2024-04-24 19:40
ftp://ftp.de.debian.org/debian/pool/main/g/gemma/gemma_0.98.5+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --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 -j1
platform: Linux-5.15.0-105-generic-x86_64-with-glibc2.35
python: 3.10.12
client-version: 1.3.56
compiler: g++ (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
cppcheck: head 2.14.0
head-info: 94f28a2 (2024-04-24 20:47:54 +0200)
count: 979 979
elapsed-time: 243.8 240.2
head-timing-info:

old-timing-info:

head results:
GEMMA-0.98.5/src/debug.h:94:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.h:103:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.h:112:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.h:117:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.h:150:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:121:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:148:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:198:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:248:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:351:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:374:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:563:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:652:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:675:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:782:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:933:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:1208:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:1234:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:1351:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:1522:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmm.cpp:1626:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gzstream.h:58:3: warning: Member variable 'gzstreambuf::file' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/gzstream.h:58:3: warning: Member variable 'gzstreambuf::mode' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/bslmm.h:98:8: style:inconclusive: Technically the member function 'BSLMM::CopyToParam' can be const. [functionConst]
GEMMA-0.98.5/src/bslmm.cpp:104:13: note: Technically the member function 'BSLMM::CopyToParam' can be const.
GEMMA-0.98.5/src/bslmm.h:98:8: note: Technically the member function 'BSLMM::CopyToParam' can be const.
GEMMA-0.98.5/src/bslmm.h:107:8: style:inconclusive: Technically the member function 'BSLMM::WriteBV' can be const. [functionConst]
GEMMA-0.98.5/src/bslmm.cpp:116:13: note: Technically the member function 'BSLMM::WriteBV' can be const.
GEMMA-0.98.5/src/bslmm.h:107:8: note: Technically the member function 'BSLMM::WriteBV' can be const.
GEMMA-0.98.5/src/bslmm.h:111:8: style:inconclusive: Technically the member function 'BSLMM::WriteResult' can be const. [functionConst]
GEMMA-0.98.5/src/bslmm.cpp:237:13: note: Technically the member function 'BSLMM::WriteResult' can be const.
GEMMA-0.98.5/src/bslmm.h:111:8: note: Technically the member function 'BSLMM::WriteResult' can be const.
GEMMA-0.98.5/src/bslmm.h:117:10: performance:inconclusive: Technically the member function 'BSLMM::CalcPveLM' can be static (but you may consider moving to unnamed namespace). [functionStatic]
GEMMA-0.98.5/src/bslmm.cpp:339:15: note: Technically the member function 'BSLMM::CalcPveLM' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/bslmm.h:117:10: note: Technically the member function 'BSLMM::CalcPveLM' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/bslmm.h:129:8: style:inconclusive: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const. [functionConst]
GEMMA-0.98.5/src/bslmm.cpp:645:13: note: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const.
GEMMA-0.98.5/src/bslmm.h:129:8: note: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const.
GEMMA-0.98.5/src/bslmm.h:131:8: style:inconclusive: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const. [functionConst]
GEMMA-0.98.5/src/bslmm.cpp:661:13: note: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const.
GEMMA-0.98.5/src/bslmm.h:131:8: note: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const.
GEMMA-0.98.5/src/bslmm.h:159:10: style:inconclusive: Technically the member function 'BSLMM::CalcPosterior' can be const. [functionConst]
GEMMA-0.98.5/src/bslmm.cpp:1447:15: note: Technically the member function 'BSLMM::CalcPosterior' can be const.
GEMMA-0.98.5/src/bslmm.h:159:10: note: Technically the member function 'BSLMM::CalcPosterior' can be const.
GEMMA-0.98.5/src/bslmm.h:164:8: performance:inconclusive: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
GEMMA-0.98.5/src/bslmm.cpp:1553:13: note: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/bslmm.h:164:8: note: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/bslmm.h:165:8: style:inconclusive: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const. [functionConst]
GEMMA-0.98.5/src/bslmm.cpp:1561:13: note: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const.
GEMMA-0.98.5/src/bslmm.h:165:8: note: Technically the member function 'BSLMM::CalcCC_PVEnZ' can be const.
GEMMA-0.98.5/src/gzstream.h:99:16: warning: The class 'igzstream' defines member function with name 'rdbuf' also defined in its parent class 'gzstreambase'. [duplInheritedMember]
GEMMA-0.98.5/src/gzstream.h:85:16: note: Parent function 'gzstreambase::rdbuf'
GEMMA-0.98.5/src/gzstream.h:99:16: note: Derived function 'igzstream::rdbuf'
GEMMA-0.98.5/src/gzstream.h:100:8: warning: The class 'igzstream' defines member function with name 'open' also defined in its parent class 'gzstreambase'. [duplInheritedMember]
GEMMA-0.98.5/src/gzstream.h:83:8: note: Parent function 'gzstreambase::open'
GEMMA-0.98.5/src/gzstream.h:100:8: note: Derived function 'igzstream::open'
GEMMA-0.98.5/src/gzstream.h:110:16: warning: The class 'ogzstream' defines member function with name 'rdbuf' also defined in its parent class 'gzstreambase'. [duplInheritedMember]
GEMMA-0.98.5/src/gzstream.h:85:16: note: Parent function 'gzstreambase::rdbuf'
GEMMA-0.98.5/src/gzstream.h:110:16: note: Derived function 'ogzstream::rdbuf'
GEMMA-0.98.5/src/gzstream.h:111:8: warning: The class 'ogzstream' defines member function with name 'open' also defined in its parent class 'gzstreambase'. [duplInheritedMember]
GEMMA-0.98.5/src/gzstream.h:83:8: note: Parent function 'gzstreambase::open'
GEMMA-0.98.5/src/gzstream.h:111:8: note: Derived function 'ogzstream::open'
GEMMA-0.98.5/src/gzstream.h:97:3: style: Class 'igzstream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
GEMMA-0.98.5/src/gzstream.h:108:3: style: Class 'ogzstream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
GEMMA-0.98.5/src/bslmm.cpp:1458:14: style: The if condition is the same as the previous if condition [duplicateCondition]
GEMMA-0.98.5/src/bslmm.cpp:1452:14: note: First condition
GEMMA-0.98.5/src/bslmm.cpp:1458:14: note: Second condition
GEMMA-0.98.5/src/bslmm.cpp:350:16: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/bslmm.cpp:561:16: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/bslmm.cpp:1232:16: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/bslmm.cpp:747:10: style:inconclusive: Same expression used in consecutive assignments of 'logp_old' and 'logp_new'. [duplicateAssignExpression]
GEMMA-0.98.5/src/bslmm.cpp:747:36: note: Same expression used in consecutive assignments of 'logp_old' and 'logp_new'.
GEMMA-0.98.5/src/bslmm.cpp:747:10: note: Same expression used in consecutive assignments of 'logp_old' and 'logp_new'.
GEMMA-0.98.5/src/bslmm.cpp:328:10: style: The scope of the variable 'pos' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:459:13: style: The scope of the variable 'ds' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:459:17: style: The scope of the variable 'uy' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:528:13: style: The scope of the variable 'ds' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:528:17: style: The scope of the variable 'uy' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:691:10: style: The scope of the variable 'd1' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:691:14: style: The scope of the variable 'd2' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:776:10: style: The scope of the variable 'unif' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:1246:10: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:1298:40: style: The scope of the variable 'i_add' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:1298:47: style: The scope of the variable 'j_add' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:1298:54: style: The scope of the variable 'i_flag' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:1298:62: style: The scope of the variable 'j_flag' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmm.cpp:311:32: style:inconclusive: Function 'CalcPgamma' argument 1 names different: declaration 'p_gammar' definition 'p_gamma'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/bslmm.h:115:27: note: Function 'CalcPgamma' argument 1 names different: declaration 'p_gammar' definition 'p_gamma'.
GEMMA-0.98.5/src/bslmm.cpp:311:32: note: Function 'CalcPgamma' argument 1 names different: declaration 'p_gammar' definition 'p_gamma'.
GEMMA-0.98.5/src/bslmm.cpp:368:41: style:inconclusive: Function 'InitialMCMC' argument 3 names different: declaration 'rank_old' definition 'rank'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/bslmm.h:120:36: note: Function 'InitialMCMC' argument 3 names different: declaration 'rank_old' definition 'rank'.
GEMMA-0.98.5/src/bslmm.cpp:368:41: note: Function 'InitialMCMC' argument 3 names different: declaration 'rank_old' definition 'rank'.
GEMMA-0.98.5/src/bslmm.cpp:1224:39: style:inconclusive: Function 'CalcXtX' argument 1 names different: declaration 'X_new' definition 'X'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/bslmm.h:152:34: note: Function 'CalcXtX' argument 1 names different: declaration 'X_new' definition 'X'.
GEMMA-0.98.5/src/bslmm.cpp:1224:39: note: Function 'CalcXtX' argument 1 names different: declaration 'X_new' definition 'X'.
