2022-06-21 07:31
ftp://ftp.de.debian.org/debian/pool/main/c/clonalframeml/clonalframeml_1.12.orig.tar.gz
cppcheck-options: --library=posix --library=gnu  --showtime=top5 --check-library --inconclusive --enable=style,information --template=daca2 -D__GNUC__ --platform=unix64 -rp=temp -j2
platform: Linux-5.10.0-15-cloud-amd64-x86_64-with-glibc2.31
python: 3.9.2
client-version: 1.3.24
compiler: g++ (Debian 10.2.1-6) 10.2.1 20210110
cppcheck: head 2.8
head-info: de2509f (2022-06-21 00:12:11 +0200)
count: 296 297
elapsed-time: 21.5 17.2
head-timing-info:
 Overall time: 0s

old-timing-info:
 Overall time: 0s

head results:
ClonalFrameML-1.12/src/myutils/mydouble.h:161:44: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
ClonalFrameML-1.12/src/myutils/mydouble.h:162:25: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
ClonalFrameML-1.12/src/myutils/mydouble.h:175:42: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
ClonalFrameML-1.12/src/myutils/mydouble.h:176:17: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
ClonalFrameML-1.12/src/main.h:235:67: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
ClonalFrameML-1.12/src/main.h:363:67: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:38:2: warning: Member variable 'mt_node::id' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:38:2: warning: Member variable 'mt_node::in_use' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:38:2: warning: Member variable 'mt_node::time' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:38:2: warning: Member variable 'mt_node::edge_time' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:38:2: warning: Member variable 'mt_node::last_update' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:38:2: warning: Member variable 'mt_node::ancestor' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:38:2: warning: Member variable 'mt_node::descendant' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:75:2: warning: Member variable 'marginal_tree::id' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:75:2: warning: Member variable 'marginal_tree::k' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:75:2: warning: Member variable 'marginal_tree::size' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:75:2: warning: Member variable 'marginal_tree::n' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:75:2: warning: Member variable 'marginal_tree::node' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:75:2: warning: Member variable 'marginal_tree::genotype' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:75:2: warning: Member variable 'marginal_tree::next_free_node' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:75:2: warning: Member variable 'marginal_tree::nco' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::pc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::plog' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::pclog' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::en' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::oldg' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::sq' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::alxm' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::g' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/random.h:200:2: warning: Member variable 'Random::gset' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/DNA.h:67:2: warning: Member variable 'DNA::nseq' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/DNA.h:67:2: warning: Member variable 'DNA::lseq' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/mydouble.h:38:2: warning: Member variable 'mydouble::_log' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::evala_BrentFunc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::evalb_BrentFunc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::evalc_BrentFunc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::pointa' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::pointb' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::pointc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::tolerance' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::ZEPS' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::function_minimum' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::bracketed' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:77:2: warning: Member variable 'Brent::fail' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::evala_BrentFunc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::evalb_BrentFunc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::evalc_BrentFunc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::pointa' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::pointb' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::pointc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::tolerance' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::ZEPS' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::function_minimum' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::min_x' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:323:2: