.3/src/apps/helix_toolbox.cpp:1096:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/helix_toolbox.cpp:911:13: style: Local variable 'Xdim' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/helix_toolbox.cpp:91:6: note: Shadowed declaration
relion-3.1.3/src/apps/helix_toolbox.cpp:911:13: note: Shadow variable
relion-3.1.3/src/apps/helix_toolbox.cpp:911:19: style: Local variable 'Ydim' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/helix_toolbox.cpp:91:12: note: Shadowed declaration
relion-3.1.3/src/apps/helix_toolbox.cpp:911:19: note: Shadow variable
relion-3.1.3/src/apps/maingui.cpp:98:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/helix_toolbox.cpp:256:20: style: Variable 'init_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/helix_toolbox.cpp:259:23: style: Variable 'options_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/helix_toolbox.cpp:278:27: style: Variable 'options_old_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/helix_toolbox.cpp:293:22: style: Variable 'params_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/maingui.cpp:39:8: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
relion-3.1.3/src/apps/maingui.cpp:39:8: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/manualpick.cpp:47:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/manualpick.cpp:44:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/mask_create.cpp:43:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/mask_create.cpp:99:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/mask_create.cpp:133:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/mask_create.cpp:228:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/merge_particles.cpp:9:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/mask_create.cpp:226:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/mask_create.cpp:123:42: style: Parameter 'Iout' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/apps/mask_create.cpp:130:39: style: Parameter 'Iout' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/apps/mask_create.cpp:51:22: style: Variable 'create_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/mask_create.cpp:69:22: style: Variable 'denovo_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/motion_refine.cpp:36:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/motion_refine.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/merge_particles.cpp:5:26: style: Parameter 'argv' can be declared as const array [constParameter]
relion-3.1.3/src/apps/motion_refine_mpi.cpp:33:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/motion_refine_mpi.cpp:37:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/movie_reconstruct.cpp:328:4: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/apps/mrc2vtk.cpp:8:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/mrc2vtk.cpp:4:26: style: Parameter 'argv' can be declared as const array [constParameter]
relion-3.1.3/src/apps/paper_data_synth.cpp:90:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/particle_FCC.cpp:57:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/particle_FCC.cpp:55:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/particle_FCC.cpp:27:6: style: The scope of the variable 'minMG' can be reduced. [variableScope]
relion-3.1.3/src/apps/paper_data_synth.cpp:41:17: style: Local variable 'refOut' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/paper_data_synth.cpp:23:16: note: Shadowed declaration
relion-3.1.3/src/apps/paper_data_synth.cpp:41:17: note: Shadow variable
relion-3.1.3/src/apps/particle_reposition.cpp:287:8: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/apps/particle_select.cpp:41:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/particle_subtract.cpp:48:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/particle_subtractor.h:31:1: style: The class 'ParticleSubtractor' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
relion-3.1.3/src/apps/particle_subtract.cpp:46:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/particle_subtract_mpi.cpp:32:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/particle_subtract_mpi.cpp:71:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/particle_select.cpp:13:6: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/pipeliner.cpp:46:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/pipeliner.cpp:81:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/pipeliner.cpp:166:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/particle_symmetry_expand.cpp:47:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/particle_symmetry_expand.cpp:112:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/particle_symmetry_expand.cpp:224:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/pipeliner.cpp:164:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/pipeliner.cpp:54:21: style: Variable 'check_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/pipeliner.cpp:56:19: style: Variable 'add_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/pipeliner.cpp:61:19: style: Variable 'run_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/pipeliner.cpp:69:22: style: Variable 'expert_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/plot_delocalisation.cpp:51:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/particle_symmetry_expand.cpp:221:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/particle_symmetry_expand.cpp:54:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/particle_symmetry_expand.cpp:61:23: style: Variable 'helical_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/postprocess.cpp:39:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/postprocess.cpp:36:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/plot_delocalisation.cpp:49:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/postprocess_mpi.cpp:31:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/postprocess_mpi.cpp:46:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/plot_delocalisation.cpp:24:9: style: The scope of the variable 'threads' can be reduced. [variableScope]
relion-3.1.3/src/apps/preprocess.cpp:36:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/preprocess.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/preprocess_mpi.cpp:37:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/preprocess_mpi.cpp:34:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/project.cpp:131:4: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/apps/prepare_subtomo.cpp:111:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:166:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:209:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:536:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:1111:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/reconstruct.cpp:35:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/reconstruct.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/reconstruct_mpi.cpp:37:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/reconstruct_mpi.cpp:34:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/refine.cpp:44:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/refine.cpp:41:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/refine_mpi.cpp:40:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/refine_mpi.cpp:38:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/reposition.cpp:41:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable interpolator [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/reposition.cpp:23:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/reposition.cpp:145:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/run_ctffind.cpp:36:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/run_ctffind.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/image_handler.cpp:167:70: style:inconclusive: Boolean expression 'fn_cosDPhi!=""' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
relion-3.1.3/src/apps/run_ctffind_mpi.cpp:37:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/run_ctffind_mpi.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/run_motioncorr.cpp:36:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/run_motioncorr.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:37:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/run_motioncorr_mpi.cpp:33:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/image_handler.cpp:167:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
relion-3.1.3/src/apps/image_handler.cpp:292:10: style: Condition 'is_first' is always true [knownConditionTrueFalse]
relion-3.1.3/src/apps/image_handler.cpp:287:20: note: Assignment 'is_first=true', assigned value is 1
relion-3.1.3/src/apps/image_handler.cpp:292:10: note: Condition 'is_first' is always true
relion-3.1.3/src/apps/image_handler.cpp:1065:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/scheduler.cpp:43:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/scheduler.cpp:122:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_JOB_ABORT_NOW [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/scheduler.cpp:280:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/image_handler.cpp:175:17: style: Local variable 'Iout' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:51:16: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:175:17: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:324:25: style: Local variable 'transformer' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:56:21: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:324:25: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:438:23: style: Local variable 'transformer' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:56:21: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:438:23: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:498:24: style: Local variable 'minval' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:42:9: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:498:24: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:498:32: style: Local variable 'maxval' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:42:17: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:498:32: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:718:13: style: Local variable 'fn_img' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:37:37: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:718:13: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:759:13: style: Local variable 'fn_img' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:37:37: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:759:13: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:857:25: style: Local variable 'minval' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:42:9: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:857:25: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:857:33: style: Local variable 'maxval' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:42:17: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:857:33: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:881:13: style: Local variable 'psi' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/image_handler.cpp:770:11: note: Shadowed declaration
relion-3.1.3/src/apps/image_handler.cpp:881:13: note: Shadow variable
relion-3.1.3/src/apps/image_handler.cpp:73:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:77:19: style: Variable 'cst_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:85:19: style: Variable 'img_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:95:24: style: Variable 'subtract_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:100:20: style: Variable 'four_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:132:23: style: Variable 'three_d_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:135:26: style: Variable 'preprocess_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:144:19: style: Variable 'avg_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/image_handler.cpp:150:19: style: Variable 'png_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/scheduler.cpp:278:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/split_stack.cpp:40:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:50:7: style: The scope of the variable 'c_itrans' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:65:9: style: The scope of the variable 'x' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:65:11: style: The scope of the variable 'y' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:91:6: style: The scope of the variable 'x' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:91:8: style: The scope of the variable 'y' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:91:10: style: The scope of the variable 'z' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:308:6: style: The scope of the variable 'x' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:308:8: style: The scope of the variable 'y' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:308:10: style: The scope of the variable 'z' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:308:12: style: The scope of the variable 'xp' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:308:15: style: The scope of the variable 'yp' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:308:18: style: The scope of the variable 'zp' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:308:21: style: The scope of the variable 'xy' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:269:6: style: The scope of the variable 'x' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:269:8: style: The scope of the variable 'y' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:269:10: style: The scope of the variable 'xp' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:269:13: style: The scope of the variable 'yp' can be reduced. [variableScope]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:332:16: style: Unsigned expression 'new_voxel' can't be negative so it is unnecessary to test it. [unsignedPositive]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:287:16: style: Unsigned expression 'new_pixel' can't be negative so it is unnecessary to test it. [unsignedPositive]
relion-3.1.3/src/apps/scheduler.cpp:29:8: style: class member 'scheduler_parameters::myconstant' is never used. [unusedStructMember]
relion-3.1.3/src/apps/scheduler.cpp:32:38: style: class member 'scheduler_parameters::start_node' is never used. [unusedStructMember]
relion-3.1.3/src/apps/scheduler.cpp:32:64: style: class member 'scheduler_parameters::email' is never used. [unusedStructMember]
relion-3.1.3/src/apps/scheduler.cpp:74:19: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/scheduler.cpp:78:19: style: Variable 'add_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/scheduler.cpp:90:19: style: Variable 'set_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/scheduler.cpp:96:19: style: Variable 'run_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/scheduler.cpp:150:12: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:28:11: style: Parameter 'g_pdf_orientation' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:29:9: style: Parameter 'g_pdf_orientation_zeros' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:30:11: style: Parameter 'g_pdf_offset' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:31:9: style: Parameter 'g_pdf_offset_zeros' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:36:18: style: Parameter 'd_rot_id' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:37:18: style: Parameter 'd_trans_idx' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:38:18: style: Parameter 'd_job_idx' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:39:18: style: Parameter 'd_job_num' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:120:42: style: Parameter 'vol' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:197:14: style: Parameter 'noise' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:769:27: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:796:27: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:797:7: style: Parameter 'B' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:859:11: style: Parameter 'alphas' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:917:11: style: Parameter 'alphas' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:918:11: style: Parameter 'betas' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:919:11: style: Parameter 'gammas' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:922:11: style: Parameter 'L' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:923:11: style: Parameter 'R' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/apps/stack_create.cpp:44:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/stack_create.cpp:62:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/stack_create.cpp:80:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/stack_create.cpp:278:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:49:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/tiltpair_plot.cpp:49:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:169:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/tiltpair_plot.cpp:88:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:183:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/tiltpair_plot.cpp:199:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:214:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/tiltpair_plot.cpp:258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:237:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/tiltpair_plot.cpp:314:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:258:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:267:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:369:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:689:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_object [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:839:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:846:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X_ANGSTROM [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:917:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:987:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:1006:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:1020:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:1065:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/tiltpair_plot.cpp:117:7: performance:inconclusive: Technically the member function 'tiltpair_plot_parameters::value_to_redblue_scale' can be static (but you may consider moving to unnamed namespace). [functionStatic]
relion-3.1.3/src/apps/tiltpair_plot.cpp:312:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/tiltpair_plot.cpp:56:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/stack_create.cpp:97:8: style: Condition 'is_first' is always true [knownConditionTrueFalse]
relion-3.1.3/src/apps/stack_create.cpp:93:17: note: Assignment 'is_first=true', assigned value is 1
relion-3.1.3/src/apps/stack_create.cpp:97:8: note: Condition 'is_first' is always true
relion-3.1.3/src/apps/stack_create.cpp:111:23: style: Condition 'm<fn_mics.size()' is always false [knownConditionTrueFalse]
relion-3.1.3/src/apps/stack_create.cpp:111:18: note: Assignment 'm=0', assigned value is 0
relion-3.1.3/src/apps/stack_create.cpp:111:23: note: Condition 'm<fn_mics.size()' is always false
relion-3.1.3/src/apps/stack_create.cpp:276:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/tomo_test.cpp:36:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/stack_create.cpp:230:15: style: Local variable 'fn_img' shadows outer variable [shadowVariable]
relion-3.1.3/src/apps/stack_create.cpp:87:12: note: Shadowed declaration
relion-3.1.3/src/apps/stack_create.cpp:230:15: note: Shadow variable
relion-3.1.3/src/apps/stack_create.cpp:51:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/vis_Ewald_weight.cpp:58:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/vis_Ewald_weight.cpp:56:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/vis_Ewald_weight.cpp:31:6: style: The scope of the variable 'threads' can be reduced. [variableScope]
relion-3.1.3/src/apps/vis_delocalisation.cpp:72:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/vis_delocalisation.cpp:178:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Both [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/tomo_test.cpp:18:14: style: The scope of the variable 'tomoFn' can be reduced. [variableScope]
relion-3.1.3/src/apps/tomo_test.cpp:166:32: style: Parameter 'dest' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/apps/vis_delocalisation.cpp:70:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/vis_delocalisation.cpp:38:6: style: The scope of the variable 'threads' can be reduced. [variableScope]
relion-3.1.3/src/apps/vis_delocalisation.cpp:146:14: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/apps/vis_delocalisation.cpp:146:35: performance: Function parameter 'tag' should be passed by const reference. [passedByValue]
relion-3.1.3/src/apps/vis_delocalisation.cpp:198:58: style: Parameter 'dest' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/args.cpp:63:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:129:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable options [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:144:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:159:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:187:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_section [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:203:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_section [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:211:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_section [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:217:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable options [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:237:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:283:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:294:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:337:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:378:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable options [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:400:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optionals [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:415:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/args.cpp:433:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::continue_old' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::do_skip_ctf_correction' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::do_use_trials_for_ctffind' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::do_use_only_lower_tilt_defoci' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::is_coords_star_file' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::show_usage' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::dont_check_input_files' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::do_use_gctf' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::do_ignore_ctffind_params' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::do_EPA' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:99:2: warning: Member variable 'prepare_subtomo::do_validation' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/apps/prepare_subtomo.cpp:163:7: style:inconclusive: Technically the member function 'prepare_subtomo::showMessages' can be const. [functionConst]
relion-3.1.3/src/apps/prepare_subtomo.cpp:944:64: style: Condition 'nr_subtomo==1' is always true [knownConditionTrueFalse]
relion-3.1.3/src/apps/prepare_subtomo.cpp:936:17: note: Assignment 'nr_subtomo=0', assigned value is 0
relion-3.1.3/src/apps/prepare_subtomo.cpp:939:5: note: nr_subtomo is incremented', new value is 1
relion-3.1.3/src/apps/prepare_subtomo.cpp:944:64: note: Condition 'nr_subtomo==1' is always true
relion-3.1.3/src/apps/prepare_subtomo.cpp:1116:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/apps/prepare_subtomo.cpp:207:7: style: The scope of the variable 'res' can be reduced. [variableScope]
relion-3.1.3/src/apps/prepare_subtomo.cpp:327:22: style: The scope of the variable 'nr_frames' can be reduced. [variableScope]
relion-3.1.3/src/apps/prepare_subtomo.cpp:887:9: style: The scope of the variable 'write_star_file' can be reduced. [variableScope]
relion-3.1.3/src/args.cpp:432:14: style: The scope of the variable 'thisRankIDs' can be reduced. [variableScope]
relion-3.1.3/src/args.cpp:51:67: performance: Function parameter 'param' should be passed by const reference. [passedByValue]
relion-3.1.3/src/args.cpp:51:92: performance: Function parameter 'option' should be passed by const reference. [passedByValue]
relion-3.1.3/src/args.cpp:91:56: performance: Function parameter 'param' should be passed by const reference. [passedByValue]
relion-3.1.3/src/apps/prepare_subtomo.cpp:57:7: style: class member 'prepare_subtomo::is_coords_star_file' is never used. [unusedStructMember]
relion-3.1.3/src/apps/prepare_subtomo.cpp:118:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/prepare_subtomo.cpp:131:23: style: Variable 'ctffind_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/prepare_subtomo.cpp:147:20: style: Variable 'gctf_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker_mpi.cpp:26:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker_mpi.cpp:81:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker_mpi.cpp:108:12: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:296:15: style: Condition 'ii%100==0' is always false [knownConditionTrueFalse]
relion-3.1.3/src/apps/star_handler.cpp:278:17: note: Assignment 'ii=0', assigned value is 0
relion-3.1.3/src/apps/star_handler.cpp:295:4: note: ii is incremented', new value is 1
relion-3.1.3/src/apps/star_handler.cpp:296:15: note: Condition 'ii%100==0' is always false
relion-3.1.3/src/apps/star_handler.cpp:1063:2: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/assembly.cpp:12:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:19:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coords [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:24:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable number [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:345:37: style: The scope of the variable 'MDoptics' can be reduced. [variableScope]
relion-3.1.3/src/assembly.cpp:42:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:564:26: style: The scope of the variable 'six_zeros' can be reduced. [variableScope]
relion-3.1.3/src/assembly.cpp:88:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable number [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:576:26: style: The scope of the variable 'nine_zeros' can be reduced. [variableScope]
relion-3.1.3/src/assembly.cpp:123:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:861:8: style: The scope of the variable 'optics_group' can be reduced. [variableScope]
relion-3.1.3/src/assembly.cpp:149:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:176:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:184:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:191:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:205:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:405:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:479:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/assembly.cpp:498:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/apps/star_handler.cpp:686:21: warning: Either the condition 'size_split>0' is redundant or there is division by zero at line 686. [zerodivcond]
relion-3.1.3/src/apps/star_handler.cpp:671:39: note: Assuming that condition 'size_split>0' is not redundant
relion-3.1.3/src/apps/star_handler.cpp:686:21: note: Division by zero
relion-3.1.3/src/apps/star_handler.cpp:348:40: error: Out of bounds access in expression 'fns_in[0]' because 'fns_in' is empty. [containerOutOfBounds]
relion-3.1.3/src/apps/star_handler.cpp:338:29: note: Assuming condition is false
relion-3.1.3/src/apps/star_handler.cpp:348:40: note: Access out of bounds
relion-3.1.3/src/apps/star_handler.cpp:57:23: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:64:23: style: Variable 'compare_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:71:22: style: Variable 'subset_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:79:23: style: Variable 'discard_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:84:23: style: Variable 'combine_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:88:21: style: Variable 'split_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:95:23: style: Variable 'operate_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:103:22: style: Variable 'center_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:109:22: style: Variable 'column_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:121:25: style: Variable 'duplicate_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/apps/star_handler.cpp:995:23: style: Unused variable: values [unusedVariable]
relion-3.1.3/src/backprojector.cpp:43:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:83:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:363:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:477:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:678:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:864:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:905:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:938:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:1003:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:1055:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:1216:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:1377:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:1837:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:1856:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref_dim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:2020:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:2174:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pad_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:2239:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:57:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable opticsGroup [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:97:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kV [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:137:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kV [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:154:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable opticsGroup [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:209:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Cs [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:260:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:288:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:319:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:470:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:543:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:558:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:572:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:620:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:646:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable jp [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:666:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Axx [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:671:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Axy [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctf.cpp:676:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Ayy [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:27:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:32:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:35:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:93:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:48:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:99:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_ctffind_exe [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:58:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area_percentage [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:366:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_only_join_results [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:96:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:425:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:185:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:536:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_micrographs_ctf [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:216:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable random_seed [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:610:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_micrographs_ctf [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:897:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:691:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_micrographs_ctf [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:945:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:814:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_ctffind4 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:1061:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:830:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:1120:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable helical_tube_diameter [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:927:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:1271:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable helical_tube_diameter [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:1515:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_stddev_noise [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:1845:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:2342:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:2530:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable workSize [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:2841:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable autopick_skip_side [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:3475:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_odir [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:3487:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable micrograph_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:3561:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_fraction_expected_Pratio [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:3620:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:3683:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:3722:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_optimise_scale [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner.cpp:30:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/ctffind_runner.cpp:31:18: style: Variable 'ctf_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/ctffind_runner.cpp:41:18: style: Variable 'mic_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/ctffind_runner.cpp:48:22: style: Variable 'ctffind_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/ctffind_runner.cpp:60:23: style: Variable 'ctffind4_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/ctffind_runner.cpp:73:19: style: Variable 'gctf_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/ctffind_runner.cpp:424:19: style: Variable 'barstep' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/ctffind_runner.cpp:601:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/ctffind_runner_mpi.cpp:25:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ctffind_runner_mpi.cpp:41:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_only_join_results [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/backprojector.cpp:1510:9: style: Condition '!have_warned' is always true [knownConditionTrueFalse]
relion-3.1.3/src/backprojector.cpp:1501:22: note: Assignment 'have_warned=false', assigned value is 0
relion-3.1.3/src/backprojector.cpp:1510:9: note: Condition '!have_warned' is always true
relion-3.1.3/src/backprojector.cpp:959:6: style: The scope of the variable 'kp' can be reduced. [variableScope]
relion-3.1.3/src/backprojector.cpp:959:10: style: The scope of the variable 'ip' can be reduced. [variableScope]
relion-3.1.3/src/backprojector.cpp:959:14: style: The scope of the variable 'jp' can be reduced. [variableScope]
relion-3.1.3/src/error.cpp:58:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable backtrace_buffer [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/error.cpp:76:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/error.cpp:72:58: style: Parameter 'XE' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/euler.cpp:157:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_EPSILON [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/euler.cpp:119:47: style: Parameter 'v0' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/assembly.cpp:220:21: error: Buffer is accessed out of bounds: line [bufferAccessOutOfBounds]
relion-3.1.3/src/assembly.cpp:313:21: style: The scope of the variable 'str_resname' can be reduced. [variableScope]
relion-3.1.3/src/assembly.cpp:72:21: style: Unused variable: this_nResidues [unusedVariable]