GEMMA-0.98.5/src/bslmm.cpp:1225:54: style:inconclusive: Function 'CalcXtX' argument 4 names different: declaration 'XtX_new' definition 'XtX'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/bslmm.h:153:49: note: Function 'CalcXtX' argument 4 names different: declaration 'XtX_new' definition 'XtX'.
GEMMA-0.98.5/src/bslmm.cpp:1225:54: note: Function 'CalcXtX' argument 4 names different: declaration 'XtX_new' definition 'XtX'.
GEMMA-0.98.5/src/bslmm.cpp:1225:71: style:inconclusive: Function 'CalcXtX' argument 5 names different: declaration 'Xty_new' definition 'Xty'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/bslmm.h:153:70: note: Function 'CalcXtX' argument 5 names different: declaration 'Xty_new' definition 'Xty'.
GEMMA-0.98.5/src/bslmm.cpp:1225:71: note: Function 'CalcXtX' argument 5 names different: declaration 'Xty_new' definition 'Xty'.
GEMMA-0.98.5/src/bslmm.cpp:816:19: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmm.cpp:794:15: note: Shadowed declaration
GEMMA-0.98.5/src/bslmm.cpp:816:19: note: Shadow variable
GEMMA-0.98.5/src/bslmm.cpp:832:19: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmm.cpp:794:15: note: Shadowed declaration
GEMMA-0.98.5/src/bslmm.cpp:832:19: note: Shadow variable
GEMMA-0.98.5/src/bslmm.cpp:855:19: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmm.cpp:794:15: note: Shadowed declaration
GEMMA-0.98.5/src/bslmm.cpp:855:19: note: Shadow variable
GEMMA-0.98.5/src/bslmm.cpp:1046:21: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmm.cpp:1030:17: note: Shadowed declaration
GEMMA-0.98.5/src/bslmm.cpp:1046:21: note: Shadow variable
GEMMA-0.98.5/src/bslmm.cpp:1056:21: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmm.cpp:1030:17: note: Shadowed declaration
GEMMA-0.98.5/src/bslmm.cpp:1056:21: note: Shadow variable
GEMMA-0.98.5/src/bslmm.cpp:1077:23: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmm.cpp:1030:17: note: Shadowed declaration
GEMMA-0.98.5/src/bslmm.cpp:1077:23: note: Shadow variable
GEMMA-0.98.5/src/bslmm.cpp:1748:23: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmm.cpp:1696:17: note: Shadowed declaration
GEMMA-0.98.5/src/bslmm.cpp:1748:23: note: Shadow variable
GEMMA-0.98.5/src/debug.h:102:69: performance: Function parameter 'msg' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/debug.h:116:34: performance: Function parameter 'msg' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.h:355:55: performance: Function parameter 'suffix' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.h:356:30: performance: Function parameter 'suffix' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.h:357:61: performance: Function parameter 'suffix' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.h:358:61: performance: Function parameter 'suffix' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.h:41:33: performance: Function parameter 'file_snps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.h:90:29: performance: Function parameter 'file_geno' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.h:90:58: performance: Function parameter 'ksnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.h:97:33: performance: Function parameter 'file_geno' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.h:132:69: performance: Function parameter 'ksnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.h:148:33: performance: Function parameter 'setKSnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/lmm.h:102:34: performance: Function parameter 'gwasnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/lmm.h:106:40: performance: Function parameter 'gwasnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/lmm.h:110:39: performance: Function parameter 'gwasnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/mathfunc.h:40:35: performance: Function parameter 'v' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/bslmm.cpp:50:34: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/bslmm.cpp:142:54: style: Parameter 'beta_g' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/bslmm.cpp:327:39: style: Parameter 'rank' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/bslmm.cpp:369:55: style: Parameter 'pos_loglr' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/bslmmdap.cpp:107:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmmdap.cpp:144:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmmdap.cpp:213:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmmdap.cpp:343:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmmdap.cpp:423:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmmdap.cpp:540:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmmdap.cpp:619:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmmdap.cpp:828:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/bslmmdap.cpp:226:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/bslmmdap.cpp:177:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/bslmmdap.cpp:180:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/bslmmdap.cpp:273:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/bslmmdap.h:78:8: style:inconclusive: Technically the member function 'BSLMMDAP::CopyToParam' can be const. [functionConst]
GEMMA-0.98.5/src/bslmmdap.cpp:93:16: note: Technically the member function 'BSLMMDAP::CopyToParam' can be const.
GEMMA-0.98.5/src/bslmmdap.h:78:8: note: Technically the member function 'BSLMMDAP::CopyToParam' can be const.
GEMMA-0.98.5/src/bslmmdap.h:81:8: style:inconclusive: Technically the member function 'BSLMMDAP::WriteResult' can be const. [functionConst]
GEMMA-0.98.5/src/bslmmdap.cpp:410:16: note: Technically the member function 'BSLMMDAP::WriteResult' can be const.
GEMMA-0.98.5/src/bslmmdap.h:81:8: note: Technically the member function 'BSLMMDAP::WriteResult' can be const.
GEMMA-0.98.5/src/bslmmdap.h:83:10: style:inconclusive: Technically the member function 'BSLMMDAP::CalcMarginal' can be const. [functionConst]
GEMMA-0.98.5/src/bslmmdap.cpp:480:18: note: Technically the member function 'BSLMMDAP::CalcMarginal' can be const.
GEMMA-0.98.5/src/bslmmdap.h:83:10: note: Technically the member function 'BSLMMDAP::CalcMarginal' can be const.
GEMMA-0.98.5/src/bslmmdap.h:88:10: style:inconclusive: Technically the member function 'BSLMMDAP::CalcPrior' can be const. [functionConst]
GEMMA-0.98.5/src/bslmmdap.cpp:564:18: note: Technically the member function 'BSLMMDAP::CalcPrior' can be const.
GEMMA-0.98.5/src/bslmmdap.h:88:10: note: Technically the member function 'BSLMMDAP::CalcPrior' can be const.
GEMMA-0.98.5/src/bslmmdap.cpp:191:20: style: Condition 'flag_block==0' is always true [knownConditionTrueFalse]
GEMMA-0.98.5/src/bslmmdap.cpp:161:18: note: Assignment 'flag_block=0', assigned value is 0
GEMMA-0.98.5/src/bslmmdap.cpp:191:20: note: Condition 'flag_block==0' is always true
GEMMA-0.98.5/src/bslmmdap.cpp:119:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/bslmmdap.cpp:163:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/bslmmdap.cpp:241:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/bslmmdap.cpp:538:16: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/bslmmdap.cpp:120:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/bslmmdap.cpp:119:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/bslmmdap.cpp:120:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/bslmmdap.cpp:122:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/bslmmdap.cpp:120:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/bslmmdap.cpp:122:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/bslmmdap.cpp:114:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:150:16: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:155:23: style: The scope of the variable 'flag_block' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:222:19: style: The scope of the variable 'a1' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:222:23: style: The scope of the variable 'a0' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:222:32: style: The scope of the variable 'cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:485:10: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:485:13: style: The scope of the variable 'uy' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:509:13: style: The scope of the variable 'uy' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:579:15: style: The scope of the variable 'h' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:690:10: style: The scope of the variable 'h' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:690:13: style: The scope of the variable 'rho' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:690:18: style: The scope of the variable 'sigma_a2' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:690:28: style: The scope of the variable 'sigma_b2' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:690:44: style: The scope of the variable 'logm' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:691:10: style: The scope of the variable 't1' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:691:14: style: The scope of the variable 't2' can be reduced. [variableScope]
GEMMA-0.98.5/src/bslmmdap.cpp:625:17: style: Local variable 'ij' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmmdap.cpp:595:10: note: Shadowed declaration
GEMMA-0.98.5/src/bslmmdap.cpp:625:17: note: Shadow variable
GEMMA-0.98.5/src/bslmmdap.cpp:654:20: style: Local variable 'sum' shadows outer function [shadowFunction]
GEMMA-0.98.5/src/mathfunc.h:63:8: note: Shadowed declaration
GEMMA-0.98.5/src/bslmmdap.cpp:654:20: note: Shadow variable
GEMMA-0.98.5/src/bslmmdap.cpp:692:31: style: Local variable 'ns_test' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/bslmmdap.h:54:19: note: Shadowed declaration
GEMMA-0.98.5/src/bslmmdap.cpp:692:31: note: Shadow variable
GEMMA-0.98.5/src/bslmmdap.cpp:52:37: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/bslmmdap.cpp:564:44: style: Parameter 'cHyp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/bslmmdap.cpp:114:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/bslmmdap.cpp:259:12: style: Variable 'cm' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/bslmmdap.cpp:261:12: style: Variable 'a1' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/bslmmdap.cpp:263:12: style: Variable 'a0' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/debug.cpp:78:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:161:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:166:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:171:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:182:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:213:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:221:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:227:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:256:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:261:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:288:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:297:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:336:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/debug.cpp:315:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/debug.cpp:295:66: style:inconclusive: Function 'do_gsl_matrix_safe_get' argument 2 names different: declaration 'i' definition 'row'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/debug.h:72:67: note: Function 'do_gsl_matrix_safe_get' argument 2 names different: declaration 'i' definition 'row'.