warning: Member variable 'ConstrainedBrent::max_x' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/powell.h:65:2: warning: Member variable 'Powell::N' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/powell.h:65:2: warning: Member variable 'Powell::function_minimum' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/powell.h:65:2: warning: Member variable 'Powell::n_iterations' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/powell.h:65:2: warning: Member variable 'Powell::fail' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:69:2: warning: Member variable 'ArgumentWizard::got_required' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:69:2: warning: Member variable 'ArgumentWizard::switcher' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:69:2: warning: Member variable 'ArgumentWizard::argc' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:69:2: warning: Member variable 'ArgumentWizard::argn' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/main.h:177:2: warning: Member variable 'ClonalFrameBaumWelch::ML' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/main.h:177:2: warning: Member variable 'ClonalFrameBaumWelch::ML0' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/main.h:177:2: warning: Member variable 'ClonalFrameBaumWelch::priorL' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/main.h:177:2: warning: Member variable 'ClonalFrameBaumWelch::PR' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/main.h:295:2: warning: Member variable 'ClonalFrameBaumWelchRhoPerBranch::ML' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/main.h:295:2: warning: Member variable 'ClonalFrameBaumWelchRhoPerBranch::PR' is not initialized in the constructor. [uninitMemberVar]
ClonalFrameML-1.12/src/brent.h:65:7: style:inconclusive: Member variable 'Brent::coutput' is in the wrong place in the initializer list. [initializerList]
ClonalFrameML-1.12/src/brent.h:77:104: note: Member variable 'Brent::coutput' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/brent.h:65:7: note: Member variable 'Brent::coutput' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/brent.h:313:7: style:inconclusive: Member variable 'ConstrainedBrent::coutput' is in the wrong place in the initializer list. [initializerList]
ClonalFrameML-1.12/src/brent.h:323:115: note: Member variable 'ConstrainedBrent::coutput' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/brent.h:313:7: note: Member variable 'ConstrainedBrent::coutput' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/powell.h:47:7: style:inconclusive: Member variable 'Powell::coutput' is in the wrong place in the initializer list. [initializerList]
ClonalFrameML-1.12/src/powell.h:65:100: note: Member variable 'Powell::coutput' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/powell.h:47:7: note: Member variable 'Powell::coutput' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/powell.h:45:8: style:inconclusive: Member variable 'Powell::brent' is in the wrong place in the initializer list. [initializerList]
ClonalFrameML-1.12/src/powell.h:65:116: note: Member variable 'Powell::brent' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/powell.h:45:8: note: Member variable 'Powell::brent' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/main.h:161:38: style:inconclusive: Member variable 'ClonalFrameBaumWelch::is_imported' is in the wrong place in the initializer list. [initializerList]
ClonalFrameML-1.12/src/main.h:181:21: note: Member variable 'ClonalFrameBaumWelch::is_imported' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/main.h:161:38: note: Member variable 'ClonalFrameBaumWelch::is_imported' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/main.h:170:15: style:inconclusive: Member variable 'ClonalFrameBaumWelch::informative' is in the wrong place in the initializer list. [initializerList]
ClonalFrameML-1.12/src/main.h:182:98: note: Member variable 'ClonalFrameBaumWelch::informative' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/main.h:170:15: note: Member variable 'ClonalFrameBaumWelch::informative' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/main.h:278:38: style:inconclusive: Member variable 'ClonalFrameBaumWelchRhoPerBranch::is_imported' is in the wrong place in the initializer list. [initializerList]
ClonalFrameML-1.12/src/main.h:299:21: note: Member variable 'ClonalFrameBaumWelchRhoPerBranch::is_imported' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/main.h:278:38: note: Member variable 'ClonalFrameBaumWelchRhoPerBranch::is_imported' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/main.h:287:15: style:inconclusive: Member variable 'ClonalFrameBaumWelchRhoPerBranch::informative' is in the wrong place in the initializer list. [initializerList]
ClonalFrameML-1.12/src/main.h:300:98: note: Member variable 'ClonalFrameBaumWelchRhoPerBranch::informative' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/main.h:287:15: note: Member variable 'ClonalFrameBaumWelchRhoPerBranch::informative' is in the wrong place in the initializer list.