relion-3.1.3/src/assembly.cpp:312:33: style: Variable 'str_atomname' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:44:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable img_data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:81:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable colour_scheme [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:147:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scale [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:272:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable selected [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:282:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable selected [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:289:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable selected [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:296:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable selected [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:316:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MULTIVIEWER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:392:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_selection_type [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:442:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ncol [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:634:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xoff [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:652:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:657:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FL_PUSH [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:862:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:895:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_selected_imgs [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:952:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:960:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:968:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:976:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:984:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_class [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1019:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1066:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1151:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1174:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1193:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULTPDFVIEWER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1226:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1275:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_selected_parts [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1319:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1427:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MULTIVIEWER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1451:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1510:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_selected_imgs [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1593:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GUI_BACKGROUND_COLOR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1614:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FL_PUSH [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1704:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1753:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:1841:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FL_PUSH [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2000:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_coords [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2038:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_coords [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2051:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_color [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2124:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2130:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2138:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2153:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2316:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2361:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2403:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2511:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2574:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2579:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_gui [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2682:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/displayer.cpp:2782:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_gui [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/fftw.cpp:358:3: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/exp_model.cpp:28:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_particles_subset1 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:38:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:76:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:81:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:86:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:91:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:96:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:100:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:109:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:155:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_images_per_optics_group [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:202:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_particles_subset1 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:360:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:412:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_bodies [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:445:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:483:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_scratch [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:523:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_scratch [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:541:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable free_space_Gb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:581:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_scratch [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:597:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:815:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WRITE_READONLY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:1165:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:91:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:98:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:296:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:308:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:325:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:334:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:488:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:497:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:520:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:550:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/filename.cpp:513:14: style: The scope of the variable 'dir' can be reduced. [variableScope]
relion-3.1.3/src/filename.cpp:534:9: warning: Uninitialized variable: mdret [uninitvar]
relion-3.1.3/src/filename.cpp:520:38: note: Assuming condition is false
relion-3.1.3/src/filename.cpp:534:9: note: Uninitialized variable: mdret
relion-3.1.3/src/flex_analyser.cpp:62:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:182:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:193:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DONT_WRAP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:220:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:348:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:466:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:571:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:660:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:702:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:710:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/exp_model.cpp:1134:25: style: Redundant condition: have_tiltpsi. '!have_tiltpsi || (have_tiltpsi && ABS(tilt)<0.001)' is equivalent to '!have_tiltpsi || ABS(tilt)<0.001' [redundantCondition]
relion-3.1.3/src/exp_model.cpp:624:12: style: The scope of the variable 'imgno' can be reduced. [variableScope]
relion-3.1.3/src/exp_model.cpp:776:37: style: The scope of the variable 'part_id' can be reduced. [variableScope]
relion-3.1.3/src/exp_model.cpp:1111:7: style: The scope of the variable 'izero' can be reduced. [variableScope]
relion-3.1.3/src/exp_model.cpp:685:15: style: Local variable 'fn_ctf' shadows outer variable [shadowVariable]
relion-3.1.3/src/exp_model.cpp:625:20: note: Shadowed declaration
relion-3.1.3/src/exp_model.cpp:685:15: note: Shadow variable
relion-3.1.3/src/exp_model.cpp:811:18: style: Local variable 'img' shadows outer variable [shadowVariable]
relion-3.1.3/src/exp_model.cpp:791:17: note: Shadowed declaration
relion-3.1.3/src/exp_model.cpp:811:18: note: Shadow variable
relion-3.1.3/src/exp_model.cpp:978:13: style: Local variable 'part_id' shadows outer variable [shadowVariable]
relion-3.1.3/src/exp_model.cpp:776:37: note: Shadowed declaration
relion-3.1.3/src/exp_model.cpp:978:13: note: Shadow variable
relion-3.1.3/src/exp_model.cpp:231:26: style: Unused variable: img_name [unusedVariable]
relion-3.1.3/src/exp_model.cpp:540:21: style: Variable 'myhost' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/exp_model.cpp:262:62: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/funcs.cpp:75:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:119:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable w [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:238:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:261:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:337:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:514:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:590:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:611:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:765:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/flex_analyser.cpp:232:23: style: The scope of the variable 'datarow' can be reduced. [variableScope]
relion-3.1.3/src/flex_analyser.cpp:706:70: style:inconclusive: Function 'principalComponentsAnalysis' argument 2 names different: declaration 'eigenvectors' definition 'eigenvec'. [funcArgNamesDifferent]
relion-3.1.3/src/flex_analyser.h:133:70: note: Function 'principalComponentsAnalysis' argument 2 names different: declaration 'eigenvectors' definition 'eigenvec'.
relion-3.1.3/src/flex_analyser.cpp:706:70: note: Function 'principalComponentsAnalysis' argument 2 names different: declaration 'eigenvectors' definition 'eigenvec'.
relion-3.1.3/src/flex_analyser.cpp:707:55: style:inconclusive: Function 'principalComponentsAnalysis' argument 3 names different: declaration 'eigenvalues' definition 'eigenval'. [funcArgNamesDifferent]
relion-3.1.3/src/flex_analyser.h:134:55: note: Function 'principalComponentsAnalysis' argument 3 names different: declaration 'eigenvalues' definition 'eigenval'.
relion-3.1.3/src/flex_analyser.cpp:707:55: note: Function 'principalComponentsAnalysis' argument 3 names different: declaration 'eigenvalues' definition 'eigenval'.
relion-3.1.3/src/flex_analyser.cpp:515:12: style: Local variable 'fn_eps' shadows outer variable [shadowVariable]
relion-3.1.3/src/flex_analyser.cpp:453:11: note: Shadowed declaration
relion-3.1.3/src/flex_analyser.cpp:515:12: note: Shadow variable
relion-3.1.3/src/flex_analyser.cpp:517:12: style: Local variable 'plot2D' shadows outer variable [shadowVariable]
relion-3.1.3/src/flex_analyser.cpp:455:11: note: Shadowed declaration
relion-3.1.3/src/flex_analyser.cpp:517:12: note: Shadow variable
relion-3.1.3/src/flex_analyser.cpp:518:12: style: Local variable 'dataSet' shadows outer variable [shadowVariable]
relion-3.1.3/src/flex_analyser.cpp:456:11: note: Shadowed declaration
relion-3.1.3/src/flex_analyser.cpp:518:12: note: Shadow variable
relion-3.1.3/src/flex_analyser.cpp:810:19: style: Local variable 'z' shadows outer variable [shadowVariable]
relion-3.1.3/src/flex_analyser.cpp:760:22: note: Shadowed declaration
relion-3.1.3/src/flex_analyser.cpp:810:19: note: Shadow variable
relion-3.1.3/src/flex_analyser.cpp:450:93: style: Parameter 'means' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/flex_analyser.cpp:555:93: style: Parameter 'eigenvectors' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/flex_analyser.cpp:555:128: style: Parameter 'means' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/flex_analyser.cpp:656:79: style: Parameter 'projected_input' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/flex_analyser.cpp:680:80: style: Parameter 'projected_input' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/flex_analyser.cpp:27:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/flex_analyser.cpp:33:20: style: Variable 'model_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/flex_analyser.cpp:37:18: style: Variable 'pca_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/flex_analyser.cpp:772:11: style: Variable 'nrot' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/flex_analyser.cpp:881:11: style: Variable 'nrot' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/funcs.cpp:668:11: style: The scope of the variable 'p1' can be reduced. [variableScope]
relion-3.1.3/src/funcs.cpp:668:15: style: The scope of the variable 'p2' can be reduced. [variableScope]
relion-3.1.3/src/funcs.cpp:714:11: style: The scope of the variable 'p1' can be reduced. [variableScope]
relion-3.1.3/src/funcs.cpp:714:15: style: The scope of the variable 'p2' can be reduced. [variableScope]
relion-3.1.3/src/funcs.cpp:754:21: style: The scope of the variable 't' can be reduced. [variableScope]
relion-3.1.3/src/funcs.cpp:302:19: style: Local variable 'i_n' shadows outer function [shadowFunction]
relion-3.1.3/src/funcs.cpp:280:8: note: Shadowed declaration
relion-3.1.3/src/funcs.cpp:302:19: note: Shadow variable
relion-3.1.3/src/funcs.cpp:674:12: style: Variable 'p1' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/funcs.cpp:675:12: style: Variable 'p2' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/gui_entries.cpp:61:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable deactivate_option [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:720:12: style: Variable 'p1' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/gui_entries.cpp:108:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable joboption_type [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/funcs.cpp:721:12: style: Variable 'p2' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/gui_entries.cpp:209:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable deactivate_option [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/gui_entries.cpp:223:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/gui_entries.cpp:255:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inp [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/gui_entries.cpp:309:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SINGLE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/gui_entries.cpp:350:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SINGLE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/gui_entries.cpp:400:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable my_deactivate_group [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/gui_jobwindow.cpp:891:448: error: No pair for character ("). Can't process file. File is either invalid or unicode, which is currently not supported. [syntaxError]
relion-3.1.3/src/gui_entries.cpp:286:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/gui_entries.cpp:300:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/gui_entries.cpp:343:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/gui_entries.cpp:387:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/gui_entries.cpp:416:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/gui_entries.cpp:435:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/gui_entries.cpp:293:21: style: Variable 'help' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/gui_mainwindow.cpp:3516:40: error: There is an unknown macro here somewhere. Configuration is required. If RELION_SHORT_VERSION is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/displayer.cpp:54:17: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/displayer.cpp:2391:24: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/displayer.cpp:103:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
relion-3.1.3/src/displayer.cpp:122:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
relion-3.1.3/src/displayer.cpp:2163:62: style: The scope of the variable 'inputwidth2' can be reduced. [variableScope]
relion-3.1.3/src/displayer.cpp:704:19: style: Local variable 'rclick_menu' shadows outer variable [shadowVariable]
relion-3.1.3/src/displayer.cpp:700:18: note: Shadowed declaration
relion-3.1.3/src/displayer.cpp:704:19: note: Shadow variable
relion-3.1.3/src/displayer.cpp:777:19: style: Local variable 'rclick_menu' shadows outer variable [shadowVariable]
relion-3.1.3/src/displayer.cpp:700:18: note: Shadowed declaration
relion-3.1.3/src/displayer.cpp:777:19: note: Shadow variable
relion-3.1.3/src/displayer.cpp:936:16: style: Local variable 'ipos' shadows outer variable [shadowVariable]
relion-3.1.3/src/displayer.cpp:929:11: note: Shadowed declaration
relion-3.1.3/src/displayer.cpp:936:16: note: Shadow variable
relion-3.1.3/src/displayer.cpp:1376:8: style: Local variable 'nr_parts' shadows outer variable [shadowVariable]
relion-3.1.3/src/displayer.cpp:1350:11: note: Shadowed declaration
relion-3.1.3/src/displayer.cpp:1376:8: note: Shadow variable
relion-3.1.3/src/displayer.cpp:1084:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:1166:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:1187:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:1211:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:1217:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:2007:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:2503:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:2510:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:2532:20: style: Variable 'disp_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/displayer.cpp:2550:20: style: Variable 'pick_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/helix_inimodel2d.cpp:225:4: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/healpix_sampling.cpp:27:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:63:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:170:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable random_perturbation [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:179:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:237:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:307:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset_step [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:468:128: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3d_trans [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:485:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable healpix_order [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:570:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:607:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:639:101: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:677:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1053:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable healpix_order [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1128:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1495:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sym [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1507:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable directions_ipix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1550:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset_step [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1555:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable helical_offset_step [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1560:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1596:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3d_trans [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1615:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1624:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3d_trans [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1641:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rot_angles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1654:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable psi_angles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1666:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translations_x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1712:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translations_x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1844:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rot_angles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1925:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable psi_angles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1948:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:1995:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:2083:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable limit_tilt [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:2152:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rot_angles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/healpix_sampling.cpp:2231:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pg_CN [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/image.cpp:127:3: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/jaz/Fourier_helper.cpp:31:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/aberration_fit.cpp:115:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_VOLTAGE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/aberration_fit.cpp:196:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coefficients [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/aberration_fit.cpp:113:55: style: Unused variable: scale [unusedVariable]
relion-3.1.3/src/jaz/aberration_fit.cpp:113:66: style: Unused variable: phase_shift [unusedVariable]
relion-3.1.3/src/healpix_sampling.cpp:489:13: style: The if condition is the same as the previous if condition [duplicateCondition]
relion-3.1.3/src/healpix_sampling.cpp:484:13: note: First condition
relion-3.1.3/src/healpix_sampling.cpp:489:13: note: Second condition
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:142:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/apps/ref_aberration_plot.cpp:53:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optReference [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/apps/ref_aberration_plot.cpp:75:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable noReference [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/apps/ref_aberration_plot.cpp:91:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/apps/ref_aberration_plot.cpp:96:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_omp_threads [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/apps/ref_aberration_plot.cpp:96:40: style: Variable 'fts' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:1868:121: style: The scope of the variable 'helical_segments' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:2043:9: style: The scope of the variable 'id_peak_dist_max' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:2182:9: style: The scope of the variable 'id_peak_dist_max' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:2340:8: style: The scope of the variable 'x_int' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:2340:15: style: The scope of the variable 'y_int' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:3376:7: style: The scope of the variable 'peak_r_min' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:3377:24: style: The scope of the variable 'ccf_peak_list' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:3378:38: style: The scope of the variable 'tube_coord_list' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:3378:55: style: The scope of the variable 'tube_track_list' can be reduced. [variableScope]
relion-3.1.3/src/autopicker.cpp:3379:23: style: The scope of the variable 'tube_len_list' can be reduced. [variableScope]
relion-3.1.3/src/jaz/archive/apps/update_angles.cpp:90:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/autopicker.cpp:95:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:117:18: style: Variable 'ref_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:131:18: style: Variable 'log_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:147:20: style: Variable 'helix_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:155:19: style: Variable 'peak_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:162:21: style: Variable 'expert_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:922:12: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:1108:27: style: Variable 'new_micrograph_xsize' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:1109:30: style: Variable 'new_micrograph_ysize' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:1110:23: style: Variable 'skip_side_pix' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:1151:29: style: Variable 'max_depths' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:1152:33: style: Variable 'max_sumfoms' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:2063:25: style: Variable 'id_peak_dist_max' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/autopicker.cpp:2202:25: style: Variable 'id_peak_dist_max' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/archive/frame_merge.cpp:65:13: style: Condition '!(vb==vb)' is always false [knownConditionTrueFalse]
relion-3.1.3/src/jaz/archive/frame_merge.cpp:65:18: style: Same expression on both sides of '=='. [duplicateExpression]
relion-3.1.3/src/jaz/archive/motion_em.cpp:75:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s_pos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_em.cpp:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable posProb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_em.cpp:197:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_em.cpp:231:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_em.cpp:333:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_em.cpp:387:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s_vel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_em.cpp:426:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_em.cpp:498:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable initialized [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_em.cpp:543:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/apps/update_angles.cpp:95:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/apps/update_angles.cpp:134:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/apps/update_angles.cpp:143:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/apps/update_angles.cpp:175:9: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:52:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable starFn [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:427:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sh [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:432:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sh [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:437:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable preextracted [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:516:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable preextracted [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:630:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mdts [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:543:22: warning: Return value of function mgFn.substr() is not used. [ignoredReturnValue]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:177:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:192:9: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:204:13: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:242:13: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:538:25: style: Local variable 'mgFn' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:524:21: note: Shadowed declaration
relion-3.1.3/src/jaz/archive/refinement_program.cpp:538:25: note: Shadow variable
relion-3.1.3/src/jaz/archive/refinement_program.cpp:543:58: warning:inconclusive: Found suspicious operator '+', result is not used. [constStatement]
relion-3.1.3/src/jaz/archive/refinement_program.cpp:631:11: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
relion-3.1.3/src/jaz/convolution_helper.cpp:31:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:80:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:176:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:36:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:68:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:99:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:114:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:145:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:220:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:259:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:286:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:311:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:365:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:413:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:603:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:652:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:694:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_NUMBER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:732:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_NUMBER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:771:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:820:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:841:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1046:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1077:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1118:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1181:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1210:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1250:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1302:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1319:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1383:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1452:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1485:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1619:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1688:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1719:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::kmin' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::aberr_n_max' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::xring0' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::xring1' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::diag' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:26:22: warning: Member variable 'AberrationEstimator::obsModel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:316:22: style: Local variable 'sts' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:187:21: note: Shadowed declaration
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:316:22: note: Shadow variable
relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:46:38: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/helix.cpp:83:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable twist_deg [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:174:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:353:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:659:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:977:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:1305:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:1353:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:1397:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:1511:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CART_TO_HELICAL_COORDS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:1609:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:1745:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:1785:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_STAR_FORMAT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:1832:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNIMODAL_PSI_PRIOR_FLIP_RATIO [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2029:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2150:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2175:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_TILT_PRIOR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2204:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_TILT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2241:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_PSI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2289:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XIMDISP_COORDS_FORMAT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2322:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNIMODAL_PSI_PRIOR_FLIP_RATIO [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2397:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2510:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2653:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:2777:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3079:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3346:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3421:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3479:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3513:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3625:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3846:184: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3897:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:3984:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4003:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MDobjectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4021:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4039:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable psi_deg [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4100:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable helical_tube_name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4391:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4550:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_TILT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4584:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_PSI_PRIOR_FLIP_RATIO [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4596:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4622:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4658:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4691:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4714:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_Z_ANGSTROM [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4762:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_TILT_PRIOR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:4927:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:5122:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:5512:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:5554:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:5674:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:185:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_BFACTOR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:316:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_BFACTOR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:457:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:140:9: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:150:9: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:156:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:192:9: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:372:9: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:48:73: style: The scope of the variable 'fn_sym' can be reduced. [variableScope]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:66:36: style: The scope of the variable 'nr_helical_asu' can be reduced. [variableScope]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:66:52: style: The scope of the variable 'evalFrames' can be reduced. [variableScope]
relion-3.1.3/src/jaz/archive/apps/em_motion.cpp:764:41: style: Variable 'centVisTracks[p][f]' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::kmin' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::min_scale' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::min_B' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::max_B' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::perMicrograph' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::diag' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:21:17: warning: Member variable 'BFactorRefiner::obsModel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:39:8: style:inconclusive: Technically the member function 'BFactorRefiner::writePerParticleEPS' can be const. [functionConst]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:433:22: note: Technically the member function 'BFactorRefiner::writePerParticleEPS' can be const.
relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:39:8: note: Technically the member function 'BFactorRefiner::writePerParticleEPS' can be const.
relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:41:8: style:inconclusive: Technically the member function 'BFactorRefiner::writePerMicrographEPS' can be const. [functionConst]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:295:22: note: Technically the member function 'BFactorRefiner::writePerMicrographEPS' can be const.
relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:41:8: note: Technically the member function 'BFactorRefiner::writePerMicrographEPS' can be const.
relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:55:8: style:inconclusive: Technically the member function 'BFactorRefiner::isFinished' can be const. [functionConst]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:485:22: note: Technically the member function 'BFactorRefiner::isFinished' can be const.
relion-3.1.3/src/jaz/ctf/bfactor_refiner.h:55:8: note: Technically the member function 'BFactorRefiner::isFinished' can be const.
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:103:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable writeMrc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:126:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:249:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:416:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:437:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:497:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:45:38: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:60:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.h:28:1: style: The class 'CtfRefinerMpi' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:23:21: warning: The class 'CtfRefinerMpi' defines member function with name 'read' also defined in its parent class 'CtfRefiner'. [duplInheritedMember]
relion-3.1.3/src/jaz/ctf/ctf_refiner.h:41:8: note: Parent function 'CtfRefiner::read'
relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:23:21: note: Derived function 'CtfRefinerMpi::read'
relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:45:21: warning: The class 'CtfRefinerMpi' defines member function with name 'run' also defined in its parent class 'CtfRefiner'. [duplInheritedMember]
relion-3.1.3/src/jaz/ctf/ctf_refiner.h:43:8: note: Parent function 'CtfRefiner::run'
relion-3.1.3/src/jaz/ctf/ctf_refiner_mpi.cpp:45:21: note: Derived function 'CtfRefinerMpi::run'
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:110:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:185:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:308:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::only_do_unfinished' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::do_defocus_fit' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::do_bfac_fit' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::do_tilt_fit' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::do_aberr_fit' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::do_mag_fit' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::do_ctf_padding' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::diag' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::maxMG' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::minMG' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:45:13: warning: Member variable 'CtfRefiner::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/ctf_refiner.h:47:7: style:inconclusive: Technically the member function 'CtfRefiner::getVerbosityLevel' can be const. [functionConst]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:489:17: note: Technically the member function 'CtfRefiner::getVerbosityLevel' can be const.
relion-3.1.3/src/jaz/ctf/ctf_refiner.h:47:7: note: Technically the member function 'CtfRefiner::getVerbosityLevel' can be const.
relion-3.1.3/src/jaz/ctf/ctf_refiner.h:91:30: style:inconclusive: Technically the member function 'CtfRefiner::merge' can be const. [functionConst]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:430:40: note: Technically the member function 'CtfRefiner::merge' can be const.
relion-3.1.3/src/jaz/ctf/ctf_refiner.h:91:30: note: Technically the member function 'CtfRefiner::merge' can be const.
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:738:9: style: The scope of the variable 'fc' can be reduced. [variableScope]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:768:27: style:inconclusive: Function 'measureValueScaleReal' argument 1 names different: declaration 'obs' definition 'data'. [funcArgNamesDifferent]
relion-3.1.3/src/jaz/archive/motion_refinement.h:142:39: note: Function 'measureValueScaleReal' argument 1 names different: declaration 'obs' definition 'data'.
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:768:27: note: Function 'measureValueScaleReal' argument 1 names different: declaration 'obs' definition 'data'.
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:817:27: style:inconclusive: Function 'measureValueScale' argument 1 names different: declaration 'obs' definition 'data'. [funcArgNamesDifferent]
relion-3.1.3/src/jaz/archive/motion_refinement.h:146:39: note: Function 'measureValueScale' argument 1 names different: declaration 'obs' definition 'data'.
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:817:27: note: Function 'measureValueScale' argument 1 names different: declaration 'obs' definition 'data'.
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:663:18: style: Local variable 'dummy' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:658:14: note: Shadowed declaration
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:663:18: note: Shadow variable
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1394:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/archive/motion_refinement.h:63:16: note: Shadowed declaration
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1394:18: note: Shadow variable
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1463:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/archive/motion_refinement.h:63:16: note: Shadowed declaration
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1463:18: note: Shadow variable
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1493:14: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/archive/motion_refinement.h:63:16: note: Shadowed declaration
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1493:14: note: Shadow variable
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1501:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/archive/motion_refinement.h:63:16: note: Shadowed declaration
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1501:18: note: Shadow variable
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:433:6: style: The scope of the variable 'barstep' can be reduced. [variableScope]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:494:82: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::defocusRange' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::kmin' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::max_iters' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::fitAstigmatism' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::bruteForcePre' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::bruteForcePost' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::bruteForceOnly' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::diag' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:39:19: warning: Member variable 'DefocusEstimator::obsModel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/defocus_estimator.h:55:8: style:inconclusive: Technically the member function 'DefocusEstimator::writeEPS' can be const. [functionConst]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:160:24: note: Technically the member function 'DefocusEstimator::writeEPS' can be const.
relion-3.1.3/src/jaz/ctf/defocus_estimator.h:55:8: note: Technically the member function 'DefocusEstimator::writeEPS' can be const.
relion-3.1.3/src/jaz/ctf/defocus_estimator.h:58:8: style:inconclusive: Technically the member function 'DefocusEstimator::isFinished' can be const. [functionConst]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:230:24: note: Technically the member function 'DefocusEstimator::isFinished' can be const.
relion-3.1.3/src/jaz/ctf/defocus_estimator.h:58:8: note: Technically the member function 'DefocusEstimator::isFinished' can be const.
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:53:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:65:18: style: Variable 'fit_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:71:19: style: Variable 'bfac_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:77:19: style: Variable 'tilt_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:83:20: style: Variable 'aberr_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:89:20: style: Variable 'aniso_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:95:19: style: Variable 'comp_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:118:11: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:195:8: style: Variable 's' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:254:40: style: Variable 'fts' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:277:12: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:439:11: style: Variable 'barstep' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1068:31: performance: Function parameter 'positions' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1702:21: performance: Function parameter 'filenameFull' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1702:47: performance: Function parameter 'filenameBlocks' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:76:38: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:246:15: performance: Function parameter 'tag' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:738:12: style: Variable 'fc' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:25:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:78:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1459:22: style: Variable 'eps' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:269:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:234:5: performance: Variable 'data' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:272:5: performance: Variable 'data' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:316:15: style: Local variable 'x' shadows outer argument [shadowArgument]
relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:294:65: note: Shadowed declaration
relion-3.1.3/src/jaz/ctf/defocus_helper.cpp:316:15: note: Shadow variable
relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:63:34: style: Parameter 'mask' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:93:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:151:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:122:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable real [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:179:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Axx [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:329:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Axx [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:429:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:311:47: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:338:80: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:101:49: style: Parameter 'eqs' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:139:24: style: Parameter 'eqs' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:386:19: style: Variable 'xf' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:387:19: style: Variable 'yf' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:473:32: style: Variable 'groupToIndex[optGroups[i]]' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::kmin' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::adaptAstig' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::perMgAstig' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::diag' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::ready' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:37:25: warning: Member variable 'MagnificationEstimator::obsModel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:192:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:55:15: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:157:7: style: Variable 'hasMagMatrices' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:105:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:176:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:125:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:199:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:273:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:404:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:595:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:708:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::kmin' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::aberr_n_max' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::xring0' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::xring1' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::diag' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:46:16: warning: Member variable 'TiltEstimator::obsModel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:332:22: style: Local variable 'sts' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:190:21: note: Shadowed declaration
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:332:22: note: Shadow variable
relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:70:38: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf_helper.cpp:47:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:853:28: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:908:28: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:866:11: style: Local variable 'x' shadows outer argument [shadowArgument]
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:851:56: note: Shadowed declaration
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:866:11: note: Shadow variable
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:921:11: style: Local variable 'x' shadows outer argument [shadowArgument]
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:906:61: note: Shadowed declaration
relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:921:11: note: Shadow variable
relion-3.1.3/src/jaz/d3x3/dsyevh3.c:82:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_EPSILON [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/d3x3/dsyevd3.c:145:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_EPSILON [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:177:29: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:381:29: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:18:14: performance: Function parameter 'modeStr' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:612:61: performance: Function parameter 'mode' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:627:91: performance: Function parameter 's' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/d3x3/dsyevj3.c:70:6: style: Variable 'sd' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/d3x3/slvsec3.c:185:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_EPSILON [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:86:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:183:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:312:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:387:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:462:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:479:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:666:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable y [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:714:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable y [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:825:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable t0 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:848:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:889:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:914:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k1 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/d3x3/dsyevv3.c:111:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_EPSILON [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/damage_helper.cpp:571:22: style: Local variable 'eps' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/damage_helper.cpp:550:18: note: Shadowed declaration
relion-3.1.3/src/jaz/damage_helper.cpp:571:22: note: Shadow variable
relion-3.1.3/src/jaz/d3x3/slvsec3.c:162:14: style: Local variable 't' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/d3x3/slvsec3.c:54:10: note: Shadowed declaration
relion-3.1.3/src/jaz/d3x3/slvsec3.c:162:14: note: Shadow variable
relion-3.1.3/src/jaz/d3x3/slvsec3.c:32:21: style: Parameter 'd' can be declared as const array [constParameter]
relion-3.1.3/src/jaz/d3x3/slvsec3.c:32:34: style: Parameter 'z' can be declared as const array [constParameter]
relion-3.1.3/src/jaz/damage_helper.cpp:48:21: style: Variable 'fSum' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/damage_helper.cpp:68:18: style: Variable 'fSum' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/fsc_helper.cpp:32:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:91:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:153:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:184:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:223:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:251:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:304:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:334:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:452:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/fsc_helper.cpp:639:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Bscale [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:29:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:39:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:769:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:788:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixedNu [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:817:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixedNu [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:850:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixedNu [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:898:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixedNu0 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:979:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:1047:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/distribution_helper.cpp:1099:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/color_helper.cpp:23:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/color_helper.cpp:50:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/color_helper.cpp:21:73: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/img_proc/color_helper.cpp:27:74: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/img_proc/color_helper.cpp:46:48: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/distribution_helper.cpp:797:49: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
relion-3.1.3/src/jaz/distribution_helper.cpp:921:26: error: Uninitialized variable: nu0 [legacyUninitvar]
relion-3.1.3/src/jaz/interpolation.cpp:35:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/io/star_converter.cpp:40:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_Q0 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/io/star_converter.cpp:255:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DETECTOR_PIXEL_SIZE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/io/star_converter.cpp:288:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:660:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:718:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:821:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:895:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:919:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:939:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:1179:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:1702:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:1929:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2022:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2120:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2144:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2305:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2368:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2519:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable z [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2627:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable z [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2745:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2923:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable real [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2986:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:3009:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/io/star_converter.cpp:226:5: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/io/star_converter.cpp:294:19: style: The scope of the variable 'd' can be reduced. [variableScope]
relion-3.1.3/src/jaz/io/star_converter.cpp:253:74: performance: Function parameter 'tablename' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/legacy_obs_model.cpp:32:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/legacy_obs_model.cpp:126:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/legacy_obs_model.cpp:183:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beamtilt_xx [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/legacy_obs_model.cpp:191:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/legacy_obs_model.cpp:196:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/legacy_obs_model.cpp:201:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/local_motion_fit.cpp:49:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/local_motion_fit.cpp:113:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:66:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:121:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:169:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:221:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:254:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:373:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:411:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:709:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:748:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:785:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:811:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:27:20: warning: Member variable 'MicrographHandler::movie_angpix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:27:20: warning: Member variable 'MicrographHandler::coords_angpix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/micrograph_handler.cpp:27:20: warning: Member variable 'MicrographHandler::data_angpix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/micrograph_handler.h:39:6: style:inconclusive: Member variable 'MicrographHandler::nr_omp_threads' is in the wrong place in the initializer list. [initializerList]
relion-3.1.3/src/jaz/micrograph_handler.cpp:29:4: note: Member variable 'MicrographHandler::nr_omp_threads' is in the wrong place in the initializer list.
relion-3.1.3/src/jaz/micrograph_handler.h:39:6: note: Member variable 'MicrographHandler::nr_omp_threads' is in the wrong place in the initializer list.
relion-3.1.3/src/jaz/micrograph_handler.h:45:14: style:inconclusive: Member variable 'MicrographHandler::corrMicFn' is in the wrong place in the initializer list. [initializerList]
relion-3.1.3/src/jaz/micrograph_handler.cpp:37:4: note: Member variable 'MicrographHandler::corrMicFn' is in the wrong place in the initializer list.
relion-3.1.3/src/jaz/micrograph_handler.h:45:14: note: Member variable 'MicrographHandler::corrMicFn' is in the wrong place in the initializer list.
relion-3.1.3/src/jaz/micrograph_handler.h:41:6: style:inconclusive: Member variable 'MicrographHandler::eer_upsampling' is in the wrong place in the initializer list. [initializerList]
relion-3.1.3/src/jaz/micrograph_handler.cpp:38:4: note: Member variable 'MicrographHandler::eer_upsampling' is in the wrong place in the initializer list.
relion-3.1.3/src/jaz/micrograph_handler.h:41:6: note: Member variable 'MicrographHandler::eer_upsampling' is in the wrong place in the initializer list.