GEMMA-0.98.5/src/debug.cpp:295:66: note: Function 'do_gsl_matrix_safe_get' argument 2 names different: declaration 'i' definition 'row'.
GEMMA-0.98.5/src/debug.cpp:295:84: style:inconclusive: Function 'do_gsl_matrix_safe_get' argument 3 names different: declaration 'j' definition 'col'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/debug.h:72:83: note: Function 'do_gsl_matrix_safe_get' argument 3 names different: declaration 'j' definition 'col'.
GEMMA-0.98.5/src/debug.cpp:295:84: note: Function 'do_gsl_matrix_safe_get' argument 3 names different: declaration 'j' definition 'col'.
GEMMA-0.98.5/src/debug.cpp:327:53: style:inconclusive: Function 'do_validate_K' argument 2 names different: declaration '__pretty_func' definition '__pretty_function'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/debug.h:85:52: note: Function 'do_validate_K' argument 2 names different: declaration '__pretty_func' definition '__pretty_function'.
GEMMA-0.98.5/src/debug.cpp:327:53: note: Function 'do_validate_K' argument 2 names different: declaration '__pretty_func' definition '__pretty_function'.
GEMMA-0.98.5/src/debug.cpp:306:7: performance: Passing the result of c_str() to a function that takes std::string as argument no. 3 is slow and redundant. [stlcstrParam]
GEMMA-0.98.5/src/fastblas.cpp:50:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/fastblas.cpp:109:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/fastblas.cpp:179:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma.cpp:73:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma.cpp:84:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma.cpp:90:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma.cpp:156:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma.cpp:1127:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma.cpp:1645:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma.cpp:3141:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma.cpp:3178:13: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
GEMMA-0.98.5/src/gemma.cpp:3180:30: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled]
GEMMA-0.98.5/src/gemma.h:61:8: style:inconclusive: Technically the member function 'GEMMA::PrintHeader' can be const. [functionConst]
GEMMA-0.98.5/src/gemma.cpp:82:13: note: Technically the member function 'GEMMA::PrintHeader' can be const.
GEMMA-0.98.5/src/gemma.h:61:8: note: Technically the member function 'GEMMA::PrintHeader' can be const.
GEMMA-0.98.5/src/gemma.h:62:8: performance:inconclusive: Technically the member function 'GEMMA::PrintHelp' can be static (but you may consider moving to unnamed namespace). [functionStatic]
GEMMA-0.98.5/src/gemma.cpp:153:13: note: Technically the member function 'GEMMA::PrintHelp' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/gemma.h:62:8: note: Technically the member function 'GEMMA::PrintHelp' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/gemma.h:63:8: performance:inconclusive: Technically the member function 'GEMMA::PrintLicense' can be static (but you may consider moving to unnamed namespace). [functionStatic]
GEMMA-0.98.5/src/gemma.cpp:89:13: note: Technically the member function 'GEMMA::PrintLicense' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/gemma.h:63:8: note: Technically the member function 'GEMMA::PrintLicense' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/gemma.h:64:8: performance:inconclusive: Technically the member function 'GEMMA::Assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
GEMMA-0.98.5/src/gemma.cpp:754:13: note: Technically the member function 'GEMMA::Assign' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/gemma.h:64:8: note: Technically the member function 'GEMMA::Assign' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/gemma.h:65:8: performance:inconclusive: Technically the member function 'GEMMA::BatchRun' can be static (but you may consider moving to unnamed namespace). [functionStatic]
GEMMA-0.98.5/src/gemma.cpp:1638:13: note: Technically the member function 'GEMMA::BatchRun' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/gemma.h:65:8: note: Technically the member function 'GEMMA::BatchRun' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/gemma.h:66:8: style:inconclusive: Technically the member function 'GEMMA::WriteLog' can be const. [functionConst]
GEMMA-0.98.5/src/gemma.cpp:3136:13: note: Technically the member function 'GEMMA::WriteLog' can be const.
GEMMA-0.98.5/src/gemma.h:66:8: note: Technically the member function 'GEMMA::WriteLog' can be const.
GEMMA-0.98.5/src/gemma.cpp:1713:14: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma.cpp:2337:16: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma.cpp:2596:19: style: The scope of the variable 'wi' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma.cpp:2627:16: style: The scope of the variable 'wi' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma.cpp:2758:18: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma.cpp:2758:21: style: The scope of the variable 'u' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma.cpp:2758:24: style: The scope of the variable 'e' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma.cpp:3136:52: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma.cpp:3178:7: style: Variable 'ptm' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma.cpp:2337:18: style: Variable 'd' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma.cpp:2435:20: style: Unused variable: vec_z [unusedVariable]
GEMMA-0.98.5/src/gemma_io.cpp:66:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:89:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:143:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eofbit [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:153:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:181:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:239:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:282:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:342:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:386:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:444:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:511:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:558:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:643:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:865:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1054:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1105:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1172:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1282:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1307:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1356:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1405:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1585:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1728:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1834:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:1942:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2074:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2209:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2275:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2292:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2351:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2619:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2705:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2744:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:2937:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3163:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3239:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3266:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3352:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3539:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3703:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3857:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3880:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3908:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3947:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3973:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:3997:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:4088:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gemma_io.cpp:195:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:1062:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:1432:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:1756:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:1866:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:2636:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:2787:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:3285:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:3377:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:3560:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:3868:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:3891:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:3919:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:3929:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/gemma_io.cpp:94:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:166:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:206:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:221:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:253:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:256:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:258:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:295:26: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:300:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:311:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:320:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:361:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:414:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:429:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:462:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:472:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:618:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:1202:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:1215:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:1331:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:1343:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:1382:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:2254:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:2315:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:2328:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:2438:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:2589:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:2693:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:3319:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:3472:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:3656:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:3896:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:3924:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:3934:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/gemma_io.cpp:89:16: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:166:21: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:206:21: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:252:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:295:33: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:359:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:414:21: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:462:21: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:532:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:589:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:697:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:1066:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:1202:23: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:1243:16: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:1331:21: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:1379:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:1761:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:1871:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:2231:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:2312:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:2438:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:2662:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:2795:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:3254:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:3292:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:3399:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:3581:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:3869:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:3892:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:3920:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:3930:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/gemma_io.cpp:253:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:252:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:253:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:590:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:589:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:590:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:593:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:592:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:593:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:594:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:593:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:594:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:595:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:594:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:595:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:1067:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:1066:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:1067:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:1068:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:1067:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:1068:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:1762:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:1761:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:1762:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:1763:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:1762:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:1763:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:1872:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:1871:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:1872:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:1873:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:1872:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:1873:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:2796:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:2795:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:2796:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:2797:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:2796:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/gemma_io.cpp:2797:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/gemma_io.cpp:3674:9: style: Redundant assignment of 'z' to itself. [selfAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:163:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:247:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:353:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:397:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:454:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:523:10: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:524:12: style: The scope of the variable 'b_pos' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:525:10: style: The scope of the variable 'chr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:526:10: style: The scope of the variable 'cM' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:527:10: style: The scope of the variable 'major' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:528:10: style: The scope of the variable 'minor' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:572:10: style: The scope of the variable 'id' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:673:10: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:676:10: style: The scope of the variable 'major' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:677:10: style: The scope of the variable 'minor' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1058:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1118:13: style: The scope of the variable 'b' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1237:12: style: The scope of the variable 'id1' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1237:17: style: The scope of the variable 'id2' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1290:10: style: The scope of the variable 'file_kin' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1315:57: style: The scope of the variable 'i_col' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1320:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1369:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1370:10: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1750:7: style: The scope of the variable 'ns_test' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:1955:10: style: The scope of the variable 'ns_test' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2222:10: style: The scope of the variable 'alpha' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2222:17: style: The scope of the variable 'beta' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2222:23: style: The scope of the variable 'gamma' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2222:30: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2304:10: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2306:21: style: The scope of the variable 't' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2435:10: style: The scope of the variable 'type' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2631:19: style: The scope of the variable 'a1' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2631:23: style: The scope of the variable 'a0' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2631:32: style: The scope of the variable 'cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:2632:10: style: The scope of the variable 'i_cat' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3249:16: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3250:10: style: The scope of the variable 'weight' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3281:25: style: The scope of the variable 'a1' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3281:29: style: The scope of the variable 'a0' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3281:38: style: The scope of the variable 'cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3371:19: style: The scope of the variable 'a1' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3371:23: style: The scope of the variable 'a0' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3371:32: style: The scope of the variable 'cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3553:23: style: The scope of the variable 'a0' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3553:32: style: The scope of the variable 'cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3749:10: style: The scope of the variable 't' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3749:17: style: The scope of the variable 'b' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3749:24: style: The scope of the variable 'n_snp' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3865:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3888:9: style: The scope of the variable 'ch_ptr' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3958:10: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:3982:10: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/gemma_io.cpp:279:34: style:inconclusive: Function 'ReadFile_anno' argument 1 names different: declaration 'file_bim' definition 'file_anno'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/gemma_io.h:52:34: note: Function 'ReadFile_anno' argument 1 names different: declaration 'file_bim' definition 'file_anno'.