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:180:6: style:inconclusive: Technically the member function 'marginal_tree::get_k' can be const. [functionConst]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:181:7: performance:inconclusive: Technically the member function 'marginal_tree::error' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:188:9: style:inconclusive: Technically the member function 'marginal_tree::height' can be const. [functionConst]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:191:9: style:inconclusive: Technically the member function 'marginal_tree::branch_length' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/random.h:58:6: performance:inconclusive: Technically the member function 'myutils::Random::autosetseed' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/random.h:105:7: performance:inconclusive: Technically the member function 'myutils::Random::rerror' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/random.h:182:9: performance:inconclusive: Technically the member function 'myutils::Random::gammln' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/random.h:314:6: style:inconclusive: Technically the member function 'myutils::Random::getseed' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/random.h:343:6: style:inconclusive: Technically the member function 'myutils::Random::ncalls' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/DNA.h:331:9: style:inconclusive: Technically the member function 'DNA::S' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/DNA.h:375:9: style:inconclusive: Technically the member function 'DNA::pi' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/DNA.h:389:9: style:inconclusive: Technically the member function 'DNA::Varpi' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/DNA.h:409:9: style:inconclusive: Technically the member function 'DNA::Tajima' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/DNA.h:446:9: style:inconclusive: Technically the member function 'DNA::pi' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/DNA.h:793:7: performance:inconclusive: Technically the member function 'DNA::codonToPeptide' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:171:14: performance:inconclusive: Technically the member function 'Brent::shft3' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:176:14: performance:inconclusive: Technically the member function 'Brent::shft2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:230:14: performance:inconclusive: Technically the member function 'Brent::SWAP' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:233:16: performance:inconclusive: Technically the member function 'Brent::SIGN' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:236:16: performance:inconclusive: Technically the member function 'Brent::MAX' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:239:16: performance:inconclusive: Technically the member function 'Brent::FABS' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:352:14: performance:inconclusive: Technically the member function 'ConstrainedBrent::shft3' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:357:14: performance:inconclusive: Technically the member function 'ConstrainedBrent::shft2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:424:14: performance:inconclusive: Technically the member function 'ConstrainedBrent::SWAP' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:427:16: performance:inconclusive: Technically the member function 'ConstrainedBrent::SIGN' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:430:16: performance:inconclusive: Technically the member function 'ConstrainedBrent::MAX' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/brent.h:433:16: performance:inconclusive: Technically the member function 'ConstrainedBrent::FABS' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/powell.h:156:16: performance:inconclusive: Technically the member function 'Powell::FABS' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/powell.h:159:16: performance:inconclusive: Technically the member function 'Powell::SQR' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:127:7: performance:inconclusive: Technically the member function 'myutils::ArgumentWizard::remove_case' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:158:7: style:inconclusive: Technically the member function 'myutils::ArgumentWizard::auto_check_required' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:163:7: style:inconclusive: Technically the member function 'myutils::ArgumentWizard::function_get_unrecognised' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:215:7: performance:inconclusive: Technically the member function 'myutils::ArgumentWizard::function_get_external_vector_double' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/main.h:383:17: performance:inconclusive: Technically the member function 'ClonalFrameBaumWelchRhoPerBranch::simulate_posterior' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:124:6: style:inconclusive: Technically the member function 'LowerTriangularMatrix < double >::n' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:125:6: style:inconclusive: Technically the member function 'LowerTriangularMatrix < double >::size' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:128:7: performance:inconclusive: Technically the member function 'LowerTriangularMatrix < double >::error' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:124:6: style:inconclusive: Technically the member function 'LowerTriangularMatrix < int >::n' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:125:6: style:inconclusive: Technically the member function 'LowerTriangularMatrix < int >::size' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:128:7: performance:inconclusive: Technically the member function 'LowerTriangularMatrix < int >::error' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:124:6: style:inconclusive: Technically the member function 'LowerTriangularMatrix < std :: vector < double > >::n' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:125:6: style:inconclusive: Technically the member function 'LowerTriangularMatrix < std :: vector < double > >::size' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:128:7: performance:inconclusive: Technically the member function 'LowerTriangularMatrix < std :: vector < double > >::error' can be static (but you may consider moving to unnamed namespace). [functionStatic]