relion-3.1.3/src/jaz/micrograph_handler.cpp:53:19: style: Redundant assignment of 'this->firstFrame' to itself. [selfAssignment]
relion-3.1.3/src/jaz/micrograph_handler.cpp:54:18: style: Redundant assignment of 'this->lastFrame' to itself. [selfAssignment]
relion-3.1.3/src/jaz/micrograph_handler.cpp:408:12: style: Local variable 'nr_omp_threads' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/micrograph_handler.h:39:6: note: Shadowed declaration
relion-3.1.3/src/jaz/micrograph_handler.cpp:408:12: note: Shadow variable
relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:1252:14: style: Variable 'd' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/motion/alignment_set.h:155:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:61:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:200:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:240:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:439:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:640:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_POSTPROCESS_BFACTOR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/alignment_set.h:223:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:124:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:197:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:267:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:373:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:528:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:180:23: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:362:23: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:120:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:120:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:131:14: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:131:14: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:147:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:147:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:194:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:194:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:206:14: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:206:14: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:222:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:222:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:263:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:263:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:279:14: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:279:14: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:297:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:297:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:308:14: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:308:14: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:322:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:322:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:369:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:369:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:390:14: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:390:14: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:408:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:408:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:419:14: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:419:14: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:433:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:433:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:497:18: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:497:18: note: Shadow variable
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:532:14: style: Local variable 'f' shadows outer function [shadowFunction]
relion-3.1.3/src/jaz/motion/gp_motion_fit.h:42:16: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:532:14: note: Shadow variable
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:118:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:198:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:392:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:553:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:605:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:709:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:830:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::doCombineFrames' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::bfac_diag' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::do_ctf_multiply' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::do_recenter' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::k0' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::k1' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::box_arg' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::scale_arg' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::crop_arg' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::k0a' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::k1a' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::recenter_x' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::recenter_y' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::recenter_z' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::s_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::sh_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::fc' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::angpix_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::maxFreq' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::obsModel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:36:18: warning: Member variable 'FrameRecombiner::micrographHandler' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/alignment_set.h:71:18: warning: Member variable 'AlignmentSet < float >::accPix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/frame_recombiner.h:52:8: style:inconclusive: Technically the member function 'FrameRecombiner::doingRecombination' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:690:23: note: Technically the member function 'FrameRecombiner::doingRecombination' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:52:8: note: Technically the member function 'FrameRecombiner::doingRecombination' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:55:8: style:inconclusive: Technically the member function 'FrameRecombiner::outerFreqKnown' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:695:23: note: Technically the member function 'FrameRecombiner::outerFreqKnown' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:55:8: note: Technically the member function 'FrameRecombiner::outerFreqKnown' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:60:10: style:inconclusive: Technically the member function 'FrameRecombiner::getOutputPixelSize' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:720:25: note: Technically the member function 'FrameRecombiner::getOutputPixelSize' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:60:10: note: Technically the member function 'FrameRecombiner::getOutputPixelSize' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:61:7: style:inconclusive: Technically the member function 'FrameRecombiner::getOutputBoxSize' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:725:22: note: Technically the member function 'FrameRecombiner::getOutputBoxSize' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:61:7: note: Technically the member function 'FrameRecombiner::getOutputBoxSize' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:62:15: style:inconclusive: Technically the member function 'FrameRecombiner::getOutputSuffix' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:738:30: note: Technically the member function 'FrameRecombiner::getOutputSuffix' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:62:15: note: Technically the member function 'FrameRecombiner::getOutputSuffix' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:63:8: style:inconclusive: Technically the member function 'FrameRecombiner::isCtfMultiplied' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:733:23: note: Technically the member function 'FrameRecombiner::isCtfMultiplied' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:63:8: note: Technically the member function 'FrameRecombiner::isCtfMultiplied' can be const.
relion-3.1.3/src/jaz/motion/alignment_set.h:63:14: style:inconclusive: Technically the member function 'AlignmentSet < float >::accelerate' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/alignment_set.h:189:23: note: Technically the member function 'AlignmentSet < float >::accelerate' can be const.
relion-3.1.3/src/jaz/motion/alignment_set.h:63:14: note: Technically the member function 'AlignmentSet < float >::accelerate' can be const.
relion-3.1.3/src/jaz/motion/alignment_set.h:65:26: style:inconclusive: Technically the member function 'AlignmentSet < float >::updateTsc' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/alignment_set.h:199:35: note: Technically the member function 'AlignmentSet < float >::updateTsc' can be const.
relion-3.1.3/src/jaz/motion/alignment_set.h:65:26: note: Technically the member function 'AlignmentSet < float >::updateTsc' can be const.
relion-3.1.3/src/jaz/motion/frame_recombiner.h:62:15: performance: Function 'getOutputSuffix()' should return member 'suffix' by const reference. [returnByReference]
relion-3.1.3/src/jaz/motion/alignment_set.h:160:13: error: Shifting by a negative value is undefined behaviour [shiftNegative]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:547:29: style: Local variable 'freqWeights' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/motion/frame_recombiner.h:88:43: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:547:29: note: Shadow variable
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:626:29: style: Local variable 'freqWeights' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/motion/frame_recombiner.h:88:43: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:626:29: note: Shadow variable
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:100:34: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:435:37: performance: Function parameter 'og_name' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:701:55: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:743:49: performance: Function parameter 'filenameRoot' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::maxEDs' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::maxIters' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::globOffMax' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::group' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::unregGlob' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::globOff' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::cutoffOut' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::diag' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::expKer' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::global_init' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::debugOpt' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::params_scaled_by_dose' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::dmga' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::dmgb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::dmgc' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::dosePerFrame' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::sig_vel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::sig_div' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::sig_acc' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::optEps' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::cc_pad' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::fc' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::s_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::sh_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::angpix_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::no_whitening' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::all_groups' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::obsModel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:39:18: warning: Member variable 'MotionEstimator::micrographHandler' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_estimator.h:85:14: style:inconclusive: Technically the member function 'MotionEstimator::isReady' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:805:23: note: Technically the member function 'MotionEstimator::isReady' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:85:14: note: Technically the member function 'MotionEstimator::isReady' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:87:16: style:inconclusive: Technically the member function 'MotionEstimator::getDosePerFrame' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:810:25: note: Technically the member function 'MotionEstimator::getDosePerFrame' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:87:16: note: Technically the member function 'MotionEstimator::getDosePerFrame' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:90:10: style:inconclusive: Technically the member function 'MotionEstimator::getCCPad' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:845:25: note: Technically the member function 'MotionEstimator::getCCPad' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:90:10: note: Technically the member function 'MotionEstimator::getCCPad' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:97:16: style:inconclusive: Technically the member function 'MotionEstimator::normalizeSigVel' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:870:25: note: Technically the member function 'MotionEstimator::normalizeSigVel' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:97:16: note: Technically the member function 'MotionEstimator::normalizeSigVel' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:98:16: style:inconclusive: Technically the member function 'MotionEstimator::normalizeSigDiv' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:875:25: note: Technically the member function 'MotionEstimator::normalizeSigDiv' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:98:16: note: Technically the member function 'MotionEstimator::normalizeSigDiv' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:99:16: style:inconclusive: Technically the member function 'MotionEstimator::normalizeSigAcc' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:880:25: note: Technically the member function 'MotionEstimator::normalizeSigAcc' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.h:99:16: note: Technically the member function 'MotionEstimator::normalizeSigAcc' can be const.
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:295:3: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:433:47: style: Local variable 'initialTracks' shadows outer argument [shadowArgument]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:382:39: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:433:47: note: Shadow variable
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:520:12: style: Local variable 'fc' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/motion/motion_estimator.h:121:17: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:520:12: note: Shadow variable
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:552:12: style: Local variable 'fc' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/motion/motion_estimator.h:121:17: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:552:12: note: Shadow variable
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:633:12: style: Local variable 'fc' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/motion/motion_estimator.h:121:17: note: Shadowed declaration
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:633:12: note: Shadow variable
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:89:27: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:627:15: performance: Function parameter 'fn_root' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:815:67: performance: Function parameter 'metaFn' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:851:55: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:885:49: performance: Function parameter 'filenameRoot' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:45:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:228:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:255:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:281:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:334:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:389:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_NUMBER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:428:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_NUMBER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_estimator.cpp:265:12: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:434:9: style: The scope of the variable 'fc' can be reduced. [variableScope]
relion-3.1.3/src/jaz/motion/motion_helper.cpp:434:12: style: Variable 'fc' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:113:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:268:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable floatfield [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:345:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:366:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:417:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:491:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/alignment_set.h:92:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sh [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/alignment_set.h:178:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable accPix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/alignment_set.h:191:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable accPix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/alignment_set.h:210:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fc [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:102:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:122:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:389:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:506:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:519:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::s_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::sh_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::fc' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::findShortestMovie' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::only_do_unfinished' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::estimateParams' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::estimateMotion' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::recombineFrames' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::generateStar' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::maxMG' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:43:16: warning: Member variable 'MotionRefiner::minMG' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_refiner.h:56:7: style:inconclusive: Technically the member function 'MotionRefiner::getVerbosityLevel' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:377:20: note: Technically the member function 'MotionRefiner::getVerbosityLevel' can be const.
relion-3.1.3/src/jaz/motion/motion_refiner.h:56:7: note: Technically the member function 'MotionRefiner::getVerbosityLevel' can be const.
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:307:6: style: Condition 'needsReference' is always true [knownConditionTrueFalse]
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:304:6: note: Assuming that condition '!doAnything' is not redundant
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:302:22: note: needsReference is assigned 'doAnything' here.
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:307:6: note: Condition 'needsReference' is always true
relion-3.1.3/src/jaz/motion/motion_refiner.cpp:503:59: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::estim2' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::estim3' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::minParticles' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::maxRange' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::maxIters' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::seed' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::group' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::sV' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::sD' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::sA' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::iniStep' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::conv' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::align_frac' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::eval_frac' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::k_cutoff' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::k_eval' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::motionEstimator' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::obsModel' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::reference' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::fc' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::k_out' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::verb' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::nr_omp_threads' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::s_ref' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::s' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::sh' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::allGroups' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:38:23: warning: Member variable 'MotionParamEstimator::debug' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/motion/motion_param_estimator.h:65:14: style:inconclusive: Technically the member function 'MotionParamEstimator::anythingToDo' can be const. [functionConst]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:337:28: note: Technically the member function 'MotionParamEstimator::anythingToDo' can be const.
relion-3.1.3/src/jaz/motion/motion_param_estimator.h:65:14: note: Technically the member function 'MotionParamEstimator::anythingToDo' can be const.
relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.h:33:9: style: Class 'ThreeHyperParameterProblem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:538:9: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:69:17: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:311:10: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:252:24: style:inconclusive: Function 'lbfgs' argument 7 names different: declaration 'param' definition '_param'. [funcArgNamesDifferent]
relion-3.1.3/src/jaz/lbfgs/lbfgs.h:484:24: note: Function 'lbfgs' argument 7 names different: declaration 'param' definition '_param'.
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:252:24: note: Function 'lbfgs' argument 7 names different: declaration 'param' definition '_param'.
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:654:22: style:inconclusive: Function 'line_search_backtracking' argument 9 names different: declaration 'wa' definition 'wp'. [funcArgNamesDifferent]
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:145:22: note: Function 'line_search_backtracking' argument 9 names different: declaration 'wa' definition 'wp'.
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:654:22: note: Function 'line_search_backtracking' argument 9 names different: declaration 'wa' definition 'wp'.
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:650:22: style: Parameter 's' can be declared as pointer to const. However it seems that 'line_search_backtracking' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:359:26: note: You might need to cast the function pointer here
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:650:22: note: Parameter 's' can be declared as pointer to const
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:743:22: style: Parameter 's' can be declared as pointer to const. However it seems that 'line_search_backtracking_owlqn' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:345:26: note: You might need to cast the function pointer here
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:743:22: note: Parameter 's' can be declared as pointer to const
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:817:22: style: Parameter 's' can be declared as pointer to const. However it seems that 'line_search_morethuente' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:354:26: note: You might need to cast the function pointer here
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:817:22: note: Parameter 's' can be declared as pointer to const
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:1133:22: style: Parameter 'ft' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:1134:22: style: Parameter 'dt' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/jaz/lbfgs/lbfgs.c:753:39: style: Variable 'norm' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:72:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:59:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/motion_refiner_mpi.h:29:1: style: The class 'MotionRefinerMpi' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:23:24: warning: The class 'MotionRefinerMpi' defines member function with name 'read' also defined in its parent class 'MotionRefiner'. [duplInheritedMember]
relion-3.1.3/src/jaz/motion/motion_refiner.h:48:8: note: Parent function 'MotionRefiner::read'
relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:23:24: note: Derived function 'MotionRefinerMpi::read'
relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:50:24: warning: The class 'MotionRefinerMpi' defines member function with name 'run' also defined in its parent class 'MotionRefiner'. [duplInheritedMember]
relion-3.1.3/src/jaz/motion/motion_refiner.h:54:8: note: Parent function 'MotionRefiner::run'
relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:50:24: note: Derived function 'MotionRefinerMpi::run'
relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:67:21: style: Variable 'my_nr_micrographs' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:82:27: style: Variable 'my_nr_micrographs' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:53:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:72:20: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:84:20: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/new_ft.cpp:365:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fftw_plan_mutex_new [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/new_ft.cpp:406:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fftw_plan_mutex_new [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/new_ft.cpp:446:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fftw_plan_mutex_new [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/new_ft.cpp:487:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fftw_plan_mutex_new [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/new_ft.h:229:17: style: Class 'DoublePlan' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/jaz/new_ft.h:297:17: style: Class 'FloatPlan' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/jaz/new_ft.h:256:38: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.h:323:38: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:254:29: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:282:21: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:304:30: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:332:22: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:370:4: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:375:4: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:397:13: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:411:4: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:416:4: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:451:4: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:456:4: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:478:13: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:492:4: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/new_ft.cpp:497:4: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/optimization/gradient_descent.cpp:46:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/optimization/optimization.h:51:12: style: The function 'f' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
relion-3.1.3/src/jaz/optimization/optimization.h:32:20: note: Virtual function in base class
relion-3.1.3/src/jaz/optimization/optimization.h:51:12: note: Function in derived class
relion-3.1.3/src/jaz/optimization/optimization.h:52:10: style: The function 'grad' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
relion-3.1.3/src/jaz/optimization/optimization.h:42:18: note: Virtual function in base class
relion-3.1.3/src/jaz/optimization/optimization.h:52:10: note: Function in derived class
relion-3.1.3/src/jaz/obs_model.cpp:71:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:190:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_PIXEL_SIZE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:334:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:445:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:507:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:520:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hasMultipleMtfs [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:575:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:588:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable oddZernikeCoeffs [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:617:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:633:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxSizes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:645:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:650:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:660:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:672:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:677:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:682:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lambda [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:687:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lambda [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:692:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Cs [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:697:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Cs [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:707:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxSizes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:719:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hasBoxSizes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:729:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hasBoxSizes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:746:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magMatrices [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:751:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magMatrices [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:756:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magMatrices [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:762:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:773:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CtfPremultiplied [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:783:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CtfPremultiplied [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:790:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable groupNames [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:858:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:876:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:905:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:930:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:959:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1005:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1020:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mtfImage [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1104:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable avgMtfImage [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1122:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable phaseCorr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1168:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gammaOffset [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1214:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hasMagMatrices [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1237:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxSizes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1244:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X_ANGSTROM [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/noise_helper.cpp:45:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/noise_helper.cpp:664:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/noise_helper.cpp:764:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/noise_helper.cpp:902:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:67:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:95:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:200:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/optimization/lbfgs.h:86:21: style:inconclusive: Technically the member function 'LBFGS::LibLbfgsAdapter::progress' can be const. [functionConst]
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:192:29: note: Technically the member function 'LBFGS::LibLbfgsAdapter::progress' can be const.
relion-3.1.3/src/jaz/optimization/lbfgs.h:86:21: note: Technically the member function 'LBFGS::LibLbfgsAdapter::progress' can be const.
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:144:32: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:154:32: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:91:16: style: Variable 'initial[0]' is reassigned a value before the old one has been used. [redundantAssignment]
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:90:16: note: initial[0] is assigned
relion-3.1.3/src/jaz/optimization/lbfgs.cpp:91:16: note: initial[0] is overwritten
relion-3.1.3/src/jaz/optimization/nelder_mead.cpp:61:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/optimization/nelder_mead.cpp:217:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/obs_model.cpp:1058:19: style: Variable 'img' can be declared as reference to const [constVariableReference]
relion-3.1.3/src/jaz/optimization/optimization.cpp:63:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/optimization/optimization.h:44:7: style:inconclusive: Technically the member function 'DifferentiableOptimization::testGradient' can be const. [functionConst]
relion-3.1.3/src/jaz/optimization/optimization.cpp:47:34: note: Technically the member function 'DifferentiableOptimization::testGradient' can be const.
relion-3.1.3/src/jaz/optimization/optimization.h:44:7: note: Technically the member function 'DifferentiableOptimization::testGradient' can be const.
relion-3.1.3/src/jaz/parallel_ft.cpp:298:9: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/jaz/optimization/nelder_mead.cpp:213:16: style: Variable 'initial[0]' is reassigned a value before the old one has been used. [redundantAssignment]
relion-3.1.3/src/jaz/optimization/nelder_mead.cpp:212:16: note: initial[0] is assigned
relion-3.1.3/src/jaz/optimization/nelder_mead.cpp:213:16: note: initial[0] is overwritten
relion-3.1.3/src/jaz/reference_map.cpp:63:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_POSTPROCESS_UNFIL_HALFMAP1 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/reference_map.cpp:255:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_RANDOM_SUBSET [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/reference_map.cpp:295:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_RANDOM_SUBSET [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/reference_map.cpp:334:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_RANDOM_SUBSET [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/refinement_helper.cpp:44:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SPECTRAL_IDX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/refinement_helper.cpp:78:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SPECTRAL_IDX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/refinement_helper.cpp:116:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SPECTRAL_IDX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/refinement_helper.cpp:169:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/reference_map.cpp:35:15: warning: Member variable 'ReferenceMap::k_out' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/reference_map.cpp:35:15: warning: Member variable 'ReferenceMap::s' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/reference_map.cpp:35:15: warning: Member variable 'ReferenceMap::sh' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/reference_map.cpp:35:15: warning: Member variable 'ReferenceMap::angpix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/noise_helper.cpp:200:37: style: Obsolescent function 'rand_r' called. It is recommended to use 'rand' instead. [prohibitedrand_rCalled]
relion-3.1.3/src/jaz/noise_helper.cpp:201:37: style: Obsolescent function 'rand_r' called. It is recommended to use 'rand' instead. [prohibitedrand_rCalled]
relion-3.1.3/src/jaz/noise_helper.cpp:130:20: style: Local variable 'dm' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/noise_helper.cpp:56:26: note: Shadowed declaration
relion-3.1.3/src/jaz/noise_helper.cpp:130:20: note: Shadow variable
relion-3.1.3/src/jaz/noise_helper.cpp:162:24: style: Local variable 'dm' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/noise_helper.cpp:56:26: note: Shadowed declaration
relion-3.1.3/src/jaz/noise_helper.cpp:162:24: note: Shadow variable
relion-3.1.3/src/jaz/slice_helper.cpp:63:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/slice_helper.cpp:274:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/slice_helper.cpp:328:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/slice_helper.cpp:438:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/slice_helper.cpp:579:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/slice_helper.cpp:651:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/slice_helper.cpp:676:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/slice_helper.cpp:698:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:43:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:95:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:145:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:178:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:227:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:247:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:307:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:547:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:668:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:679:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:700:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:720:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:769:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:809:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:879:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/imod_helper.cpp:39:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/imod_helper.cpp:28:66: performance: Function parameter 'fn' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/tomo/imod_helper.cpp:61:68: performance: Function parameter 'fn' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:43:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:153:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:295:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:357:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:437:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:507:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:594:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:676:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/projection_helper.cpp:123:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/stack_helper.cpp:103:27: style: Checking if unsigned expression 'testString.find("@")' is less than zero. [unsignedLessThanZero]
relion-3.1.3/src/jaz/stack_helper.cpp:208:14: style: Local variable 's' shadows outer variable [shadowVariable]
relion-3.1.3/src/jaz/stack_helper.cpp:189:12: note: Shadowed declaration
relion-3.1.3/src/jaz/stack_helper.cpp:208:14: note: Shadow variable
relion-3.1.3/src/jaz/tomo/projection_helper.cpp:30:21: performance: Function parameter 'tiltFile' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/tomo/projection_helper.cpp:71:21: performance: Function parameter 'tiltFile' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/tomo/projection_helper.cpp:121:74: performance: Function parameter 'xformFile' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/stack_helper.cpp:103:6: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
relion-3.1.3/src/jaz/stack_helper.cpp:150:8: style: Variable 'name' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:39:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:143:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:217:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:232:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:262:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:280:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/volume_converter.cpp:39:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable z [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:338:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.h:34:9: warning:inconclusive: Member variable 'TomoStack::angpix' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.h:34:9: warning:inconclusive: Member variable 'TomoStack::scaleFactor' is not initialized in the constructor. [uninitMemberVar]
relion-3.1.3/src/jaz/tomo/tomo_stack.h:61:53: style:inconclusive: Technically the member function 'TomoStack::loadFiducials' can be const. [functionConst]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:303:56: note: Technically the member function 'TomoStack::loadFiducials' can be const.
relion-3.1.3/src/jaz/tomo/tomo_stack.h:61:53: note: Technically the member function 'TomoStack::loadFiducials' can be const.