GEMMA-0.98.5/src/gemma_io.cpp:279:34: note: Function 'ReadFile_anno' argument 1 names different: declaration 'file_bim' definition 'file_anno'.
GEMMA-0.98.5/src/gemma_io.cpp:1306:36: style:inconclusive: Function 'ReadFile_eigenU' argument 1 names different: declaration 'file_u' definition 'file_ku'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/gemma_io.h:87:36: note: Function 'ReadFile_eigenU' argument 1 names different: declaration 'file_u' definition 'file_ku'.
GEMMA-0.98.5/src/gemma_io.cpp:1306:36: note: Function 'ReadFile_eigenU' argument 1 names different: declaration 'file_u' definition 'file_ku'.
GEMMA-0.98.5/src/gemma_io.cpp:1355:36: style:inconclusive: Function 'ReadFile_eigenD' argument 1 names different: declaration 'file_d' definition 'file_kd'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/gemma_io.h:88:36: note: Function 'ReadFile_eigenD' argument 1 names different: declaration 'file_d' definition 'file_kd'.
GEMMA-0.98.5/src/gemma_io.cpp:1355:36: note: Function 'ReadFile_eigenD' argument 1 names different: declaration 'file_d' definition 'file_kd'.
GEMMA-0.98.5/src/gemma_io.cpp:3238:66: style:inconclusive: Function 'ReadFile_wsnp' argument 2 names different: declaration 'mapRS2double' definition 'mapRS2weight'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/gemma_io.h:156:66: note: Function 'ReadFile_wsnp' argument 2 names different: declaration 'mapRS2double' definition 'mapRS2weight'.
GEMMA-0.98.5/src/gemma_io.cpp:3238:66: note: Function 'ReadFile_wsnp' argument 2 names different: declaration 'mapRS2double' definition 'mapRS2weight'.
GEMMA-0.98.5/src/gemma_io.cpp:3265:49: style:inconclusive: Function 'ReadFile_wsnp' argument 3 names different: declaration 'mapRS2vector' definition 'mapRS2wvector'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/gemma_io.h:158:49: note: Function 'ReadFile_wsnp' argument 3 names different: declaration 'mapRS2vector' definition 'mapRS2wvector'.
GEMMA-0.98.5/src/gemma_io.cpp:3265:49: note: Function 'ReadFile_wsnp' argument 3 names different: declaration 'mapRS2vector' definition 'mapRS2wvector'.
GEMMA-0.98.5/src/gemma_io.cpp:3945:59: style:inconclusive: Function 'ReadFile_study' argument 2 names different: declaration 'Vq' definition 'Vq_mat'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/gemma_io.h:173:59: note: Function 'ReadFile_study' argument 2 names different: declaration 'Vq' definition 'Vq_mat'.
GEMMA-0.98.5/src/gemma_io.cpp:3945:59: note: Function 'ReadFile_study' argument 2 names different: declaration 'Vq' definition 'Vq_mat'.
GEMMA-0.98.5/src/gemma_io.cpp:3995:61: style:inconclusive: Function 'ReadFile_mstudy' argument 2 names different: declaration 'Vq' definition 'Vq_mat'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/gemma_io.h:177:61: note: Function 'ReadFile_mstudy' argument 2 names different: declaration 'Vq' definition 'Vq_mat'.
GEMMA-0.98.5/src/gemma_io.cpp:3995:61: note: Function 'ReadFile_mstudy' argument 2 names different: declaration 'Vq' definition 'Vq_mat'.
GEMMA-0.98.5/src/gemma_io.cpp:742:10: style: Local variable 'infilen' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/gemma_io.cpp:695:8: note: Shadowed declaration
GEMMA-0.98.5/src/gemma_io.cpp:742:10: note: Shadow variable
GEMMA-0.98.5/src/gemma_io.cpp:1788:17: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/gemma_io.cpp:1755:12: note: Shadowed declaration
GEMMA-0.98.5/src/gemma_io.cpp:1788:17: note: Shadow variable
GEMMA-0.98.5/src/gemma_io.cpp:2887:15: style: Local variable 'i_vc' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/gemma_io.cpp:2773:46: note: Shadowed declaration
GEMMA-0.98.5/src/gemma_io.cpp:2887:15: note: Shadow variable
GEMMA-0.98.5/src/gemma_io.cpp:3113:15: style: Local variable 'i_vc' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/gemma_io.cpp:2968:46: note: Shadowed declaration
GEMMA-0.98.5/src/gemma_io.cpp:3113:15: note: Shadow variable
GEMMA-0.98.5/src/gemma_io.cpp:55:25: performance: Function parameter 'str' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.cpp:86:45: performance: Function parameter 'line' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.cpp:152:33: performance: Function parameter 'file_snps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.cpp:1401:29: performance: Function parameter 'file_geno' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.cpp:1401:58: performance: Function parameter 'ksnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.cpp:1725:33: performance: Function parameter 'file_geno' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.cpp:2736:69: performance: Function parameter 'ksnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.cpp:3156:33: performance: Function parameter 'setKSnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/gemma_io.cpp:860:53: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1169:56: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1402:29: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1582:52: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1725:57: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1726:33: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1829:58: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1830:33: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1939:56: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:1940:32: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:2070:56: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:2071:32: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/gemma_io.cpp:247:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:353:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:397:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:454:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:1058:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:1320:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:1369:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:1736:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:1848:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:2753:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:3865:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/gemma_io.cpp:1294:5: performance: Assigning the result of c_str() to a std::string is slow and redundant. [stlcstrAssignment]
GEMMA-0.98.5/src/gemma_io.cpp:355:10: style: Unused variable: id [unusedVariable]
GEMMA-0.98.5/src/gemma_io.cpp:399:10: style: Unused variable: id [unusedVariable]
GEMMA-0.98.5/src/gemma_io.cpp:457:15: style: Variable 'flag_na' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:1068:12: style: Variable 'ch_ptr' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:1315:63: style: Variable 'i_col' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:1477:19: style: Variable 'sfield' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:2306:23: style: Variable 't' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:2405:22: style: Variable 'var_set' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:2674:12: style: Variable 'cm' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:2676:12: style: Variable 'a1' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:2678:12: style: Variable 'a0' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/gemma_io.cpp:3369:10: style: Unused variable: type [unusedVariable]
GEMMA-0.98.5/src/gemma_io.cpp:3551:10: style: Unused variable: type [unusedVariable]
GEMMA-0.98.5/src/gzstream.cpp:50:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ate [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gzstream.cpp:82:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gzstream.cpp:108:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gzstream.cpp:114:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gzstream.cpp:130:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gzstream.cpp:149:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable badbit [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gzstream.cpp:155:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable badbit [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/gzstream.h:100:8: warning: The class 'igzstream' defines member function with name 'open' also defined in its parent class 'gzstreambase'. [duplInheritedMember]
GEMMA-0.98.5/src/gzstream.cpp:147:20: note: Parent function 'gzstreambase::open'
GEMMA-0.98.5/src/gzstream.h:100:8: note: Derived function 'igzstream::open'
GEMMA-0.98.5/src/gzstream.h:111:8: warning: The class 'ogzstream' defines member function with name 'open' also defined in its parent class 'gzstreambase'. [duplInheritedMember]
GEMMA-0.98.5/src/gzstream.cpp:147:20: note: Parent function 'gzstreambase::open'
GEMMA-0.98.5/src/gzstream.h:111:8: note: Derived function 'ogzstream::open'
GEMMA-0.98.5/src/gzstream.cpp:140:50: style:inconclusive: Function 'gzstreambase' argument 2 names different: declaration 'open_mode' definition 'mode'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/gzstream.h:81:38: note: Function 'gzstreambase' argument 2 names different: declaration 'open_mode' definition 'mode'.
GEMMA-0.98.5/src/gzstream.cpp:140:50: note: Function 'gzstreambase' argument 2 names different: declaration 'open_mode' definition 'mode'.
GEMMA-0.98.5/src/lapack.cpp:54:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:75:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:101:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:156:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:283:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:309:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:328:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:342:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:350:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lapack.cpp:341:36: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lapack.cpp:50:7: style:inconclusive: Same expression used in consecutive assignments of 'N' and 'LDA'. [duplicateAssignExpression]
GEMMA-0.98.5/src/lapack.cpp:50:21: note: Same expression used in consecutive assignments of 'N' and 'LDA'.
GEMMA-0.98.5/src/lapack.cpp:50:7: note: Same expression used in consecutive assignments of 'N' and 'LDA'.
GEMMA-0.98.5/src/lapack.cpp:152:9: style: Same expression used in consecutive assignments of 'N' and 'LDA'. [duplicateAssignExpression]
GEMMA-0.98.5/src/lapack.cpp:152:23: note: Same expression used in consecutive assignments of 'N' and 'LDA'.
GEMMA-0.98.5/src/lapack.cpp:152:9: note: Same expression used in consecutive assignments of 'N' and 'LDA'.