ClonalFrameML-1.12/src/myutils/matrix.h:144:6: style:inconclusive: Technically the member function 'Matrix < double >::nrows' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:145:6: style:inconclusive: Technically the member function 'Matrix < double >::ncols' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:144:6: style:inconclusive: Technically the member function 'Matrix < int >::nrows' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:145:6: style:inconclusive: Technically the member function 'Matrix < int >::ncols' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:144:6: style:inconclusive: Technically the member function 'Matrix < Nucleotide >::nrows' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:145:6: style:inconclusive: Technically the member function 'Matrix < Nucleotide >::ncols' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:144:6: style:inconclusive: Technically the member function 'Matrix < mydouble >::nrows' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:145:6: style:inconclusive: Technically the member function 'Matrix < mydouble >::ncols' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:144:6: style:inconclusive: Technically the member function 'Matrix < bool >::nrows' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:145:6: style:inconclusive: Technically the member function 'Matrix < bool >::ncols' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:144:6: style:inconclusive: Technically the member function 'Matrix < ImportationState >::nrows' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/matrix.h:145:6: style:inconclusive: Technically the member function 'Matrix < ImportationState >::ncols' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/vector.h:89:6: style:inconclusive: Technically the member function 'Vector < double >::size' can be const. [functionConst]
ClonalFrameML-1.12/src/myutils/newick.h:211:2: style: Class 'NewickTree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/myutils/DNA.h:71:2: style: Class 'DNA' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/myutils/mydouble.h:42:2: style: Class 'mydouble' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/brent.h:77:2: style: Class 'Brent' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/brent.h:323:2: style: Class 'ConstrainedBrent' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/powell.h:65:2: style: Class 'Powell' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:69:20: style: Class 'LowerTriangularMatrix < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:69:20: style: Class 'LowerTriangularMatrix < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:69:20: style: Class 'LowerTriangularMatrix < std :: vector < double > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/myutils/vector.h:52:20: style: Class 'Vector < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
ClonalFrameML-1.12/src/powell.h:86:9: style: The function 'f' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
ClonalFrameML-1.12/src/brent.h:42:17: note: Virtual function in base class
ClonalFrameML-1.12/src/powell.h:86:9: note: Function in derived class
ClonalFrameML-1.12/src/main.h:134:9: style: The function 'f' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
ClonalFrameML-1.12/src/powell.h:39:17: note: Virtual function in base class
ClonalFrameML-1.12/src/main.h:134:9: note: Function in derived class
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:96:9: style: C-style pointer casting [cstyleCast]
ClonalFrameML-1.12/src/myutils/random.h:544:10: style: C-style pointer casting [cstyleCast]
ClonalFrameML-1.12/src/myutils/random.h:575:10: style: C-style pointer casting [cstyleCast]
ClonalFrameML-1.12/src/myutils/random.h:118:10: style: The scope of the variable 'U' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:118:12: style: The scope of the variable 'V' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:118:14: style: The scope of the variable 'W' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:139:10: style: The scope of the variable 'U' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:139:12: style: The scope of the variable 'V' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:139:14: style: The scope of the variable 'W' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:139:18: style: The scope of the variable 'Y' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:157:7: style: The scope of the variable 'j' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:158:10: style: The scope of the variable 'am' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:158:13: style: The scope of the variable 'e' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:158:15: style: The scope of the variable 's' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:158:17: style: The scope of the variable 'v1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:158:20: style: The scope of the variable 'v2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:158:25: style: The scope of the variable 'y' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:549:21: style: The scope of the variable 'pnow' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:556:12: style: The scope of the variable 'rnum2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:557:10: style: The scope of the variable 'rnum1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:557:16: style: The scope of the variable 'ratio' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:579:12: style: The scope of the variable 'rnum2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:580:10: style: The scope of the variable 'rnum1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:580:16: style: The scope of the variable 'ratio' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:601:21: style: The scope of the variable 'pnow' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:608:12: style: The scope of the variable 'rnum2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:609:10: style: The scope of the variable 'rnum1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:609:16: style: The scope of the variable 'ratio' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:630:12: style: The scope of the variable 'rnum2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:631:10: style: The scope of the variable 'rnum1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:631:16: style: The scope of the variable 'ratio' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:652:21: style: The scope of the variable 'pnow' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:659:12: style: The scope of the variable 'rnum2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:660:10: style: The scope of the variable 'rnum1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:660:16: style: The scope of the variable 'ratio' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:776:15: style: The scope of the variable 'y' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:831:10: style: The scope of the variable 'fac' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:831:14: style: The scope of the variable 'rsq' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:831:18: style: The scope of the variable 'v1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/random.h:831:21: style: The scope of the variable 'v2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/DNA.h:357:8: style: The scope of the variable 'unique' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/DNA.h:415:8: style: The scope of the variable 'segregating' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/DNA.h:468:8: style: The scope of the variable 'segregating' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/DNA.h:539:8: style: The scope of the variable 'segregating' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:104:58: style: The scope of the variable 'tol1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:104:63: style: The scope of the variable 'xm' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:182:10: style: The scope of the variable 'ulim' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:182:15: style: The scope of the variable 'u' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:182:17: style: The scope of the variable 'r' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:182:19: style: The scope of the variable 'q' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:246:26: style: The scope of the variable 'fu' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:247:16: style: The scope of the variable 'tol1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:247:21: style: The scope of the variable 'tol2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:247:34: style: The scope of the variable 'xm' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:363:10: style: The scope of the variable 'ulim' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:363:15: style: The scope of the variable 'u' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:363:17: style: The scope of the variable 'r' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:363:19: style: The scope of the variable 'q' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:440:26: style: The scope of the variable 'fu' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:441:16: style: The scope of the variable 'tol1' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:441:21: style: The scope of the variable 'tol2' can be reduced. [variableScope]
ClonalFrameML-1.12/src/brent.h:441:34: style: The scope of the variable 'xm' can be reduced. [variableScope]
ClonalFrameML-1.12/src/powell.h:96:11: style: The scope of the variable 'ibig' can be reduced. [variableScope]
ClonalFrameML-1.12/src/powell.h:97:10: style: The scope of the variable 'del' can be reduced. [variableScope]
ClonalFrameML-1.12/src/powell.h:97:14: style: The scope of the variable 'fp' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:185:15: style: The scope of the variable 'word' can be reduced. [variableScope]
ClonalFrameML-1.12/src/main.cpp:259:7: style: The scope of the variable 'debug_last_elem' can be reduced. [variableScope]
ClonalFrameML-1.12/src/main.cpp:1783:10: style: The scope of the variable 'pat' can be reduced. [variableScope]
ClonalFrameML-1.12/src/main.cpp:2184:9: style: The scope of the variable 'new_ML' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/matrix.h:236:10: style: The scope of the variable 'big' can be reduced. [variableScope]
ClonalFrameML-1.12/src/myutils/matrix.h:236:18: style: The scope of the variable 'pivinv' can be reduced. [variableScope]
ClonalFrameML-1.12/src/main.cpp:979:59: style:inconclusive: Function 'compute_compatibility' argument 2 names different: declaration 'tree' definition 'ctree'. [funcArgNamesDifferent]
ClonalFrameML-1.12/src/main.h:54:59: note: Function 'compute_compatibility' argument 2 names different: declaration 'tree' definition 'ctree'.
ClonalFrameML-1.12/src/main.cpp:979:59: note: Function 'compute_compatibility' argument 2 names different: declaration 'tree' definition 'ctree'.
ClonalFrameML-1.12/src/main.cpp:1335:68: style:inconclusive: Function 'compute_HKY85_ptrans' argument 2 names different: declaration 'k' definition 'kappa'. [funcArgNamesDifferent]
ClonalFrameML-1.12/src/main.h:59:68: note: Function 'compute_HKY85_ptrans' argument 2 names different: declaration 'k' definition 'kappa'.
ClonalFrameML-1.12/src/main.cpp:1335:68: note: Function 'compute_HKY85_ptrans' argument 2 names different: declaration 'k' definition 'kappa'.
ClonalFrameML-1.12/src/main.cpp:1880:226: style:inconclusive: Function 'maximum_likelihood_ClonalFrame_branch_allsites' argument 7 names different: declaration 'pi' definition 'pinuc'. [funcArgNamesDifferent]
ClonalFrameML-1.12/src/main.h:78:226: note: Function 'maximum_likelihood_ClonalFrame_branch_allsites' argument 7 names different: declaration 'pi' definition 'pinuc'.