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:205:11: warning:inconclusive: Found suspicious operator '+', result is not used. [constStatement]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:32:36: performance: Function parameter 'imagesFn' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:32:72: performance: Function parameter 'angles' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:33:21: performance: Function parameter 'affineTransforms' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:277:42: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/vtk_helper.cpp:27:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:52:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:95:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:135:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:183:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:227:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:272:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:319:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:366:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:413:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:466:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:515:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RFLOAT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:559:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RFLOAT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:689:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/vtk_helper.cpp:717:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RFLOAT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:37:49: performance: Function parameter 'tiltAngles' should be passed by const reference. [passedByValue]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:37:77: style: Parameter 'dest' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:37:106: style: Parameter 'maskDest' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:132:25: style: Parameter 'dest' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:132:47: style: Parameter 'maskDest' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:579:25: style: Parameter 'dest' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:658:55: style: Parameter 'vol' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/jaz/vtk_helper.cpp:78:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:121:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:165:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:213:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:257:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:302:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:349:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:393:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:440:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:492:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:539:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:583:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:741:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/jaz/vtk_helper.cpp:692:9: style:inconclusive: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
relion-3.1.3/src/jaz/vtk_helper.cpp:687:9: warning: Uninitialized variable: size [uninitvar]
relion-3.1.3/src/jaz/vtk_helper.cpp:642:19: note: Assuming condition is true
relion-3.1.3/src/jaz/vtk_helper.cpp:687:9: note: Uninitialized variable: size
relion-3.1.3/src/jaz/vtk_helper.cpp:687:26: warning: Uninitialized variable: dimx [uninitvar]
relion-3.1.3/src/jaz/vtk_helper.cpp:642:19: note: Assuming condition is false
relion-3.1.3/src/jaz/vtk_helper.cpp:687:26: note: Uninitialized variable: dimx
relion-3.1.3/src/jaz/vtk_helper.cpp:687:41: warning: Uninitialized variable: dimy [uninitvar]
relion-3.1.3/src/jaz/vtk_helper.cpp:642:19: note: Assuming condition is false
relion-3.1.3/src/jaz/vtk_helper.cpp:687:41: note: Uninitialized variable: dimy
relion-3.1.3/src/jaz/vtk_helper.cpp:687:56: warning: Uninitialized variable: dimz [uninitvar]
relion-3.1.3/src/jaz/vtk_helper.cpp:642:19: note: Assuming condition is false
relion-3.1.3/src/jaz/vtk_helper.cpp:687:56: note: Uninitialized variable: dimz
relion-3.1.3/src/local_symmetry_mpi.cpp:7:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry_mpi.cpp:49:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_apply_local_symmetry [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:223:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GUI_BACKGROUND_COLOR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:349:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:411:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:427:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:521:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:531:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:567:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:575:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_PIXEL_SIZE [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:627:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MDin [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/manualpicker.cpp:63:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/manualpicker.cpp:155:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/manualpicker.cpp:182:14: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/manualpicker.cpp:420:27: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/manualpicker.cpp:433:27: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/manualpicker.cpp:469:27: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/manualpicker.cpp:481:27: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/manualpicker.cpp:63:7: style: Variable 'iptr' can be declared as pointer to const [constVariablePointer]
relion-3.1.3/src/manualpicker.cpp:155:7: style: Variable 'iptr' can be declared as pointer to const [constVariablePointer]
relion-3.1.3/src/manualpicker.cpp:182:7: style: Variable 'iptr' can be declared as pointer to const [constVariablePointer]
relion-3.1.3/src/manualpicker.cpp:134:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/manualpicker.cpp:163:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/manualpicker.cpp:530:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/manualpicker.cpp:543:18: style: Variable 'mic_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/mask.cpp:58:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mask.cpp:173:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mask.cpp:271:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mask.cpp:313:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mask.cpp:514:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mask.cpp:532:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:40:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:93:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:106:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:131:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:147:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:159:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:171:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:189:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:214:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:237:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:295:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:321:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:381:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:526:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:668:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MASK_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:709:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:768:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:1043:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:1171:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:1366:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:1392:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CC_POS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:1425:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:1735:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:1802:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:2128:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable show_usage_for_an_option [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:2146:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:2151:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:2159:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable show_usage_for_an_option [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:2221:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_apply_local_symmetry [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/local_symmetry.cpp:2773:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/memory.cpp:32:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/memory.cpp:53:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
relion-3.1.3/src/memory.cpp:31:18: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/metadata_container.cpp:52:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:57:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:62:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ints [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:67:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ints [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:72:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bools [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:77:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubleVectors [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:82:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubleVectors [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:88:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable strings [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:93:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:98:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubles [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:103:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ints [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:108:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ints [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:113:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bools [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:118:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable strings [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:123:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubleVectors [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_container.cpp:128:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubleVectors [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:54:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:61:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable names [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:66:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:110:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNDEFINED [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:118:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:123:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:127:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:131:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:135:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:139:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:143:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:147:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:151:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:156:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_LAST_LABEL [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_label.cpp:69:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/helix.cpp:665:6: style: The if condition is the same as the previous if condition [duplicateCondition]
relion-3.1.3/src/helix.cpp:657:6: note: First condition
relion-3.1.3/src/helix.cpp:665:6: note: Second condition
relion-3.1.3/src/helix.cpp:4844:7: style: The if condition is the same as the previous if condition [duplicateCondition]
relion-3.1.3/src/helix.cpp:4837:7: note: First condition
relion-3.1.3/src/helix.cpp:4844:7: note: Second condition
relion-3.1.3/src/helix.cpp:1865:19: style: Condition 'MDobj_id%2' is always true [knownConditionTrueFalse]
relion-3.1.3/src/helix.cpp:1859:16: note: Assignment 'MDobj_id=0', assigned value is 0
relion-3.1.3/src/helix.cpp:1862:6: note: MDobj_id is incremented', new value is 1
relion-3.1.3/src/helix.cpp:1865:19: note: Condition 'MDobj_id%2' is always true
relion-3.1.3/src/helix.cpp:5162:19: style: Condition '*(char*)&num==1' is always true [knownConditionTrueFalse]
relion-3.1.3/src/helix.cpp:5160:12: note: Assignment 'num=1', assigned value is 1
relion-3.1.3/src/helix.cpp:5162:19: note: Condition '*(char*)&num==1' is always true
relion-3.1.3/src/metadata_table.cpp:86:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:98:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable label2offset [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:128:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable isList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:135:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:153:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comment [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:183:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comment [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:188:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comment [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:193:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:198:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:203:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:208:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:213:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURRENT_MDT_VERSION [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:218:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:325:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable unknownLabelPosition2Offset [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:521:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SORTED_IDX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:547:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable label2offset [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:588:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:598:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:605:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:619:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_LAST_LABEL [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:709:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNKNOWN_LABEL [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:753:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:762:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:772:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:786:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:848:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:857:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:866:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:875:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:883:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:889:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:905:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:935:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNDEFINED [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1032:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNDEFINED [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1080:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1139:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1162:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1298:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1368:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1489:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable label2offset [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1544:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1576:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNDEFINED [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1729:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1790:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNKNOWN_LABEL [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1827:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_object [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1851:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1865:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X_ANGSTROM [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/helix.cpp:5162:6: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/helix.cpp:5282:43: portability: Casting between char * and float * which have an incompatible binary data representation. [invalidPointerCast]
relion-3.1.3/src/helix.cpp:5291:43: portability: Casting between char * and float * which have an incompatible binary data representation. [invalidPointerCast]
relion-3.1.3/src/helix.cpp:5303:43: portability: Casting between char * and float * which have an incompatible binary data representation. [invalidPointerCast]
relion-3.1.3/src/helix.cpp:5015:10: style: Variable 'xa' is reassigned a value before the old one has been used. [redundantAssignment]
relion-3.1.3/src/helix.cpp:5012:10: note: xa is assigned
relion-3.1.3/src/helix.cpp:5015:10: note: xa is overwritten
relion-3.1.3/src/helix.cpp:305:112: style: The scope of the variable 'best_id' can be reduced. [variableScope]
relion-3.1.3/src/helix.cpp:1277:45: style: The scope of the variable 'dist' can be reduced. [variableScope]
relion-3.1.3/src/helix.cpp:4673:17: style: The scope of the variable 'rint' can be reduced. [variableScope]
relion-3.1.3/src/helix.cpp:4750:27: style: The scope of the variable 'is_mrcs' can be reduced. [variableScope]
relion-3.1.3/src/helix.cpp:4911:6: style: The scope of the variable 'nr_partitions' can be reduced. [variableScope]
relion-3.1.3/src/helix.cpp:5091:7: style: The scope of the variable 'contain_3d_points' can be reduced. [variableScope]
relion-3.1.3/src/helix.cpp:5091:34: style: The scope of the variable 'flip_YZ' can be reduced. [variableScope]
relion-3.1.3/src/helix.cpp:4229:14: style: Local variable 'pitch' shadows outer variable [shadowVariable]
relion-3.1.3/src/helix.cpp:4225:13: note: Shadowed declaration
relion-3.1.3/src/helix.cpp:4229:14: note: Shadow variable
relion-3.1.3/src/helix.cpp:5693:15: style: Local variable 'angpix' shadows outer variable [shadowVariable]
relion-3.1.3/src/helix.cpp:5679:9: note: Shadowed declaration
relion-3.1.3/src/helix.cpp:5693:15: note: Shadow variable
relion-3.1.3/src/helix.cpp:4067:23: performance: Function parameter 'helical_rise' should be passed by const reference. [passedByValue]
relion-3.1.3/src/helix.cpp:4068:23: performance: Function parameter 'helical_twist' should be passed by const reference. [passedByValue]
relion-3.1.3/src/helix.cpp:1759:13: style: Parameter 'suffix_out' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:2137:16: style: Parameter 'suffix_local_ctf' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:2138:16: style: Parameter 'suffix_combined' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:2266:13: style: Parameter 'suffix_out' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:3461:31: style: Parameter 'fn_in' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:3833:24: style: Parameter 'rise_A' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:3834:24: style: Parameter 'twist_deg' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:4648:16: style: Parameter 'suffix_fout' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:4746:13: style: Parameter 'fn_out_root' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:5070:13: style: Parameter 'fn_out_root' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/helix.cpp:478:22: warning: Array index -1 is out of bounds. [negativeContainerIndex]
relion-3.1.3/src/helix.cpp:439:14: note: Assignment 'best_id=-1', assigned value is -1
relion-3.1.3/src/helix.cpp:440:23: note: Assuming condition is false
relion-3.1.3/src/helix.cpp:478:22: note: Negative array index
relion-3.1.3/src/helix.cpp:480:23: warning: Array index -1 is out of bounds. [negativeContainerIndex]
relion-3.1.3/src/helix.cpp:439:14: note: Assignment 'best_id=-1', assigned value is -1
relion-3.1.3/src/helix.cpp:440:23: note: Assuming condition is false
relion-3.1.3/src/helix.cpp:480:23: note: Negative array index
relion-3.1.3/src/metadata_table.cpp:402:2: style: Struct 'MdDoubleComparator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/metadata_table.cpp:414:2: style: Struct 'MdIntComparator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/metadata_table.cpp:426:2: style: Struct 'MdStringComparator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/metadata_table.cpp:438:2: style: Struct 'MdStringAfterAtComparator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/metadata_table.cpp:454:2: style: Struct 'MdStringBeforeAtComparator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
relion-3.1.3/src/metadata_table.cpp:1148:2: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
relion-3.1.3/src/micrograph_model.cpp:66:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NUM_COEFFS_PER_DIM [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:91:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NUM_COEFFS_PER_DIM [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:158:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eer_upsampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:168:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable model [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:173:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:204:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fnGain [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:297:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fnGain [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:302:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binning [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:307:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fnMovie [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:312:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable width [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:317:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable height [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:322:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_frames [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:327:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eer_upsampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:332:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eer_grouping [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:341:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fnDefect [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:366:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable width [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:412:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_frames [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:425:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable model [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:558:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eer_upsampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:584:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable width [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:621:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable width [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/micrograph_model.cpp:658:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/metadata_table.cpp:1053:12: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
relion-3.1.3/src/metadata_table.cpp:1059:12: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
relion-3.1.3/src/metadata_table.cpp:460:9: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
relion-3.1.3/src/metadata_table.cpp:461:9: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
relion-3.1.3/src/metadata_table.cpp:1071:27: style: Unused variable: value [unusedVariable]
relion-3.1.3/src/metadata_table.cpp:1209:18: style: Unused variable: token [unusedVariable]
relion-3.1.3/src/micrograph_model.cpp:370:46: style: Same expression on both sides of '||'. [duplicateExpression]
relion-3.1.3/src/ml_optimiser.cpp:4141:6: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/ml_model.cpp:37:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:103:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:377:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_bodies [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:683:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SPECTRAL_IDX [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:706:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_DIMENSIONALITY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:916:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_classes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:933:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_BODY_MASK_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1225:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1277:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pixel_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1325:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_particles_per_group [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1391:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_classes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1404:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_classes [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1438:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pixel_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1511:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LL [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1556:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1651:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1723:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1881:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_optimiser_mpi.cpp:2104:8: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/motioncorr_runner.cpp:1266:5: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/motioncorr_runner_mpi.cpp:25:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/motioncorr_runner_mpi.cpp:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:54:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:81:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:86:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:103:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:124:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:176:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:240:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_ERR_COUNT [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:291:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/mpi.cpp:303:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/multidim_array.cpp:55:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/numerical_recipes.cpp:54:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/numerical_recipes.cpp:211:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/numerical_recipes.cpp:718:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/ml_model.cpp:1780:14: style: Checking if unsigned expression 'idx_start' is less than zero. [unsignedLessThanZero]
relion-3.1.3/src/ml_model.cpp:1779:31: note: Assignment 'ori_idx=0', assigned value is 0
relion-3.1.3/src/ml_model.cpp:1780:14: note: Unsigned less than zero
relion-3.1.3/src/ml_model.cpp:1901:14: style: Checking if unsigned expression 'idx_start' is less than zero. [unsignedLessThanZero]
relion-3.1.3/src/ml_model.cpp:1895:31: note: Assignment 'ori_idx=0', assigned value is 0
relion-3.1.3/src/ml_model.cpp:1901:14: note: Unsigned less than zero
relion-3.1.3/src/ml_model.cpp:275:11: style: Local variable 'iclass' shadows outer variable [shadowVariable]
relion-3.1.3/src/ml_model.cpp:196:6: note: Shadowed declaration
relion-3.1.3/src/ml_model.cpp:275:11: note: Shadow variable
relion-3.1.3/src/ml_model.cpp:298:11: style: Local variable 'igroup' shadows outer variable [shadowVariable]
relion-3.1.3/src/ml_model.cpp:260:11: note: Shadowed declaration
relion-3.1.3/src/ml_model.cpp:298:11: note: Shadow variable
relion-3.1.3/src/ml_model.cpp:327:12: style: Local variable 'iclass' shadows outer variable [shadowVariable]
relion-3.1.3/src/ml_model.cpp:196:6: note: Shadowed declaration
relion-3.1.3/src/ml_model.cpp:327:12: note: Shadow variable
relion-3.1.3/src/ml_model.cpp:354:12: style: Local variable 'iclass' shadows outer variable [shadowVariable]
relion-3.1.3/src/ml_model.cpp:196:6: note: Shadowed declaration
relion-3.1.3/src/ml_model.cpp:354:12: note: Shadow variable
relion-3.1.3/src/parallel.cpp:55:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:60:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:65:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:71:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable needed [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:79:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:85:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:103:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable thread_id [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:110:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable thread_id [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:134:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:148:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:163:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:187:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable workFunction [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:209:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable workFunction [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:233:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:246:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable assignedTasks [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:253:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable blockSize [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:259:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable blockSize [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:272:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numberOfTasks [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:294:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable assignedTasks [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/parallel.cpp:132:10: style: Exception should be caught by reference. [catchExceptionByValue]
relion-3.1.3/src/parallel.cpp:117:30: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/parallel.cpp:173:61: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/parallel.cpp:161:9: style: The scope of the variable 'result' can be reduced. [variableScope]
relion-3.1.3/src/particle_subtractor.cpp:694:4: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/pipeline_control.cpp:33:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_JOB_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeline_control.cpp:70:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_JOB_ABORT_NOW [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeline_control.cpp:84:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_JOB_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeline_jobs.cpp:2834:871: error: No pair for character ("). Can't process file. File is either invalid or unicode, which is currently not supported. [syntaxError]
relion-3.1.3/src/pipeliner.cpp:36:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:78:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodeList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:120:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:139:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:162:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodeList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:173:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:186:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:194:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:239:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:254:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:290:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:303:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:324:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:433:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:518:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:677:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROC_IMPORT_NAME [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:728:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROC_MOTIONCORR [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:764:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:805:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable app [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1044:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1080:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1128:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1159:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1252:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1360:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULTPDFVIEWER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1398:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1434:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1679:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1742:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1780:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1805:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1897:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2078:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2292:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inputNodeList [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2394:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alias [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2633:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_branches [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2666:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_short_names [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2712:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2727:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2738:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:2758:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/numerical_recipes.cpp:502:5: warning:inconclusive: Possible null pointer dereference: xt [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:499:16: note: Assignment 'xt=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:502:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:502:5: warning:inconclusive: Possible null pointer dereference: pcom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:672:18: note: Assignment 'pcom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:684:59: note: Calling function 'mnbrak', 10th argument 'pcom' value is 0
relion-3.1.3/src/numerical_recipes.cpp:502:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:502:5: warning:inconclusive: Possible null pointer dereference: xicom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:673:19: note: Assignment 'xicom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:684:65: note: Calling function 'mnbrak', 11th argument 'xicom' value is 0
relion-3.1.3/src/numerical_recipes.cpp:502:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:503:5: warning:inconclusive: Possible null pointer dereference: xt [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:499:16: note: Assignment 'xt=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:503:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:503:5: warning:inconclusive: Possible null pointer dereference: pcom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:672:18: note: Assignment 'pcom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:684:59: note: Calling function 'mnbrak', 10th argument 'pcom' value is 0
relion-3.1.3/src/numerical_recipes.cpp:503:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:503:5: warning:inconclusive: Possible null pointer dereference: xicom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:673:19: note: Assignment 'xicom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:684:65: note: Calling function 'mnbrak', 11th argument 'xicom' value is 0
relion-3.1.3/src/numerical_recipes.cpp:503:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:510:5: warning:inconclusive: Possible null pointer dereference: pcom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:672:18: note: Assignment 'pcom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:684:59: note: Calling function 'mnbrak', 10th argument 'pcom' value is 0
relion-3.1.3/src/numerical_recipes.cpp:510:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:510:5: warning:inconclusive: Possible null pointer dereference: xicom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:673:19: note: Assignment 'xicom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:684:65: note: Calling function 'mnbrak', 11th argument 'xicom' value is 0
relion-3.1.3/src/numerical_recipes.cpp:510:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:585:5: warning:inconclusive: Possible null pointer dereference: xt [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:579:16: note: Assignment 'xt=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:585:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:585:5: warning:inconclusive: Possible null pointer dereference: pcom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:672:18: note: Assignment 'pcom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:685:59: note: Calling function 'brent', 9th argument 'pcom' value is 0
relion-3.1.3/src/numerical_recipes.cpp:585:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:585:5: warning:inconclusive: Possible null pointer dereference: xicom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:673:19: note: Assignment 'xicom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:685:65: note: Calling function 'brent', 10th argument 'xicom' value is 0
relion-3.1.3/src/numerical_recipes.cpp:585:5: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:678:9: warning:inconclusive: Possible null pointer dereference: pcom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:672:18: note: Assignment 'pcom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:678:9: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:679:9: warning:inconclusive: Possible null pointer dereference: xicom [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:673:19: note: Assignment 'xicom=NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:679:9: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:826:9: warning:inconclusive: Possible null pointer dereference: rv1 [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:813:19: note: Assignment 'rv1=(RFLOAT*)NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:826:9: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:903:36: warning:inconclusive: Possible null pointer dereference: rv1 [nullPointer]
relion-3.1.3/src/numerical_recipes.cpp:813:19: note: Assignment 'rv1=(RFLOAT*)NULL', assigned value is 0
relion-3.1.3/src/numerical_recipes.cpp:903:36: note: Null pointer dereference
relion-3.1.3/src/numerical_recipes.cpp:701:12: style: The scope of the variable 'ibig' can be reduced. [variableScope]
relion-3.1.3/src/numerical_recipes.cpp:1134:9: style: The scope of the variable 'n' can be reduced. [variableScope]
relion-3.1.3/src/numerical_recipes.cpp:147:42: style: Parameter 'c' can be declared as const array [constParameter]
relion-3.1.3/src/numerical_recipes.cpp:407:19: style: Variable 'cof' can be declared as const array [constVariable]