GEMMA-0.98.5/src/lapack.cpp:177:9: style: Same expression used in consecutive assignments of 'N' and 'LDA'. [duplicateAssignExpression]
GEMMA-0.98.5/src/lapack.cpp:177:23: note: Same expression used in consecutive assignments of 'N' and 'LDA'.
GEMMA-0.98.5/src/lapack.cpp:177:9: note: Same expression used in consecutive assignments of 'N' and 'LDA'.
GEMMA-0.98.5/src/lapack.cpp:177:23: style: Same expression used in consecutive assignments of 'LDA' and 'LDZ'. [duplicateAssignExpression]
GEMMA-0.98.5/src/lapack.cpp:177:39: note: Same expression used in consecutive assignments of 'LDA' and 'LDZ'.
GEMMA-0.98.5/src/lapack.cpp:177:23: note: Same expression used in consecutive assignments of 'LDA' and 'LDZ'.
GEMMA-0.98.5/src/lapack.cpp:293:53: style: Parameter 'Xty' can be declared as pointer to const [constParameterPointer]
GEMMA-0.98.5/src/lapack.cpp:265:34: style: Variable 'count_negative_eigenvalues' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/lapack.cpp:274:34: style: Variable 'count_negative_eigenvalues' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/ldr.h:63:8: performance:inconclusive: Technically the member function 'LDR::CopyToParam' can be static (but you may consider moving to unnamed namespace). [functionStatic]
GEMMA-0.98.5/src/ldr.cpp:72:11: note: Technically the member function 'LDR::CopyToParam' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/ldr.h:63:8: note: Technically the member function 'LDR::CopyToParam' can be static (but you may consider moving to unnamed namespace).
GEMMA-0.98.5/src/ldr.cpp:49:32: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/ldr.cpp:72:30: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/lm.cpp:88:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lm.cpp:234:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lm.cpp:255:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lm.cpp:291:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lm.cpp:383:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lm.cpp:498:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lm.h:66:8: style:inconclusive: Technically the member function 'LM::CopyToParam' can be const. [functionConst]
GEMMA-0.98.5/src/lm.cpp:77:10: note: Technically the member function 'LM::CopyToParam' can be const.
GEMMA-0.98.5/src/lm.h:66:8: note: Technically the member function 'LM::CopyToParam' can be const.
GEMMA-0.98.5/src/lm.cpp:336:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lm.cpp:430:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lm.cpp:431:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/lm.cpp:430:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/lm.cpp:431:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/lm.cpp:432:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/lm.cpp:431:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/lm.cpp:432:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/lm.cpp:304:7: style: The scope of the variable 'c_phen' can be reduced. [variableScope]
GEMMA-0.98.5/src/lm.cpp:305:10: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/lm.cpp:643:25: style: The scope of the variable 'log_lr' can be reduced. [variableScope]
GEMMA-0.98.5/src/lm.cpp:49:31: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/lm.cpp:393:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:101:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:333:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:380:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:448:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:523:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:625:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:694:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:773:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:843:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:919:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1002:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1092:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1150:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1193:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1251:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1327:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1358:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1365:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1481:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1659:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1710:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1914:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1949:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:2146:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:2196:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:2236:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:2279:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:2430:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/lmm.cpp:1396:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/lmm.cpp:2317:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/lmm.h:94:8: style:inconclusive: Technically the member function 'LMM::CopyToParam' can be const. [functionConst]
GEMMA-0.98.5/src/lmm.cpp:90:11: note: Technically the member function 'LMM::CopyToParam' can be const.
GEMMA-0.98.5/src/lmm.h:94:8: note: Technically the member function 'LMM::CopyToParam' can be const.
GEMMA-0.98.5/src/lmm.cpp:483:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:542:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:640:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:717:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:797:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:864:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:943:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:1033:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:1400:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:1677:20: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2027:28: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2036:43: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2057:30: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2060:45: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2066:37: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2085:31: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2086:33: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2112:27: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2113:29: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2325:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/lmm.cpp:2326:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/lmm.cpp:2325:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/lmm.cpp:2326:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/lmm.cpp:2327:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/lmm.cpp:2326:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/lmm.cpp:2327:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/lmm.cpp:605:18: style: The comparison 'n_index == (n_cvt+2+1)*(n_cvt+2)/2' is always true because 'n_index' and '(n_cvt+2+1)*(n_cvt+2)/2' represent the same value. [knownConditionTrueFalse]
GEMMA-0.98.5/src/lmm.cpp:545:50: note: 'n_index' is assigned value '(n_cvt+2+1)*(n_cvt+2)/2' here.
GEMMA-0.98.5/src/lmm.cpp:605:18: note: The comparison 'n_index == (n_cvt+2+1)*(n_cvt+2)/2' is always true because 'n_index' and '(n_cvt+2+1)*(n_cvt+2)/2' represent the same value.
GEMMA-0.98.5/src/lmm.cpp:495:35: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:916:10: style: The scope of the variable 'ps_ww' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:916:17: style: The scope of the variable 'ps2_ww' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:999:10: style: The scope of the variable 'ps_ww' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:999:17: style: The scope of the variable 'ps2_ww' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:999:25: style: The scope of the variable 'ps3_ww' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1089:10: style: The scope of the variable 'ps_ww' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1089:17: style: The scope of the variable 'ps2_ww' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1089:25: style: The scope of the variable 'ps3_ww' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1257:10: style: The scope of the variable 'index_ab' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1334:10: style: The scope of the variable 'index_ab' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1380:7: style: The scope of the variable 'c_phen' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1381:10: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1904:28: style: The scope of the variable 'log_lr' can be reduced. [variableScope]
GEMMA-0.98.5/src/lmm.cpp:1124:35: style:inconclusive: Function 'CalcRLWald' argument 1 names different: declaration 'lambda' definition 'l'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/lmm.h:121:32: note: Function 'CalcRLWald' argument 1 names different: declaration 'lambda' definition 'l'.
GEMMA-0.98.5/src/lmm.cpp:1124:35: note: Function 'CalcRLWald' argument 1 names different: declaration 'lambda' definition 'l'.
GEMMA-0.98.5/src/lmm.cpp:1126:10: style: Local variable 'n_cvt' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/lmm.h:74:10: note: Shadowed declaration
GEMMA-0.98.5/src/lmm.cpp:1126:10: note: Shadow variable
GEMMA-0.98.5/src/lmm.cpp:1169:10: style: Local variable 'n_cvt' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/lmm.h:74:10: note: Shadowed declaration
GEMMA-0.98.5/src/lmm.cpp:1169:10: note: Shadow variable
GEMMA-0.98.5/src/lmm.cpp:144:32: performance: Function parameter 'st' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/lmm.cpp:1475:37: performance: Function parameter 'gwasnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/lmm.cpp:1658:43: performance: Function parameter 'gwasnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/lmm.cpp:1708:42: performance: Function parameter 'gwasnps' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/lmm.cpp:54:32: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/lmm.cpp:1471:59: style: Parameter 'fetch_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/lmm.cpp:483:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:542:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:640:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:717:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:797:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:864:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:943:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:1033:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/lmm.cpp:2290:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/logistic.cpp:84:26: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:134:26: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:195:26: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:329:24: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:369:24: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:427:24: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:558:25: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:595:25: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:644:25: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/logistic.cpp:214:10: style: The scope of the variable 'maxchange' can be reduced. [variableScope]
GEMMA-0.98.5/src/logistic.cpp:445:10: style: The scope of the variable 'maxchange' can be reduced. [variableScope]
GEMMA-0.98.5/src/logistic.cpp:664:10: style: The scope of the variable 'maxchange' can be reduced. [variableScope]
GEMMA-0.98.5/src/logistic.cpp:644:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/logistic.cpp:214:20: style: Variable 'maxchange' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/logistic.cpp:445:20: style: Variable 'maxchange' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/logistic.cpp:664:20: style: Variable 'maxchange' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/main.cpp:64:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:118:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:127:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:154:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:186:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:235:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:289:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:308:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:327:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:412:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:461:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:501:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:509:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:560:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mathfunc.cpp:558:23: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/mathfunc.cpp:135:10: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/mathfunc.cpp:479:10: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/mathfunc.cpp:413:10: style: Local variable 't' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/mathfunc.cpp:402:8: note: Shadowed declaration
GEMMA-0.98.5/src/mathfunc.cpp:413:10: note: Shadow variable
GEMMA-0.98.5/src/mathfunc.cpp:433:10: style: Local variable 'sum' shadows outer function [shadowFunction]
GEMMA-0.98.5/src/mathfunc.h:63:8: note: Shadowed declaration
GEMMA-0.98.5/src/mathfunc.cpp:433:10: note: Shadow variable
GEMMA-0.98.5/src/mathfunc.cpp:582:10: style: Local variable 'sum' shadows outer function [shadowFunction]
GEMMA-0.98.5/src/mathfunc.h:63:8: note: Shadowed declaration
GEMMA-0.98.5/src/mathfunc.cpp:582:10: note: Shadow variable
GEMMA-0.98.5/src/mathfunc.cpp:63:35: performance: Function parameter 'v' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/mathfunc.cpp:66:3: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
GEMMA-0.98.5/src/mathfunc.cpp:248:12: style: Variable 'd' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/mathfunc.cpp:479:12: style: Variable 'd' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/mvlmm.cpp:122:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:241:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasUpper [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:428:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:461:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasUpper [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:492:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:586:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:607:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:798:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:883:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:1027:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:1086:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:1095:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:1805:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:1825:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:2019:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:2367:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:2582:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:2615:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:2770:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:2973:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:3411:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:3964:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:4410:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/mvlmm.cpp:3210:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/mvlmm.cpp:4202:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/mvlmm.h:80:8: style:inconclusive: Technically the member function 'MVLMM::CopyToParam' can be const. [functionConst]
GEMMA-0.98.5/src/mvlmm.cpp:93:13: note: Technically the member function 'MVLMM::CopyToParam' can be const.