ClonalFrameML-1.12/src/main.cpp:1880:226: note: Function 'maximum_likelihood_ClonalFrame_branch_allsites' argument 7 names different: declaration 'pi' definition 'pinuc'.
ClonalFrameML-1.12/src/myutils/random.h:118:10: style: Local variable 'U' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/random.h:818:16: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/random.h:118:10: note: Shadow variable
ClonalFrameML-1.12/src/myutils/random.h:139:10: style: Local variable 'U' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/random.h:818:16: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/random.h:139:10: note: Shadow variable
ClonalFrameML-1.12/src/myutils/random.h:139:20: style: Local variable 'Z' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/random.h:826:9: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/random.h:139:20: note: Shadow variable
ClonalFrameML-1.12/src/myutils/random.h:381:16: style: Local variable 'g' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/myutils/random.h:52:17: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/random.h:381:16: note: Shadow variable
ClonalFrameML-1.12/src/myutils/random.h:381:30: style: Local variable 'sq' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/myutils/random.h:52:9: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/random.h:381:30: note: Shadow variable
ClonalFrameML-1.12/src/myutils/DNA.h:390:15: style: Local variable 'pi' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/DNA.h:375:9: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/DNA.h:390:15: note: Shadow variable
ClonalFrameML-1.12/src/myutils/DNA.h:414:39: style: Local variable 'S' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/DNA.h:331:9: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/DNA.h:414:39: note: Shadow variable
ClonalFrameML-1.12/src/myutils/DNA.h:466:7: style: Local variable 'S' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/DNA.h:331:9: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/DNA.h:466:7: note: Shadow variable
ClonalFrameML-1.12/src/myutils/DNA.h:537:7: style: Local variable 'S' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/DNA.h:331:9: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/DNA.h:537:7: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:256:11: style: Local variable 'i' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:159:6: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:256:11: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:344:18: style: Local variable 'empirical_nucleotide_frequencies' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:306:17: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:344:18: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:345:22: style: Local variable 'nuc' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:307:21: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:345:22: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:347:18: style: Local variable 'pat' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:309:17: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:347:18: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:348:15: style: Local variable 'pat1' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:310:14: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:348:15: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:348:21: style: Local variable 'cpat' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:310:20: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:348:21: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:348:27: style: Local variable 'ipat' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:310:26: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:348:27: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:349:16: style: Local variable 'nuc_ispoly' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:311:15: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:349:16: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:352:22: style: Local variable 'node_nuc' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:314:21: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:352:22: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:354:12: style: Local variable 'ML' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:324:11: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:354:12: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:368:11: style: Local variable 'ML' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:354:12: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:368:11: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:415:11: style: Local variable 'ML' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:354:12: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:415:11: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:499:11: style: Local variable 'ML' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:354:12: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:499:11: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:2618:11: style: Local variable 'j' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:2550:6: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:2618:11: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:2656:7: style: Local variable 'j' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:2550:6: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:2656:7: note: Shadow variable
ClonalFrameML-1.12/src/main.cpp:2723:12: style: Local variable 'j' shadows outer variable [shadowVariable]
ClonalFrameML-1.12/src/main.cpp:2656:7: note: Shadowed declaration
ClonalFrameML-1.12/src/main.cpp:2723:12: note: Shadow variable
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:89:7: style: Local variable 'size' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:125:6: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:89:7: note: Shadow variable
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:106:7: style: Local variable 'size' shadows outer function [shadowFunction]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:125:6: note: Shadowed declaration
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:106:7: note: Shadow variable
ClonalFrameML-1.12/src/myutils/newick.h:40:20: performance: Function parameter 'token' should be passed by const reference. [passedByValue]
ClonalFrameML-1.12/src/myutils/newick.h:211:20: performance: Function parameter 'token' should be passed by const reference. [passedByValue]