relion-3.1.3/src/numerical_recipes.cpp:496:42: style: Parameter 'pcom' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/numerical_recipes.cpp:496:56: style: Parameter 'xicom' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/numerical_recipes.cpp:574:32: style: Parameter 'pcom' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/numerical_recipes.cpp:574:46: style: Parameter 'xicom' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/numerical_recipes.cpp:1100:21: style: Parameter 'u' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/numerical_recipes.cpp:1100:32: style: Parameter 'w' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/numerical_recipes.cpp:1100:43: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/numerical_recipes.cpp:1100:68: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
relion-3.1.3/src/postprocessing.cpp:27:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_I1 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:83:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:88:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_I1 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:113:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_I2 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:186:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_mask [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:248:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_mtf [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:370:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:448:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable guinierin [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:544:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:563:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fsc_masked [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:585:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:616:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:661:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:862:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:885:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_out [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:930:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:1167:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_ampl_corr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:49:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_star_in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:103:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:112:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_extract [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:259:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_extract [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:280:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:426:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:496:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:577:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:639:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_part_dir [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:747:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:1023:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LARGE_NUMBER [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:1065:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_rescale [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:1150:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MDimg [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:1277:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_coord_dir [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing.cpp:1286:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_part_dir [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/postprocessing.cpp:26:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/postprocessing.cpp:35:19: style: Variable 'mask_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/postprocessing.cpp:43:20: style: Variable 'sharp_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/postprocessing.cpp:50:21: style: Variable 'filter_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/postprocessing.cpp:55:21: style: Variable 'locres_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/postprocessing.cpp:63:21: style: Variable 'expert_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/preprocessing_mpi.cpp:25:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing_mpi.cpp:46:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing_mpi.cpp:120:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_extract [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/preprocessing_mpi.cpp:30:18: style: Variable 'mpi_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/projector.cpp:270:3: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_ELEMENTS_IN_ARRAY3D is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/preprocessing.cpp:279:6: style: The scope of the variable 'og' can be reduced. [variableScope]
relion-3.1.3/src/preprocessing.cpp:435:7: style: The scope of the variable 'micIsUsed' can be reduced. [variableScope]
relion-3.1.3/src/preprocessing.cpp:202:14: style: Local variable 'fn_mic' shadows outer variable [shadowVariable]
relion-3.1.3/src/preprocessing.cpp:147:12: note: Shadowed declaration
relion-3.1.3/src/preprocessing.cpp:202:14: note: Shadow variable
relion-3.1.3/src/preprocessing.cpp:947:8: style: Local variable 'optics_group' shadows outer variable [shadowVariable]
relion-3.1.3/src/preprocessing.cpp:764:6: note: Shadowed declaration
relion-3.1.3/src/preprocessing.cpp:947:8: note: Shadow variable
relion-3.1.3/src/preprocessing.cpp:804:28: warning: Uninitialized variable: zF [uninitvar]
relion-3.1.3/src/preprocessing.cpp:794:22: note: Assuming condition is false
relion-3.1.3/src/preprocessing.cpp:804:28: note: Uninitialized variable: zF
relion-3.1.3/src/preprocessing.cpp:804:38: warning: Uninitialized variable: z0 [uninitvar]
relion-3.1.3/src/preprocessing.cpp:794:22: note: Assuming condition is false
relion-3.1.3/src/preprocessing.cpp:804:38: note: Uninitialized variable: z0
relion-3.1.3/src/preprocessing.cpp:48:18: style: Variable 'gen_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/preprocessing.cpp:63:22: style: Variable 'extract_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/preprocessing.cpp:76:22: style: Variable 'perpart_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/preprocessing.cpp:89:20: style: Variable 'helix_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/preprocessing.cpp:531:19: style: Variable 'is_data' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/reconstructor_mpi.cpp:25:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor_mpi.cpp:47:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_debug [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:27:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sel [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:99:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:104:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_reconstruct_ctf [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:217:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_debug [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:232:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:282:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sub [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:327:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_RANDOM_SUBSET [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:689:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_boxsize [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:798:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_sectors [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:47:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable prevTIFFWarningHandler [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:53:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable prevTIFFWarningHandler [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:102:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:112:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:188:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buf [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:228:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable read_data [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:272:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buf [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:278:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:286:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:294:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/renderEER.cpp:303:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/reconstructor.cpp:633:14: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use replace() instead. [uselessCallsSubstr]
relion-3.1.3/src/reconstructor.cpp:26:22: style: Variable 'general_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/reconstructor.cpp:37:18: style: Variable 'ctf_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/reconstructor.cpp:43:20: style: Variable 'ewald_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/reconstructor.cpp:56:22: style: Variable 'helical_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/reconstructor.cpp:61:21: style: Variable 'expert_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:1460:26: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
relion-3.1.3/src/pipeliner.cpp:1469:12: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
relion-3.1.3/src/pipeliner.cpp:284:6: style: Redundant initialization for 'res'. The initialized value is overwritten before it is read. [redundantInitialization]
relion-3.1.3/src/pipeliner.cpp:279:10: note: res is initialized
relion-3.1.3/src/pipeliner.cpp:284:6: note: res is overwritten
relion-3.1.3/src/pipeliner.cpp:318:6: style: Redundant initialization for 'res'. The initialized value is overwritten before it is read. [redundantInitialization]
relion-3.1.3/src/pipeliner.cpp:309:10: note: res is initialized
relion-3.1.3/src/pipeliner.cpp:318:6: note: res is overwritten
relion-3.1.3/src/pipeliner.cpp:1105:8: style: Redundant initialization for 'res'. The initialized value is overwritten before it is read. [redundantInitialization]
relion-3.1.3/src/pipeliner.cpp:1103:12: note: res is initialized
relion-3.1.3/src/pipeliner.cpp:1105:8: note: res is overwritten
relion-3.1.3/src/pipeliner.cpp:1718:8: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment]
relion-3.1.3/src/pipeliner.cpp:1714:9: note: res is assigned
relion-3.1.3/src/pipeliner.cpp:1718:8: note: res is overwritten
relion-3.1.3/src/pipeliner.cpp:223:15: style: The scope of the variable 'command' can be reduced. [variableScope]
relion-3.1.3/src/pipeliner.cpp:1693:6: style: The scope of the variable 'res' can be reduced. [variableScope]
relion-3.1.3/src/pipeliner.cpp:2430:11: style: The scope of the variable 'result' can be reduced. [variableScope]
relion-3.1.3/src/pipeliner.cpp:1110:9: style: Local variable 'res' shadows outer variable [shadowVariable]
relion-3.1.3/src/pipeliner.cpp:1103:8: note: Shadowed declaration
relion-3.1.3/src/pipeliner.cpp:1110:9: note: Shadow variable
relion-3.1.3/src/pipeliner.cpp:1458:12: style: Local variable 'fn_curr_dir' shadows outer variable [shadowVariable]
relion-3.1.3/src/pipeliner.cpp:1452:11: note: Shadowed declaration
relion-3.1.3/src/pipeliner.cpp:1458:12: note: Shadow variable
relion-3.1.3/src/pipeliner.cpp:1487:12: style: Local variable 'idir' shadows outer variable [shadowVariable]
relion-3.1.3/src/pipeliner.cpp:1453:6: note: Shadowed declaration
relion-3.1.3/src/pipeliner.cpp:1487:12: note: Shadow variable
relion-3.1.3/src/pipeliner.cpp:1513:12: style: Local variable 'idir' shadows outer variable [shadowVariable]
relion-3.1.3/src/pipeliner.cpp:1453:6: note: Shadowed declaration
relion-3.1.3/src/pipeliner.cpp:1513:12: note: Shadow variable
relion-3.1.3/src/pipeliner.cpp:1522:12: style: Local variable 'idir' shadows outer variable [shadowVariable]
relion-3.1.3/src/pipeliner.cpp:1453:6: note: Shadowed declaration
relion-3.1.3/src/pipeliner.cpp:1522:12: note: Shadow variable
relion-3.1.3/src/pipeliner.cpp:1531:12: style: Local variable 'idir' shadows outer variable [shadowVariable]
relion-3.1.3/src/pipeliner.cpp:1453:6: note: Shadowed declaration
relion-3.1.3/src/pipeliner.cpp:1531:12: note: Shadow variable
relion-3.1.3/src/pipeliner.cpp:1594:12: style: Local variable 'idir' shadows outer variable [shadowVariable]
relion-3.1.3/src/pipeliner.cpp:1453:6: note: Shadowed declaration
relion-3.1.3/src/pipeliner.cpp:1594:12: note: Shadow variable
relion-3.1.3/src/pipeliner.cpp:1621:12: style: Local variable 'idir' shadows outer variable [shadowVariable]
relion-3.1.3/src/pipeliner.cpp:1453:6: note: Shadowed declaration
relion-3.1.3/src/pipeliner.cpp:1621:12: note: Shadow variable
relion-3.1.3/src/pipeliner.cpp:227:12: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:284:6: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:318:6: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:509:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:648:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:1105:8: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:60:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1110:13: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:179:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input1 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:289:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input2 [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:532:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:576:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_fork [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:582:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:612:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:780:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:788:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:986:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1080:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1087:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1094:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1102:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1109:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1116:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1123:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1130:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1137:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1144:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1151:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1158:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1163:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1182:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1238:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1279:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable edges [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1343:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1398:129: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1329:13: style: Variable 'res2' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:1427:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1337:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:1447:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1463:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1479:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1552:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1665:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1830:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:1846:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/pipeliner.cpp:1373:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:1377:7: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:1661:12: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:1666:12: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:1718:8: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/renderEER.cpp:188:8: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/renderEER.cpp:200:30: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/renderEER.cpp:203:28: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/renderEER.cpp:232:10: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/renderEER.cpp:358:34: style: C-style pointer casting [cstyleCast]
relion-3.1.3/src/pipeliner.cpp:1733:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/pipeliner.cpp:2562:18: style: Unused variable: labelpos [unusedVariable]
relion-3.1.3/src/renderEER.cpp:347:18: style: The scope of the variable 'p' can be reduced. [variableScope]
relion-3.1.3/src/renderEER.cpp:392:18: style: The scope of the variable 'p1' can be reduced. [variableScope]
relion-3.1.3/src/renderEER.cpp:392:22: style: The scope of the variable 'p2' can be reduced. [variableScope]
relion-3.1.3/src/renderEER.cpp:392:26: style: The scope of the variable 's1' can be reduced. [variableScope]
relion-3.1.3/src/renderEER.cpp:392:30: style: The scope of the variable 's2' can be reduced. [variableScope]
relion-3.1.3/src/strings.cpp:166:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/strings.cpp:335:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/strings.cpp:686:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/strings.cpp:98:33: style: Condition 'value.find_first_of(" \t")!=-1' is always true [knownConditionTrueFalse]
relion-3.1.3/src/strings.cpp:309:27: performance: Function parameter '_input' should be passed by const reference. [passedByValue]
relion-3.1.3/src/strings.cpp:481:12: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
relion-3.1.3/src/strings.cpp:527:16: warning: Either the condition 'i==0' is redundant, otherwise there is negative array index -1. [negativeContainerIndex]
relion-3.1.3/src/strings.cpp:525:9: note: Assuming that condition 'i==0' is not redundant
relion-3.1.3/src/strings.cpp:527:16: note: Negative array index
relion-3.1.3/src/strings.cpp:319:23: error: Uninitialized variable: aux [uninitvar]
relion-3.1.3/src/strings.cpp:240:6: style: Unused variable: ok [unusedVariable]
relion-3.1.3/src/tabfuncs.cpp:24:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:33:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:40:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:47:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:56:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:63:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:69:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable radius [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:81:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:88:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:97:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable radius [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:109:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tabfuncs.cpp:116:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/tiff_converter.cpp:433:4: error: There is an unknown macro here somewhere. Configuration is required. If FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY is a macro then please configure it. [unknownMacro]
relion-3.1.3/src/scheduler.cpp:1095:38: style: Variable 'scheduler_global_floats[name].value' is reassigned a value before the old one has been used. [redundantAssignment]
relion-3.1.3/src/scheduler.cpp:1094:38: note: scheduler_global_floats[name].value is assigned
relion-3.1.3/src/scheduler.cpp:1095:38: note: scheduler_global_floats[name].value is overwritten
relion-3.1.3/src/scheduler.cpp:191:7: style: The scope of the variable 'idxmin' can be reduced. [variableScope]
relion-3.1.3/src/scheduler.cpp:191:15: style: The scope of the variable 'idxmax' can be reduced. [variableScope]
relion-3.1.3/src/scheduler.cpp:196:7: style: The scope of the variable 'ii' can be reduced. [variableScope]
relion-3.1.3/src/scheduler.cpp:1709:43: style: The scope of the variable 'dummy' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:31:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SC_CLK_TCK [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/time.cpp:61:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/time.cpp:130:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/time.cpp:197:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable counts [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/time.cpp:205:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_time [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/time.cpp:214:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start_times [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/time.cpp:221:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tv_sec [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:213:8: style: Local variable 'ival' shadows outer variable [shadowVariable]
relion-3.1.3/src/scheduler.cpp:190:6: note: Shadowed declaration
relion-3.1.3/src/scheduler.cpp:213:8: note: Shadow variable
relion-3.1.3/src/time.cpp:229:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable counts [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/scheduler.cpp:245:9: style: Local variable 'ival' shadows outer variable [shadowVariable]
relion-3.1.3/src/scheduler.cpp:190:6: note: Shadowed declaration
relion-3.1.3/src/scheduler.cpp:245:9: note: Shadow variable
relion-3.1.3/src/scheduler.cpp:463:16: style: Local variable 'mycommand' shadows outer variable [shadowVariable]
relion-3.1.3/src/scheduler.cpp:448:15: note: Shadowed declaration
relion-3.1.3/src/scheduler.cpp:463:16: note: Shadow variable
relion-3.1.3/src/scheduler.cpp:1382:15: style: Local variable 'command' shadows outer variable [shadowVariable]
relion-3.1.3/src/scheduler.cpp:1337:14: note: Shadowed declaration
relion-3.1.3/src/scheduler.cpp:1382:15: note: Shadow variable
relion-3.1.3/src/scheduler.cpp:1383:7: style: Local variable 'res' shadows outer variable [shadowVariable]
relion-3.1.3/src/scheduler.cpp:1338:6: note: Shadowed declaration
relion-3.1.3/src/scheduler.cpp:1383:7: note: Shadow variable
relion-3.1.3/src/scheduler.cpp:1714:9: style: Local variable 'dummy' shadows outer variable [shadowVariable]
relion-3.1.3/src/scheduler.cpp:1709:43: note: Shadowed declaration
relion-3.1.3/src/scheduler.cpp:1714:9: note: Shadow variable
relion-3.1.3/src/scheduler.cpp:1394:37: performance: Function parameter 'message' should be passed by const reference. [passedByValue]
relion-3.1.3/src/scheduler.cpp:1394:58: performance: Function parameter 'subject' should be passed by const reference. [passedByValue]
relion-3.1.3/src/scheduler.cpp:600:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
relion-3.1.3/src/scheduler.cpp:380:18: style: Variable 'nr_splits' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:426:17: style: Variable 'nr_splits' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:464:13: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:468:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:474:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:1242:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:1338:10: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:1383:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:1399:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:1608:18: style: Variable 'nr_splits' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/scheduler.cpp:598:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:843:84: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:858:82: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:873:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:888:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:905:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:960:84: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:966:82: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:972:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:978:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:1302:89: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:1341:141: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:1363:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/scheduler.cpp:1489:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
relion-3.1.3/src/transformations.cpp:153:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/time.cpp:97:6: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
relion-3.1.3/src/time.cpp:167:4: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
relion-3.1.3/src/time.cpp:167:4: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
relion-3.1.3/src/time.cpp:118:7: style: The scope of the variable 't1' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:118:11: style: The scope of the variable 't2' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:119:6: style: The scope of the variable 'min' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:119:14: style: The scope of the variable 'hour' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:120:8: style: The scope of the variable 'h1' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:120:12: style: The scope of the variable 'h2' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:120:16: style: The scope of the variable 'm1' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:120:20: style: The scope of the variable 'm2' can be reduced. [variableScope]
relion-3.1.3/src/time.cpp:50:36: style: Parameter 'time' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/time.cpp:65:31: style: Parameter 'time' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/time.cpp:80:29: style: Parameter 'time' can be declared as reference to const [constParameterReference]
relion-3.1.3/src/time.cpp:92:13: style: Variable 'T' can be declared as pointer to const [constVariablePointer]
relion-3.1.3/src/local_symmetry.cpp:1893:41: style: Condition 'icen<id' is always true [knownConditionTrueFalse]
relion-3.1.3/src/local_symmetry.cpp:1893:27: note: Assuming that condition 'icen<K' is not redundant
relion-3.1.3/src/local_symmetry.cpp:1882:8: note: Assuming that condition 'K!=id' is not redundant
relion-3.1.3/src/local_symmetry.cpp:1893:41: note: Condition 'icen<id' is always true
relion-3.1.3/src/local_symmetry.cpp:365:7: style: The scope of the variable 'is_maskname_found' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:1793:14: style: The scope of the variable 'int_val' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:2346:12: style: The scope of the variable 'newdim' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:2346:37: style: The scope of the variable 'z0' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:2346:45: style: The scope of the variable 'y0' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:2346:53: style: The scope of the variable 'x0' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:2346:61: style: The scope of the variable 'zf' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:2346:69: style: The scope of the variable 'yf' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:2346:77: style: The scope of the variable 'xf' can be reduced. [variableScope]
relion-3.1.3/src/local_symmetry.cpp:2608:29: style: Checking if unsigned expression 'op_samplings.size()' is less than zero. [unsignedLessThanZero]
relion-3.1.3/src/local_symmetry.cpp:1069:31: performance: Function parameter 'fn_masks' should be passed by const reference. [passedByValue]
relion-3.1.3/src/local_symmetry.cpp:1070:54: performance: Function parameter 'ops' should be passed by const reference. [passedByValue]
relion-3.1.3/src/local_symmetry.cpp:1152:31: performance: Function parameter 'fn_masks' should be passed by const reference. [passedByValue]
relion-3.1.3/src/local_symmetry.cpp:1153:54: performance: Function parameter 'ops' should be passed by const reference. [passedByValue]
relion-3.1.3/src/local_symmetry.cpp:1330:31: performance: Function parameter 'fn_masks' should be passed by const reference. [passedByValue]
relion-3.1.3/src/local_symmetry.cpp:1331:54: performance: Function parameter 'ops' should be passed by const reference. [passedByValue]
relion-3.1.3/src/local_symmetry.cpp:2158:19: style: Variable 'init_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2161:22: style: Variable 'options_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2169:21: style: Variable 'params_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2198:21: style: Variable 'expert_section' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2211:15: style: Variable 'do_sort' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2346:19: style: Variable 'newdim' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2346:40: style: Variable 'z0' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2346:48: style: Variable 'y0' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2346:56: style: Variable 'x0' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2346:64: style: Variable 'zf' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2346:72: style: Variable 'yf' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/local_symmetry.cpp:2346:80: style: Variable 'xf' is assigned a value that is never used. [unreadVariable]
relion-3.1.3/src/symmetries.cpp:90:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable true_symNo [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/symmetries.cpp:232:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __L [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/symmetries.cpp:281:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable true_symNo [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/symmetries.cpp:363:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pg_CN [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/symmetries.cpp:611:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pg_CN [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/symmetries.cpp:773:134: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/symmetries.cpp:793:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pg_CN [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/symmetries.cpp:919:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IS_INV [valueFlowBailoutIncompleteVar]
relion-3.1.3/src/symmetries.cpp:61:22: style: The scope of the variable 'pgOrder' can be reduced. [variableScope]
relion-3.1.3/src/symmetries.cpp:280:9: style: The scope of the variable 'new_chain_length' can be reduced. [variableScope]
diff:
head relion-3.1.3/src/CPlot2D.cpp:252:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/CPlot2D.cpp:60:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/CPlot2D.h:197:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/CPlot2D.h:212:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/CPlot2D.h:226:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/CPlot2D.h:334:18: performance: Function 'GetMarkerSymbol()' should return member 'm_strMarker' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:388:18: performance: Function 'GetDashedLinePattern()' should return member 'm_iDashedLinePattern' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:424:18: performance: Function 'GetDatasetTitle()' should return member 'm_strDatasetTitle' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:442:18: performance: Function 'GetDatasetLegendFont()' should return member 'm_strDatasetLegendFont' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:721:18: performance: Function 'GetXAxisLabelFont()' should return member 'm_strXAxisLabelFont' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:741:18: performance: Function 'GetYAxisLabelFont()' should return member 'm_strYAxisLabelFont' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:761:18: performance: Function 'GetXAxisTitleFont()' should return member 'm_strXAxisTitleFont' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:781:18: performance: Function 'GetYAxisTitleFont()' should return member 'm_strYAxisTitleFont' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:802:18: performance: Function 'GetXAxisTitle()' should return member 'm_strXAxisTitle' by const reference. [returnByReference]
head relion-3.1.3/src/CPlot2D.h:813:18: performance: Function 'GetYAxisTitle()' should return member 'm_strYAxisTitle' by const reference. [returnByReference]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:129:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:140:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:149:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:229:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:263:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:273:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scheme_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:298:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:306:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:325:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:353:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:371:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable twopi [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:462:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scheme_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:536:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fact2_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:586:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scheme_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:638:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scheme_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:684:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:722:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable twopi [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:73:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable twothird [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:778:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npix_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:784:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pi [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/Healpix_2.15a/healpix_base.cc:88:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nside_ [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:108:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:875:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/acc/cpu/cpu_kernels/helper.cpp:942:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/align_symmetry.cpp:138:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/align_symmetry.cpp:282:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/align_symmetry.cpp:72:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEAREST_NEIGHBOUR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/align_symmetry.cpp:94:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/convert_star.cpp:129:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/convert_star.cpp:61:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_METADATA_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/ctf_toolbox.cpp:100:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/ctf_toolbox.cpp:231:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:116:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEAREST_NEIGHBOUR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:188:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:294:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/double_reconstruct_openmp.cpp:720:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/estimate_gain.cpp:255:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/external_reconstruct.cpp:133:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/external_reconstruct.cpp:90:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRILINEAR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/find_tiltpairs.cpp:123:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/find_tiltpairs.cpp:186:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/find_tiltpairs.cpp:379:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/find_tiltpairs.cpp:403:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/find_tiltpairs.cpp:484:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/helix_toolbox.cpp:1099:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/helix_toolbox.cpp:240:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/helix_toolbox.cpp:368:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/helix_toolbox.cpp:417:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/image_handler.cpp:1068:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/image_handler.cpp:154:137: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BLACKGREYREDSCALE [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/image_handler.cpp:187:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/image_handler.cpp:713:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/import.cpp:330:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/import.cpp:98:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/interpolation_test.cpp:3:26: style: Parameter 'argv' can be declared as const array [constParameter]
head relion-3.1.3/src/apps/mask_create.cpp:133:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/mask_create.cpp:228:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/mask_create.cpp:99:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/mrc2vtk.cpp:4:26: style: Parameter 'argv' can be declared as const array [constParameter]
head relion-3.1.3/src/apps/particle_symmetry_expand.cpp:112:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/particle_symmetry_expand.cpp:224:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/pipeliner.cpp:166:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/pipeliner.cpp:81:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/prepare_subtomo.cpp:1111:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/prepare_subtomo.cpp:166:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/prepare_subtomo.cpp:209:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/prepare_subtomo.cpp:536:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/scheduler.cpp:122:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_JOB_ABORT_NOW [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/scheduler.cpp:280:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/stack_create.cpp:278:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/stack_create.cpp:62:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/stack_create.cpp:80:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:1006:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:1020:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:1065:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:169:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:183:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:214:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:237:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:258:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:267:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:369:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:689:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_object [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:839:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:846:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X_ANGSTROM [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:917:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/star_handler.cpp:987:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/tiltpair_plot.cpp:199:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/tiltpair_plot.cpp:258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/tiltpair_plot.cpp:314:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/tiltpair_plot.cpp:88:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/apps/vis_delocalisation.cpp:178:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Both [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:129:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable options [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:144:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:159:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:187:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_section [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:203:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_section [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:211:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_section [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:217:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable options [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:237:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:283:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:294:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:337:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable argc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:378:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable options [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:400:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optionals [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:415:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/args.cpp:433:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:123:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:149:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:176:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:184:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:191:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:19:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coords [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:205:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:24:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable number [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:313:21: style: The scope of the variable 'str_resname' can be reduced. [variableScope]