GEMMA-0.98.5/src/mvlmm.h:80:8: note: Technically the member function 'MVLMM::CopyToParam' can be const.
GEMMA-0.98.5/src/mvlmm.cpp:3218:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/mvlmm.cpp:4210:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/mvlmm.cpp:2853:14: style: Variable 'logl' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:2850:14: note: logl is assigned
GEMMA-0.98.5/src/mvlmm.cpp:2853:14: note: logl is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3059:11: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3056:11: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3059:11: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3125:11: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3122:11: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3125:11: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3219:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3218:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3219:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3220:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3219:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3220:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3308:17: style: Variable 'p_lrt' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3306:17: note: p_lrt is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3308:17: note: p_lrt is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3318:19: style: Variable 'p_lrt' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3316:19: note: p_lrt is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3318:19: note: p_lrt is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3499:11: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3496:11: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3499:11: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3568:11: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3565:11: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3568:11: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3791:17: style: Variable 'p_lrt' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3789:17: note: p_lrt is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3791:17: note: p_lrt is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:3801:19: style: Variable 'p_lrt' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:3799:19: note: p_lrt is assigned
GEMMA-0.98.5/src/mvlmm.cpp:3801:19: note: p_lrt is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4058:11: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4055:11: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4058:11: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4124:11: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4121:11: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4124:11: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4211:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4210:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4211:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4212:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4211:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4212:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4266:17: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4263:17: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4266:17: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4277:17: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4274:17: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4277:17: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4306:13: style: Variable 'p_lrt' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4304:13: note: p_lrt is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4306:13: note: p_lrt is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4316:15: style: Variable 'p_lrt' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4314:15: note: p_lrt is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4316:15: note: p_lrt is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4504:11: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4501:11: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4504:11: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4569:11: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4566:11: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4569:11: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4742:17: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4739:17: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4742:17: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4753:17: style: Variable 'logl_H0' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4750:17: note: logl_H0 is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4753:17: note: logl_H0 is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4783:13: style: Variable 'p_lrt' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4781:13: note: p_lrt is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4783:13: note: p_lrt is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:4793:15: style: Variable 'p_lrt' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/mvlmm.cpp:4791:15: note: p_lrt is assigned
GEMMA-0.98.5/src/mvlmm.cpp:4793:15: note: p_lrt is overwritten
GEMMA-0.98.5/src/mvlmm.cpp:342:20: style: The scope of the variable 'dl' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:366:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:451:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:497:31: style: The scope of the variable 'c_size' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:498:30: style: The scope of the variable 'dc_size' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:503:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:503:17: style: The scope of the variable 'dl' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:503:21: style: The scope of the variable 'x' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:503:24: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:569:22: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:628:10: style: The scope of the variable 'logdet_Q' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:628:20: style: The scope of the variable 'logdet_Ve' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:733:17: style: The scope of the variable 'dl' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:733:24: style: The scope of the variable 'd1' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:733:28: style: The scope of the variable 'd2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:841:17: style: The scope of the variable 'dl' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:951:27: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1118:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1118:17: style: The scope of the variable 'd1' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1118:21: style: The scope of the variable 'd2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1145:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1145:17: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1179:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1226:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1226:17: style: The scope of the variable 'd_Hiy_i1' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1226:27: style: The scope of the variable 'd_Hiy_j1' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1226:37: style: The scope of the variable 'd_Hiy_i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1226:47: style: The scope of the variable 'd_Hiy_j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1227:10: style: The scope of the variable 'd_Hi_i1i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1227:21: style: The scope of the variable 'd_Hi_i1j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1227:32: style: The scope of the variable 'd_Hi_j1i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1227:43: style: The scope of the variable 'd_Hi_j1j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1285:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1285:17: style: The scope of the variable 'd_Hiy_i' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1285:26: style: The scope of the variable 'd_Hiy_j' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1285:35: style: The scope of the variable 'd_Hi_i1i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1285:46: style: The scope of the variable 'd_Hi_i1j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1286:10: style: The scope of the variable 'd_Hi_j1i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1286:21: style: The scope of the variable 'd_Hi_j1j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1361:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1361:17: style: The scope of the variable 'd_Hi_i1i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1361:28: style: The scope of the variable 'd_Hi_i1j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1361:39: style: The scope of the variable 'd_Hi_j1i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1361:50: style: The scope of the variable 'd_Hi_j1j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1460:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1460:17: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1487:10: style: The scope of the variable 'delta' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1487:17: style: The scope of the variable 'd_Hi_i1i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1487:28: style: The scope of the variable 'd_Hi_i1j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1487:39: style: The scope of the variable 'd_Hi_j1i2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:1487:50: style: The scope of the variable 'd_Hi_j1j2' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:2068:10: style: The scope of the variable 'trCg1' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:2068:17: style: The scope of the variable 'trCe1' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:2624:42: style: The scope of the variable 'step_scale' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:2626:10: style: The scope of the variable 'step_iter' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:2776:10: style: The scope of the variable 'a' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:2776:13: style: The scope of the variable 'b' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:2776:16: style: The scope of the variable 'c' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:2897:10: style: The scope of the variable 'dl' can be reduced. [variableScope]
GEMMA-0.98.5/src/mvlmm.cpp:180:17: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/mvlmm.cpp:168:15: note: Shadowed declaration
GEMMA-0.98.5/src/mvlmm.cpp:180:17: note: Shadow variable
GEMMA-0.98.5/src/mvlmm.cpp:185:17: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/mvlmm.cpp:168:15: note: Shadowed declaration
GEMMA-0.98.5/src/mvlmm.cpp:185:17: note: Shadow variable
GEMMA-0.98.5/src/mvlmm.cpp:3349:21: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/mvlmm.cpp:3278:19: note: Shadowed declaration
GEMMA-0.98.5/src/mvlmm.cpp:3349:21: note: Shadow variable
GEMMA-0.98.5/src/mvlmm.cpp:3354:21: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/mvlmm.cpp:3278:19: note: Shadowed declaration
GEMMA-0.98.5/src/mvlmm.cpp:3354:21: note: Shadow variable
GEMMA-0.98.5/src/mvlmm.cpp:3831:21: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/mvlmm.cpp:3756:19: note: Shadowed declaration
GEMMA-0.98.5/src/mvlmm.cpp:3831:21: note: Shadow variable
GEMMA-0.98.5/src/mvlmm.cpp:3836:21: style: Local variable 'i' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/mvlmm.cpp:3756:19: note: Shadowed declaration
GEMMA-0.98.5/src/mvlmm.cpp:3836:21: note: Shadow variable
GEMMA-0.98.5/src/mvlmm.cpp:51:34: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/mvlmm.cpp:2985:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/mvlmm.cpp:3976:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/param.cpp:54:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:85:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:330:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:510:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:995:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:1254:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:1402:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:1822:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:1852:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:1893:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:1920:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:1975:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:2042:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::l_mle_null' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::l_remle_null' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::logl_mle_H0' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::logl_remle_H0' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::pve_null' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::pve_se_null' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::pve_total' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::se_pve_total' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::vg_remle_null' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ve_remle_null' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::vg_mle_null' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ve_mle_null' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::trace_G' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::cHyp_initial' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ni_total' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ni_test' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ni_cvt' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ni_study' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ni_ref' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::np_obs' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::np_miss' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ns_total' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ns_test' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ns_study' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ns_ref' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ng_total' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ng_test' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ni_control' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::ni_case' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::n_ph' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::time_hyp' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.cpp:94:8: warning: Member variable 'PARAM::time_Proposal' is not initialized in the constructor. [uninitMemberVar]
GEMMA-0.98.5/src/param.h:337:8: style:inconclusive: Technically the member function 'PARAM::PrintSummary' can be const. [functionConst]
GEMMA-0.98.5/src/param.cpp:1252:13: note: Technically the member function 'PARAM::PrintSummary' can be const.
GEMMA-0.98.5/src/param.h:337:8: note: Technically the member function 'PARAM::PrintSummary' can be const.
GEMMA-0.98.5/src/param.h:342:8: style:inconclusive: Technically the member function 'PARAM::CopyCvt' can be const. [functionConst]
GEMMA-0.98.5/src/param.cpp:2100:13: note: Technically the member function 'PARAM::CopyCvt' can be const.
GEMMA-0.98.5/src/param.h:342:8: note: Technically the member function 'PARAM::CopyCvt' can be const.
GEMMA-0.98.5/src/param.h:347:8: style:inconclusive: Technically the member function 'PARAM::CopyCvtPhen' can be const. [functionConst]
GEMMA-0.98.5/src/param.cpp:2146:13: note: Technically the member function 'PARAM::CopyCvtPhen' can be const.
GEMMA-0.98.5/src/param.h:347:8: note: Technically the member function 'PARAM::CopyCvtPhen' can be const.
GEMMA-0.98.5/src/param.h:348:8: style:inconclusive: Technically the member function 'PARAM::CopyCvtPhen' can be const. [functionConst]
GEMMA-0.98.5/src/param.cpp:2173:13: note: Technically the member function 'PARAM::CopyCvtPhen' can be const.
GEMMA-0.98.5/src/param.h:348:8: note: Technically the member function 'PARAM::CopyCvtPhen' can be const.
GEMMA-0.98.5/src/param.h:354:8: style:inconclusive: Technically the member function 'PARAM::WriteVector' can be const. [functionConst]
GEMMA-0.98.5/src/param.cpp:1814:13: note: Technically the member function 'PARAM::WriteVector' can be const.
GEMMA-0.98.5/src/param.h:354:8: note: Technically the member function 'PARAM::WriteVector' can be const.
GEMMA-0.98.5/src/param.h:357:8: style:inconclusive: Technically the member function 'PARAM::WriteMatrix' can be const. [functionConst]
GEMMA-0.98.5/src/param.cpp:1886:13: note: Technically the member function 'PARAM::WriteMatrix' can be const.
GEMMA-0.98.5/src/param.h:357:8: note: Technically the member function 'PARAM::WriteMatrix' can be const.
GEMMA-0.98.5/src/param.h:358:8: style:inconclusive: Technically the member function 'PARAM::WriteVector' can be const. [functionConst]
GEMMA-0.98.5/src/param.cpp:1913:13: note: Technically the member function 'PARAM::WriteVector' can be const.
GEMMA-0.98.5/src/param.h:358:8: note: Technically the member function 'PARAM::WriteVector' can be const.
GEMMA-0.98.5/src/param.cpp:2076:30: style: Condition 'a_mode!=M_BSLMM5' is always false [knownConditionTrueFalse]
GEMMA-0.98.5/src/param.cpp:2074:14: note: Assuming that condition 'a_mode!=M_BSLMM5' is not redundant
GEMMA-0.98.5/src/param.cpp:2076:30: note: Condition 'a_mode!=M_BSLMM5' is always false
GEMMA-0.98.5/src/param.cpp:207:9: style: The scope of the variable 'k' can be reduced. [variableScope]
GEMMA-0.98.5/src/param.cpp:447:9: style: The scope of the variable 'k' can be reduced. [variableScope]
GEMMA-0.98.5/src/param.cpp:1262:10: style: The scope of the variable 'file_str' can be reduced. [variableScope]
GEMMA-0.98.5/src/param.cpp:1282:10: style: The scope of the variable 'file_str' can be reduced. [variableScope]
GEMMA-0.98.5/src/param.cpp:1996:7: style: The scope of the variable 'k' can be reduced. [variableScope]
GEMMA-0.98.5/src/param.cpp:2304:10: style: The scope of the variable 'd' can be reduced. [variableScope]
GEMMA-0.98.5/src/param.cpp:2116:33: style:inconclusive: Function 'CopyGxe' argument 1 names different: declaration 'gxe' definition 'env'. [funcArgNamesDifferent]
GEMMA-0.98.5/src/param.h:344:28: note: Function 'CopyGxe' argument 1 names different: declaration 'gxe' definition 'env'.
GEMMA-0.98.5/src/param.cpp:2116:33: note: Function 'CopyGxe' argument 1 names different: declaration 'gxe' definition 'env'.
GEMMA-0.98.5/src/param.cpp:53:46: performance: Function parameter 'mapchr' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.cpp:53:67: performance: Function parameter 'loco' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.cpp:1815:60: performance: Function parameter 'suffix' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.cpp:1845:35: performance: Function parameter 'suffix' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.cpp:1886:66: performance: Function parameter 'suffix' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.cpp:1913:66: performance: Function parameter 'suffix' should be passed by const reference. [passedByValue]
GEMMA-0.98.5/src/param.cpp:57:14: style: Variable 'kv' can be declared as reference to const [constVariableReference]
GEMMA-0.98.5/src/param.cpp:835:9: style: Variable 'ptm' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/param.cpp:207:11: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/param.cpp:447:11: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/prdt.cpp:83:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/prdt.cpp:109:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/prdt.cpp:173:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/prdt.cpp:208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/prdt.cpp:311:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/prdt.cpp:528:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/prdt.cpp:229:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/prdt.cpp:234:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/prdt.cpp:236:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/prdt.cpp:237:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/prdt.cpp:254:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/prdt.h:58:8: style:inconclusive: Technically the member function 'PRDT::CopyToParam' can be const. [functionConst]
GEMMA-0.98.5/src/prdt.cpp:69:12: note: Technically the member function 'PRDT::CopyToParam' can be const.
GEMMA-0.98.5/src/prdt.h:58:8: note: Technically the member function 'PRDT::CopyToParam' can be const.
GEMMA-0.98.5/src/prdt.h:59:8: style:inconclusive: Technically the member function 'PRDT::WriteFiles' can be const. [functionConst]
GEMMA-0.98.5/src/prdt.cpp:76:12: note: Technically the member function 'PRDT::WriteFiles' can be const.
GEMMA-0.98.5/src/prdt.h:59:8: note: Technically the member function 'PRDT::WriteFiles' can be const.
GEMMA-0.98.5/src/prdt.h:60:8: style:inconclusive: Technically the member function 'PRDT::WriteFiles' can be const. [functionConst]
GEMMA-0.98.5/src/prdt.cpp:104:12: note: Technically the member function 'PRDT::WriteFiles' can be const.
GEMMA-0.98.5/src/prdt.h:60:8: note: Technically the member function 'PRDT::WriteFiles' can be const.
GEMMA-0.98.5/src/prdt.cpp:234:21: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/prdt.cpp:237:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/prdt.cpp:236:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/prdt.cpp:237:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/prdt.cpp:151:19: style: The scope of the variable 'o_j' can be reduced. [variableScope]
GEMMA-0.98.5/src/prdt.cpp:217:10: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/prdt.cpp:321:10: style: The scope of the variable 'rs' can be reduced. [variableScope]
GEMMA-0.98.5/src/prdt.cpp:42:33: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/prdt.cpp:151:23: style: Variable 'o_j' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/varcov.cpp:83:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/varcov.cpp:250:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/varcov.cpp:349:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/varcov.h:53:8: style:inconclusive: Technically the member function 'VARCOV::CopyToParam' can be const. [functionConst]
GEMMA-0.98.5/src/varcov.cpp:69:14: note: Technically the member function 'VARCOV::CopyToParam' can be const.
GEMMA-0.98.5/src/varcov.h:53:8: note: Technically the member function 'VARCOV::CopyToParam' can be const.
GEMMA-0.98.5/src/varcov.h:54:8: style:inconclusive: Technically the member function 'VARCOV::CalcNB' can be const. [functionConst]
GEMMA-0.98.5/src/varcov.cpp:168:14: note: Technically the member function 'VARCOV::CalcNB' can be const.
GEMMA-0.98.5/src/varcov.h:54:8: note: Technically the member function 'VARCOV::CalcNB' can be const.
GEMMA-0.98.5/src/varcov.h:55:8: style:inconclusive: Technically the member function 'VARCOV::WriteCov' can be const. [functionConst]
GEMMA-0.98.5/src/varcov.cpp:74:14: note: Technically the member function 'VARCOV::WriteCov' can be const.
GEMMA-0.98.5/src/varcov.h:55:8: note: Technically the member function 'VARCOV::WriteCov' can be const.
GEMMA-0.98.5/src/varcov.cpp:48:35: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:121:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:213:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:299:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GSL_SUCCESS [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:341:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GSL_SUCCESS [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:405:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GSL_SUCCESS [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:410:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:643:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:796:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:1012:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:1343:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:1560:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:1761:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:1995:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CblasNoTrans [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:2224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:2318:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:2445:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:2480:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:2571:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:2695:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:2912:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
GEMMA-0.98.5/src/vc.cpp:666:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/vc.cpp:826:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/vc.cpp:1060:29: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/vc.cpp:2245:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/vc.cpp:2498:31: warning: Return value of function safeGetline(infile,line).eof() is not used. [ignoredReturnValue]
GEMMA-0.98.5/src/vc.cpp:486:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/vc.cpp:611:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/vc.cpp:730:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/vc.cpp:914:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/vc.cpp:1102:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/vc.cpp:1207:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
GEMMA-0.98.5/src/vc.h:82:8: style:inconclusive: Technically the member function 'VC::CopyToParam' can be const. [functionConst]
GEMMA-0.98.5/src/vc.cpp:90:10: note: Technically the member function 'VC::CopyToParam' can be const.