head relion-3.1.3/src/assembly.cpp:405:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:42:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:479:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:498:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecules [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/assembly.cpp:88:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable number [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:1061:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:1120:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable helical_tube_diameter [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:1271:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable helical_tube_diameter [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:1515:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_stddev_noise [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:1845:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:185:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:216:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable random_seed [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:2342:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:2530:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable workSize [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:2841:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable autopick_skip_side [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:3475:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_odir [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:3487:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable micrograph_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:3561:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_fraction_expected_Pratio [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:35:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:3620:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:3683:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:3722:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_optimise_scale [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:48:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:58:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area_percentage [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:897:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:945:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker.cpp:96:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/autopicker_mpi.cpp:81:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:1003:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:1055:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:1216:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:1377:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:1837:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:1856:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref_dim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:2020:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:2174:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pad_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:2239:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:363:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:477:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:678:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:83:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding_factor [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:864:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:905:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/backprojector.cpp:938:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r_max [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:137:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kV [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:154:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable opticsGroup [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:209:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Cs [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:260:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:288:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:319:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:470:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:543:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:558:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:572:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obsModel [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:620:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:646:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable jp [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:666:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Axx [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:671:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Axy [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:676:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Ayy [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctf.cpp:97:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kV [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:366:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_only_join_results [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:425:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:536:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_micrographs_ctf [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:610:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_micrographs_ctf [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:691:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_micrographs_ctf [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:814:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_ctffind4 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:830:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:927:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:93:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner.cpp:99:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_ctffind_exe [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ctffind_runner_mpi.cpp:41:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_only_join_results [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1019:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1066:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1151:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1174:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1193:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULTPDFVIEWER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1226:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1275:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_selected_parts [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1319:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1427:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MULTIVIEWER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1451:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:147:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scale [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1510:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_selected_imgs [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1593:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GUI_BACKGROUND_COLOR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1614:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FL_PUSH [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1704:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1753:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:1841:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FL_PUSH [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2000:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_coords [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2038:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_coords [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2051:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_color [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2124:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2130:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2138:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2153:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2316:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2361:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2403:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2511:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2574:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2579:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_gui [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2682:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:272:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable selected [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:2782:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_gui [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:282:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable selected [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:289:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable selected [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:296:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable selected [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:316:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MULTIVIEWER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:392:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_selection_type [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:442:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ncol [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:634:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xoff [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:652:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:657:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FL_PUSH [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:81:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable colour_scheme [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:862:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:895:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_selected_imgs [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:952:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:960:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:968:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:976:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/displayer.cpp:984:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_class [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/error.cpp:76:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:100:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:109:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:1165:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:155:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_images_per_optics_group [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:202:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_particles_subset1 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:360:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:38:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:412:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_bodies [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:445:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:483:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_scratch [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:523:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_scratch [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:541:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable free_space_Gb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:581:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_scratch [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:597:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:76:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:815:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WRITE_READONLY [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:81:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:86:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:91:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/exp_model.cpp:96:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable particles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:296:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:308:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:325:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:334:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:488:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:497:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:520:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:550:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/filename.cpp:98:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:182:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:193:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DONT_WRAP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:220:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:348:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:450:93: style: Parameter 'means' can be declared as reference to const [constParameterReference]
head relion-3.1.3/src/flex_analyser.cpp:466:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:571:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:660:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:702:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/flex_analyser.cpp:710:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/funcs.cpp:119:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable w [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/funcs.cpp:238:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/funcs.cpp:261:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/funcs.cpp:337:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/funcs.cpp:514:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/funcs.cpp:590:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/funcs.cpp:611:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/funcs.cpp:765:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/gui_entries.cpp:108:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable joboption_type [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/gui_entries.cpp:209:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable deactivate_option [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/gui_entries.cpp:223:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/gui_entries.cpp:255:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inp [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/gui_entries.cpp:309:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SINGLE [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/gui_entries.cpp:350:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SINGLE [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/gui_entries.cpp:400:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable my_deactivate_group [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1053:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable healpix_order [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1128:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1495:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sym [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1507:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable directions_ipix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1550:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset_step [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1555:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable helical_offset_step [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1560:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1596:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3d_trans [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1615:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1624:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3d_trans [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1641:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rot_angles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1654:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable psi_angles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1666:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translations_x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:170:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable random_perturbation [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1712:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translations_x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:179:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1844:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rot_angles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1925:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable psi_angles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1948:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:1995:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:2083:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable limit_tilt [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:2152:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rot_angles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:2231:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pg_CN [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:237:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:307:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset_step [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:468:128: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3d_trans [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:485:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable healpix_order [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:570:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:607:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:639:101: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:63:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/healpix_sampling.cpp:677:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_3D [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:1305:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:1353:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:1397:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:1511:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CART_TO_HELICAL_COORDS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:1609:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:1745:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:174:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:1785:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_STAR_FORMAT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:1832:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNIMODAL_PSI_PRIOR_FLIP_RATIO [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2029:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2150:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2175:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_TILT_PRIOR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2204:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_TILT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2241:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_PSI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2289:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XIMDISP_COORDS_FORMAT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2322:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNIMODAL_PSI_PRIOR_FLIP_RATIO [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2397:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2510:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2653:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:2777:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3079:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3346:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3421:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3479:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3513:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:353:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3625:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3846:184: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3897:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:3984:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4003:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MDobjectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4021:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4039:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable psi_deg [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4100:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable helical_tube_name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4391:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4550:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_TILT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4584:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_PSI_PRIOR_FLIP_RATIO [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4596:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4622:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4658:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4691:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4714:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_Z_ANGSTROM [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4762:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_TILT_PRIOR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:4927:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:5122:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:5512:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:5554:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:5674:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:659:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/helix.cpp:977:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/aberration_fit.cpp:196:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coefficients [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/apps/ref_aberration_plot.cpp:75:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable noReference [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/apps/ref_aberration_plot.cpp:91:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/apps/ref_aberration_plot.cpp:96:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_omp_threads [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_em.cpp:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable posProb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_em.cpp:197:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_em.cpp:231:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_em.cpp:333:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_em.cpp:387:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s_vel [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_em.cpp:426:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_em.cpp:498:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable initialized [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_em.cpp:543:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1046:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1077:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1118:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:114:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1181:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1210:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1250:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1302:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1319:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1383:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1452:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:145:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1485:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1619:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1688:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:1719:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:220:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:259:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:286:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:311:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:365:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:413:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:603:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:652:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:68:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:694:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_NUMBER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:732:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_NUMBER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:771:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:820:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:841:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/motion_refinement.cpp:99:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/refinement_program.cpp:427:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sh [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/refinement_program.cpp:432:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sh [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/refinement_program.cpp:437:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable preextracted [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/refinement_program.cpp:516:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable preextracted [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/archive/refinement_program.cpp:630:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mdts [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/aberration_estimator.cpp:176:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:316:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_BFACTOR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/bfactor_refiner.cpp:457:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:126:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:249:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:416:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:437:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/ctf_refiner.cpp:497:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:185:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/defocus_estimator.cpp:308:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/delocalisation_helper.cpp:78:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/magnification_estimator.cpp:151:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:179:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Axx [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:329:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Axx [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/magnification_helper.cpp:429:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:177:29: style: C-style pointer casting [cstyleCast]
head relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:199:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:273:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:381:29: style: C-style pointer casting [cstyleCast]
head relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:404:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/modular_ctf_optimisation.cpp:595:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DEFOCUSU [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/tilt_estimator.cpp:176:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:853:28: style: C-style pointer casting [cstyleCast]
head relion-3.1.3/src/jaz/ctf/tilt_helper.cpp:908:28: style: C-style pointer casting [cstyleCast]
head relion-3.1.3/src/jaz/damage_helper.cpp:183:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:312:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:387:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:462:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:479:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:666:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable y [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:714:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable y [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:825:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable t0 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:848:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:889:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/damage_helper.cpp:914:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k1 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:1047:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:1099:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:39:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:769:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:788:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixedNu [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:817:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixedNu [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:850:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixedNu [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:898:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixedNu0 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/distribution_helper.cpp:979:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable area [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:153:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:184:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:223:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:251:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:304:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:334:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:452:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:639:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Bscale [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/fsc_helper.cpp:91:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/color_helper.cpp:50:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:1179:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:1702:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:1929:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2022:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2120:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2144:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2305:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2368:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2519:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable z [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2627:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable z [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2745:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2923:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable real [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:2986:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:3009:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:718:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:821:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:895:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:919:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/img_proc/filter_helper.cpp:939:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/io/star_converter.cpp:255:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_CTF_DETECTOR_PIXEL_SIZE [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/io/star_converter.cpp:288:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/legacy_obs_model.cpp:126:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/legacy_obs_model.cpp:183:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beamtilt_xx [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/legacy_obs_model.cpp:191:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/legacy_obs_model.cpp:196:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/legacy_obs_model.cpp:201:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/local_motion_fit.cpp:113:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:121:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:169:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:221:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:254:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:373:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:411:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:53:19: style: Redundant assignment of 'this->firstFrame' to itself. [selfAssignment]
2.13.0 relion-3.1.3/src/jaz/micrograph_handler.cpp:53:19: warning: Redundant assignment of 'this->firstFrame' to itself. [selfAssignment]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:54:18: style: Redundant assignment of 'this->lastFrame' to itself. [selfAssignment]
2.13.0 relion-3.1.3/src/jaz/micrograph_handler.cpp:54:18: warning: Redundant assignment of 'this->lastFrame' to itself. [selfAssignment]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:709:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:748:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:785:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/micrograph_handler.cpp:811:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/alignment_set.h:178:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable accPix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/alignment_set.h:191:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable accPix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/alignment_set.h:210:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fc [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/alignment_set.h:223:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/alignment_set.h:92:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sh [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:200:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:240:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:439:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:61:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/frame_recombiner.cpp:640:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_POSTPROCESS_BFACTOR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/frame_recombiner.h:62:15: performance: Function 'getOutputSuffix()' should return member 'suffix' by const reference. [returnByReference]
head relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:197:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:267:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:373:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
2.13.0 relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:485:20: style: C-style pointer casting [cstyleCast]
head relion-3.1.3/src/jaz/motion/gp_motion_fit.cpp:528:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_estimator.cpp:118:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_estimator.cpp:198:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_estimator.cpp:392:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_COORD_X [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_estimator.cpp:553:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_estimator.cpp:605:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_estimator.cpp:709:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_estimator.cpp:830:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_helper.cpp:228:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_helper.cpp:255:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_helper.cpp:281:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_helper.cpp:334:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_helper.cpp:389:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_NUMBER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_helper.cpp:428:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_NUMBER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:268:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable floatfield [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:345:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:366:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:417:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_param_estimator.cpp:491:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_refiner.cpp:102:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_refiner.cpp:122:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_refiner.cpp:389:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_refiner.cpp:506:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_refiner.cpp:519:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/motion_refiner_mpi.cpp:72:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/three_hyperparameter_fit.cpp:59:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/motion/two_hyperparameter_fit.cpp:53:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/new_ft.cpp:365:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fftw_plan_mutex_new [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/new_ft.cpp:406:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fftw_plan_mutex_new [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/new_ft.cpp:446:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fftw_plan_mutex_new [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/new_ft.cpp:487:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fftw_plan_mutex_new [valueFlowBailoutIncompleteVar]
2.13.0 relion-3.1.3/src/jaz/new_ft.h:239:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable forward [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/noise_helper.cpp:664:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/noise_helper.cpp:764:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/noise_helper.cpp:902:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:1005:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:1020:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mtfImage [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:1104:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable avgMtfImage [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:1122:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable phaseCorr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:1168:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gammaOffset [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:1214:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hasMagMatrices [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:1237:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxSizes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:1244:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X_ANGSTROM [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:190:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_PIXEL_SIZE [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:334:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:445:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:507:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:520:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hasMultipleMtfs [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:575:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:588:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable oddZernikeCoeffs [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:617:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:633:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxSizes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:645:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:650:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:660:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:672:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:677:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:682:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lambda [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:687:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lambda [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:692:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Cs [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:697:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Cs [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:707:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boxSizes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:719:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hasBoxSizes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:729:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hasBoxSizes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:746:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magMatrices [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:751:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magMatrices [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:756:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magMatrices [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:762:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:773:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CtfPremultiplied [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:783:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CtfPremultiplied [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:790:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable groupNames [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:858:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:876:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:905:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:930:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/obs_model.cpp:959:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/optimization/lbfgs.cpp:200:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/optimization/lbfgs.cpp:95:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/optimization/nelder_mead.cpp:217:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/reference_map.cpp:255:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_RANDOM_SUBSET [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/reference_map.cpp:295:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_RANDOM_SUBSET [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/reference_map.cpp:334:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_RANDOM_SUBSET [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/refinement_helper.cpp:116:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SPECTRAL_IDX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/refinement_helper.cpp:169:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/refinement_helper.cpp:78:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SPECTRAL_IDX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/slice_helper.cpp:274:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/slice_helper.cpp:328:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/slice_helper.cpp:438:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/slice_helper.cpp:579:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/slice_helper.cpp:651:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/slice_helper.cpp:676:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/slice_helper.cpp:698:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:145:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:178:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:227:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:247:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:307:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:547:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:668:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:679:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ydim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:700:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:720:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:769:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:809:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:879:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/stack_helper.cpp:95:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:153:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:295:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:357:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:437:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:507:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:594:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/backprojection_helper.cpp:676:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:143:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xdim [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:217:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:232:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:262:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:280:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/tomo/tomo_stack.cpp:338:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:135:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:183:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:227:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:272:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:319:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:366:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:413:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:466:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:515:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RFLOAT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:52:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:559:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RFLOAT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:689:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:717:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RFLOAT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/jaz/vtk_helper.cpp:95:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:1043:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:106:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:1171:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:131:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:1366:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:1392:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CC_POS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:1425:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:147:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:159:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:171:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:1735:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:1802:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:189:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:2128:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable show_usage_for_an_option [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:2146:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:214:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:2151:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:2159:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable show_usage_for_an_option [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:2221:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_apply_local_symmetry [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:237:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:2773:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:295:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XMIPP_EQUAL_ACCURACY [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:321:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:381:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:526:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:668:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MASK_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:709:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ROT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:768:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NR_LOCALSYM_PARAMETERS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry.cpp:93:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/local_symmetry_mpi.cpp:49:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_apply_local_symmetry [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/manualpicker.cpp:349:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sel [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/manualpicker.cpp:411:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sel [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/manualpicker.cpp:427:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/manualpicker.cpp:521:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/manualpicker.cpp:531:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/manualpicker.cpp:567:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/manualpicker.cpp:575:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_MICROGRAPH_PIXEL_SIZE [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/manualpicker.cpp:627:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MDin [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mask.cpp:173:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mask.cpp:271:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mask.cpp:313:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mask.cpp:514:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mask.cpp:532:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:103:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ints [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:108:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ints [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:113:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bools [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:118:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable strings [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:123:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubleVectors [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:128:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubleVectors [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:57:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:62:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ints [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:67:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ints [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:72:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bools [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:77:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubleVectors [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:82:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubleVectors [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:88:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable strings [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:93:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_container.cpp:98:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doubles [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:110:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNDEFINED [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:118:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:123:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:127:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:131:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:135:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:139:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:143:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:147:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:151:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:156:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_LAST_LABEL [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:61:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable names [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_label.cpp:66:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1032:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNDEFINED [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1080:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1139:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1162:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:128:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable isList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1298:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:135:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1368:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1489:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable label2offset [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:153:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1544:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1576:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNDEFINED [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1729:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comment [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1790:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNKNOWN_LABEL [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1827:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_object [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:183:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comment [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1851:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:1865:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_ORIENT_ORIGIN_X_ANGSTROM [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:188:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comment [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:193:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:198:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:203:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:208:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:213:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURRENT_MDT_VERSION [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:218:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
2.13.0 relion-3.1.3/src/metadata_table.cpp:234:7: style: The scope of the variable 'buffer' can be reduced. [variableScope]
head relion-3.1.3/src/metadata_table.cpp:325:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable unknownLabelPosition2Offset [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:521:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SORTED_IDX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:547:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable label2offset [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:588:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:598:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:605:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable activeLabels [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:619:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_LAST_LABEL [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:709:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNKNOWN_LABEL [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:753:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:762:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:772:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:786:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:848:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:857:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:866:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:875:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable objects [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:883:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:889:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:905:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_objectID [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:935:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_UNDEFINED [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/metadata_table.cpp:98:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable label2offset [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:158:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eer_upsampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:168:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable model [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:173:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:204:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fnGain [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:297:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fnGain [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:302:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binning [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:307:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fnMovie [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:312:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable width [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:317:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable height [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:322:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_frames [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:327:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eer_upsampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:332:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eer_grouping [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:341:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fnDefect [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:366:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable width [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:412:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_frames [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:425:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable model [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:558:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eer_upsampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:584:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable width [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:621:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable width [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:658:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/micrograph_model.cpp:91:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NUM_COEFFS_PER_DIM [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:103:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1225:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1277:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pixel_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1325:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_particles_per_group [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1391:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_classes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1404:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_classes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1438:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pixel_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1511:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LL [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1556:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1651:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1723:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:1881:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ori_size [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:377:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_bodies [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:683:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_SPECTRAL_IDX [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:706:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_DIMENSIONALITY [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:916:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_classes [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/ml_model.cpp:933:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_BODY_MASK_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/motioncorr_runner_mpi.cpp:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mpi.cpp:103:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_COMM_WORLD [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mpi.cpp:124:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_SUCCESS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mpi.cpp:176:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_SUCCESS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mpi.cpp:240:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPI_ERR_COUNT [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mpi.cpp:291:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mpi.cpp:303:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mpi.cpp:81:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/mpi.cpp:86:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/numerical_recipes.cpp:211:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PI [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/numerical_recipes.cpp:718:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.13.0 relion-3.1.3/src/numerical_recipes.cpp:936:13: warning:inconclusive: Possible null pointer dereference: rv1 [nullPointer]
     relion-3.1.3/src/numerical_recipes.cpp:813:19: note: Assignment 'rv1=(RFLOAT*)NULL', assigned value is 0
     relion-3.1.3/src/numerical_recipes.cpp:936:13: note: Null pointer dereference
2.13.0 relion-3.1.3/src/numerical_recipes.cpp:987:27: warning:inconclusive: Possible null pointer dereference: rv1 [nullPointer]
     relion-3.1.3/src/numerical_recipes.cpp:813:19: note: Assignment 'rv1=(RFLOAT*)NULL', assigned value is 0
     relion-3.1.3/src/numerical_recipes.cpp:987:27: note: Null pointer dereference
head relion-3.1.3/src/parallel.cpp:103:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable thread_id [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:110:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable thread_id [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:134:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:148:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:163:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:187:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable workFunction [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:209:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable workFunction [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:233:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:246:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable assignedTasks [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:253:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable blockSize [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:259:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable blockSize [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:272:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numberOfTasks [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:294:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable assignedTasks [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:60:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:65:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:71:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable needed [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:79:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/parallel.cpp:85:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mutex [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeline_control.cpp:70:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_JOB_ABORT_NOW [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeline_control.cpp:84:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELION_JOB_EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1044:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1080:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1128:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1159:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:120:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1252:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1360:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULTPDFVIEWER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1398:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:139:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1434:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.13.0 relion-3.1.3/src/pipeliner.cpp:1458:107: error: Out of bounds access in expression 'fns_subdir[idir]' because 'fns_subdir' is empty and 'idir' may be non-zero. [containerOutOfBounds]
head relion-3.1.3/src/pipeliner.cpp:162:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodeList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1679:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:173:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1742:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1780:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1805:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:186:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:1897:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:194:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2078:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2292:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inputNodeList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2394:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alias [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:239:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:254:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2633:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_branches [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2666:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_short_names [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2712:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2727:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2738:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:2758:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:290:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:303:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:324:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:433:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:518:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:677:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROC_IMPORT_NAME [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:728:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROC_MOTIONCORR [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:764:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable processList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:78:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodeList [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/pipeliner.cpp:805:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable app [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:113:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_I2 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:1167:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_ampl_corr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:186:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_mask [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:248:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_mtf [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:370:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:448:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable guinierin [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:544:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:563:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fsc_masked [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:585:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:616:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kp [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:661:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:83:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:862:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angpix [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:885:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_out [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:88:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_I1 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/postprocessing.cpp:930:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:1023:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LARGE_NUMBER [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:103:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:1065:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_rescale [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:112:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_extract [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:1150:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MDimg [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:1277:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_coord_dir [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:1286:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_part_dir [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:259:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_extract [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:280:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:426:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:496:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:577:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:639:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_part_dir [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing.cpp:747:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_IMAGE_OPTICS_GROUP [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing_mpi.cpp:120:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_extract [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/preprocessing_mpi.cpp:46:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor.cpp:104:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_reconstruct_ctf [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor.cpp:217:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_debug [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor.cpp:232:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor.cpp:282:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_sub [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor.cpp:327:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMDL_PARTICLE_RANDOM_SUBSET [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor.cpp:689:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_boxsize [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor.cpp:798:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nr_sectors [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor.cpp:99:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/reconstructor_mpi.cpp:47:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fn_debug [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:102:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:112:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:188:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buf [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:228:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable read_data [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:272:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buf [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:278:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:286:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:294:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:303:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ready [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/renderEER.cpp:53:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable prevTIFFWarningHandler [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1080:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1087:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1094:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1102:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1109:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1116:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1123:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1130:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1137:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1144:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1151:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1158:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1163:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1182:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1238:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1279:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable edges [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1343:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1398:129: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1427:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1447:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1463:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1479:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DO_LOCK [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1552:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1665:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1709:43: style: The scope of the variable 'dummy' can be reduced. [variableScope]
head relion-3.1.3/src/scheduler.cpp:179:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input1 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1830:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:1846:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:191:15: style: The scope of the variable 'idxmax' can be reduced. [variableScope]
head relion-3.1.3/src/scheduler.cpp:191:7: style: The scope of the variable 'idxmin' can be reduced. [variableScope]
head relion-3.1.3/src/scheduler.cpp:196:7: style: The scope of the variable 'ii' can be reduced. [variableScope]
head relion-3.1.3/src/scheduler.cpp:289:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input2 [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:532:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:576:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_fork [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:582:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verb [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:612:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:780:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:788:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable do_read_only [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/scheduler.cpp:986:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_node [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/strings.cpp:319:23: error: Uninitialized variable: aux [uninitvar]
head relion-3.1.3/src/strings.cpp:335:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/strings.cpp:686:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/symmetries.cpp:232:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __L [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/symmetries.cpp:281:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable true_symNo [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/symmetries.cpp:363:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pg_CN [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/symmetries.cpp:611:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pg_CN [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/symmetries.cpp:773:134: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/symmetries.cpp:793:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pg_CN [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/symmetries.cpp:919:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IS_INV [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:109:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:116:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:33:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:40:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:47:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:56:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:63:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:69:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable radius [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:81:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:88:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sampling [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/tabfuncs.cpp:97:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable radius [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/time.cpp:118:11: style: The scope of the variable 't2' can be reduced. [variableScope]
head relion-3.1.3/src/time.cpp:118:7: style: The scope of the variable 't1' can be reduced. [variableScope]
head relion-3.1.3/src/time.cpp:119:14: style: The scope of the variable 'hour' can be reduced. [variableScope]
head relion-3.1.3/src/time.cpp:119:6: style: The scope of the variable 'min' can be reduced. [variableScope]
head relion-3.1.3/src/time.cpp:120:12: style: The scope of the variable 'h2' can be reduced. [variableScope]
head relion-3.1.3/src/time.cpp:120:16: style: The scope of the variable 'm1' can be reduced. [variableScope]
head relion-3.1.3/src/time.cpp:120:20: style: The scope of the variable 'm2' can be reduced. [variableScope]
head relion-3.1.3/src/time.cpp:120:8: style: The scope of the variable 'h1' can be reduced. [variableScope]
head relion-3.1.3/src/time.cpp:130:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/time.cpp:197:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable counts [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/time.cpp:205:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_time [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/time.cpp:214:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start_times [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/time.cpp:221:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tv_sec [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/time.cpp:229:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable counts [valueFlowBailoutIncompleteVar]
head relion-3.1.3/src/time.cpp:61:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]


DONE