GEMMA-0.98.5/src/vc.h:82:8: note: Technically the member function 'VC::CopyToParam' can be const.
GEMMA-0.98.5/src/vc.h:83:8: style:inconclusive: Technically the member function 'VC::WriteFile_qs' can be const. [functionConst]
GEMMA-0.98.5/src/vc.cpp:114:10: note: Technically the member function 'VC::WriteFile_qs' can be const.
GEMMA-0.98.5/src/vc.h:83:8: note: Technically the member function 'VC::WriteFile_qs' can be const.
GEMMA-0.98.5/src/vc.cpp:261:17: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:303:17: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:346:17: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:486:19: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:681:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:848:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:1068:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:2253:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:2506:14: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/src/vc.cpp:1838:5: style: Variable 's' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/vc.cpp:1747:5: note: s is assigned
GEMMA-0.98.5/src/vc.cpp:1838:5: note: s is overwritten
GEMMA-0.98.5/src/vc.cpp:1862:12: style: Variable 'd1' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/vc.cpp:1861:12: note: d1 is assigned
GEMMA-0.98.5/src/vc.cpp:1862:12: note: d1 is overwritten
GEMMA-0.98.5/src/vc.cpp:1886:14: style: Variable 'd2' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/vc.cpp:1885:14: note: d2 is assigned
GEMMA-0.98.5/src/vc.cpp:1886:14: note: d2 is overwritten
GEMMA-0.98.5/src/vc.cpp:2254:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/vc.cpp:2253:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/vc.cpp:2254:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/vc.cpp:2255:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/vc.cpp:2254:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/vc.cpp:2255:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/vc.cpp:2507:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/vc.cpp:2506:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/vc.cpp:2507:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/vc.cpp:2508:12: style: Variable 'ch_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
GEMMA-0.98.5/src/vc.cpp:2507:12: note: ch_ptr is assigned
GEMMA-0.98.5/src/vc.cpp:2508:12: note: ch_ptr is overwritten
GEMMA-0.98.5/src/vc.cpp:744:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
GEMMA-0.98.5/src/vc.cpp:746:7: note: Found duplicate branches for 'if' and 'else'.
GEMMA-0.98.5/src/vc.cpp:744:5: note: Found duplicate branches for 'if' and 'else'.
GEMMA-0.98.5/src/vc.cpp:749:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
GEMMA-0.98.5/src/vc.cpp:751:7: note: Found duplicate branches for 'if' and 'else'.
GEMMA-0.98.5/src/vc.cpp:749:5: note: Found duplicate branches for 'if' and 'else'.
GEMMA-0.98.5/src/vc.cpp:483:10: style: The scope of the variable 'type' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:658:19: style: The scope of the variable 'a1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:658:23: style: The scope of the variable 'a0' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:658:32: style: The scope of the variable 'cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:659:10: style: The scope of the variable 'af' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:659:18: style: The scope of the variable 'var_x' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:659:29: style: The scope of the variable 'd_pos' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:659:36: style: The scope of the variable 'd_cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:660:10: style: The scope of the variable 'n_total' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:660:23: style: The scope of the variable 'n_mis' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:660:34: style: The scope of the variable 'n_obs' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:809:19: style: The scope of the variable 'a1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:809:23: style: The scope of the variable 'a0' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:809:32: style: The scope of the variable 'cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:810:10: style: The scope of the variable 'z' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:810:17: style: The scope of the variable 'beta' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:810:27: style: The scope of the variable 'se_beta' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:810:40: style: The scope of the variable 'chisq' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:810:51: style: The scope of the variable 'pvalue' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:811:10: style: The scope of the variable 'af' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:811:18: style: The scope of the variable 'var_x' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:812:10: style: The scope of the variable 'n_total' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:812:23: style: The scope of the variable 'n_mis' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:812:34: style: The scope of the variable 'n_obs' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1022:10: style: The scope of the variable 'rs1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1049:19: style: The scope of the variable 'a1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1049:23: style: The scope of the variable 'a0' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1049:38: style: The scope of the variable 'cm' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1051:10: style: The scope of the variable 'd_pos1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1051:33: style: The scope of the variable 'd_cm1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:10: style: The scope of the variable 'a' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:13: style: The scope of the variable 'b' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:16: style: The scope of the variable 'x' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:19: style: The scope of the variable 'y' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:22: style: The scope of the variable 'n' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:25: style: The scope of the variable 'var_y' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:32: style: The scope of the variable 'var_x' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:39: style: The scope of the variable 'mean_y' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:47: style: The scope of the variable 'mean_x' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:55: style: The scope of the variable 'cov_xy' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1220:63: style: The scope of the variable 'crt_factor' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1400:10: style: The scope of the variable 'd1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:2752:17: style: The scope of the variable 's1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:2890:10: style: The scope of the variable 'd1' can be reduced. [variableScope]
GEMMA-0.98.5/src/vc.cpp:1506:10: style: Local variable 'n_vc' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/vc.h:63:10: note: Shadowed declaration
GEMMA-0.98.5/src/vc.cpp:1506:10: note: Shadow variable
GEMMA-0.98.5/src/vc.cpp:1729:10: style: Local variable 'n_vc' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/vc.h:63:10: note: Shadowed declaration
GEMMA-0.98.5/src/vc.cpp:1729:10: note: Shadow variable
GEMMA-0.98.5/src/vc.cpp:1936:10: style: Local variable 'n_vc' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/vc.h:63:10: note: Shadowed declaration
GEMMA-0.98.5/src/vc.cpp:1936:10: note: Shadow variable
GEMMA-0.98.5/src/vc.cpp:2071:9: style: Local variable 'sig' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/vc.cpp:1961:7: note: Shadowed declaration
GEMMA-0.98.5/src/vc.cpp:2071:9: note: Shadow variable
GEMMA-0.98.5/src/vc.cpp:2072:22: style: Local variable 'pmt' shadows outer variable [shadowVariable]
GEMMA-0.98.5/src/vc.cpp:1962:20: note: Shadowed declaration
GEMMA-0.98.5/src/vc.cpp:2072:22: note: Shadow variable
GEMMA-0.98.5/src/vc.cpp:59:31: style: Parameter 'cPar' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2221:29: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2221:57: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2315:28: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2315:56: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2478:31: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2478:59: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2569:30: style: Parameter 'indicator_idv' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2569:58: style: Parameter 'indicator_snp' can be declared as reference to const [constParameterReference]
GEMMA-0.98.5/src/vc.cpp:2232:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/vc.cpp:2488:9: style: Variable 'ch_ptr' can be declared as pointer to const [constVariablePointer]
GEMMA-0.98.5/src/vc.cpp:2052:42: warning: Uninitialized variable: d [uninitvar]
GEMMA-0.98.5/src/vc.cpp:1991:24: note: Assuming condition is false
GEMMA-0.98.5/src/vc.cpp:2052:42: note: Uninitialized variable: d
GEMMA-0.98.5/src/vc.cpp:326:18: style: Variable 'sigma2_j' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:389:18: style: Variable 'sigma2_j' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:456:22: style: Variable 'var_set' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:659:13: style: Variable 'af' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:659:24: style: Variable 'var_x' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:660:18: style: Variable 'n_total' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:660:29: style: Variable 'n_mis' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:660:40: style: Variable 'n_obs' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:703:12: style: Variable 'cm' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:707:12: style: Variable 'a1' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:710:12: style: Variable 'a0' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:810:12: style: Variable 'z' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:810:22: style: Variable 'beta' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:810:35: style: Variable 'se_beta' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:810:46: style: Variable 'chisq' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:810:58: style: Variable 'pvalue' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:810:71: style: Variable 'zsquare' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:811:13: style: Variable 'af' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:811:24: style: Variable 'var_x' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:812:18: style: Variable 'n_total' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:812:29: style: Variable 'n_mis' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:812:40: style: Variable 'n_obs' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:872:12: style: Variable 'cm' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:875:12: style: Variable 'a1' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:878:12: style: Variable 'a0' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:807:10: style: Unused variable: type [unusedVariable]
GEMMA-0.98.5/src/vc.cpp:1082:12: style: Variable 'cm' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:1086:12: style: Variable 'a1' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:1089:12: style: Variable 'a0' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:1227:15: style: Variable 'var_y' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:1245:19: style: Variable 'var_y' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:1256:17: style: Variable 'var_y' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/src/vc.cpp:1259:17: style: Variable 'var_y' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/test/src/unittests-math.cpp:90:8: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/test/src/unittests-math.cpp:91:8: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/test/src/unittests-math.cpp:92:8: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/test/src/unittests-math.cpp:138:8: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/test/src/unittests-math.cpp:139:8: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/test/src/unittests-math.cpp:140:8: style: C-style pointer casting [cstyleCast]
GEMMA-0.98.5/test/src/unittests-math.cpp:63:20: style: Variable 'v' is assigned a value that is never used. [unreadVariable]
GEMMA-0.98.5/test/src/unittests-math.cpp:76:20: style: Unused variable: j [unusedVariable]
GEMMA-0.98.5/test/src/unittests-math.cpp:124:20: style: Unused variable: j [unusedVariable]
diff:


DONE