ClonalFrameML-1.12/src/main.cpp:1818:34: performance: Function parameter 's' should be passed by const reference. [passedByValue]
ClonalFrameML-1.12/src/main.cpp:1818:50: performance: Function parameter 'label' should be passed by const reference. [passedByValue]
ClonalFrameML-1.12/src/myutils/lotri_matrix.h:73:51: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:34: style: Parameter 'time' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:45: style: Parameter 'id1' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:55: style: Parameter 'id2' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:42: style: Parameter 'time' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:53: style: Parameter 'id1' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:63: style: Parameter 'id2' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:173:53: style: Parameter 'id' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/myutils/DNA.h:260:32: style: Parameter 'code' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/myutils/DNA.h:273:34: style: Parameter 'code' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/myutils/DNA.h:734:29: style: Parameter 'tri' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/myutils/DNA.h:750:31: style: Parameter 'tri' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/myutils/DNA.h:772:39: style: Parameter 'tri' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:152:32: style: Parameter 'label' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:979:40: style: Parameter 'fa' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:979:59: style: Parameter 'ctree' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:1127:45: style: Parameter 'fa' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:1205:69: style: Parameter 'iscompat' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:1729:69: style: Parameter 'all_node_names' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:1753:63: style: Parameter 'imported' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:1753:96: style: Parameter 'ignore_site' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:1776:51: style: Parameter 'iscompat' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:1776:74: style: Parameter 'ipat' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:1830:103: style: Parameter 'all_node_names' can be declared as reference to const [constParameter]
ClonalFrameML-1.12/src/coalesce/coalescent_record.h:173:39: style: Parameter 'time_in' can be declared as pointer to const [constParameter]
ClonalFrameML-1.12/src/main.cpp:543:11: style: Variable 'pname' can be declared as const array [constVariable]
ClonalFrameML-1.12/src/main.cpp:209:9: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:223:6: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:259:23: style: Variable 'debug_last_elem' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:270:20: style: Variable 'debug_last_elem' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:354:15: style: Variable 'ML' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2042:7: style: Variable 'pI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2079:7: style: Variable 'pI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2268:13: style: Variable 'mutI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2269:13: style: Variable 'numU' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2269:23: style: Variable 'numI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2270:13: style: Variable 'nsiI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2271:13: style: Variable 'lenU' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2271:23: style: Variable 'lenI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2286:9: style: Variable 'mutI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2287:9: style: Variable 'nsiI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2290:9: style: Variable 'numI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2291:9: style: Variable 'lenU' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2292:9: style: Variable 'numU' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/main.cpp:2293:9: style: Variable 'lenI' is assigned a value that is never used. [unreadVariable]
ClonalFrameML-1.12/src/myutils/argumentwizard.h:112:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
diff:
head ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:34: style: Parameter 'time' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:34: style: Parameter 'time' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:45: style: Parameter 'id1' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:45: style: Parameter 'id1' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:55: style: Parameter 'id2' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/coalesce/coalescent_record.h:115:55: style: Parameter 'id2' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:42: style: Parameter 'time' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:42: style: Parameter 'time' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:53: style: Parameter 'id1' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:53: style: Parameter 'id1' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:63: style: Parameter 'id2' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/coalesce/coalescent_record.h:144:63: style: Parameter 'id2' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/coalesce/coalescent_record.h:173:39: style: Parameter 'time_in' can be declared as pointer to const [constParameter]
2.8 ClonalFrameML-1.12/src/coalesce/coalescent_record.h:173:39: style: Parameter 'time_in' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/coalesce/coalescent_record.h:173:53: style: Parameter 'id' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/coalesce/coalescent_record.h:173:53: style: Parameter 'id' can be declared with const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1073:26: style: The scope of the variable 'hap' can be reduced. [variableScope]
head ClonalFrameML-1.12/src/main.cpp:1127:45: style: Parameter 'fa' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1127:45: style: Parameter 'fa' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:1205:69: style: Parameter 'iscompat' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1205:69: style: Parameter 'iscompat' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:1729:69: style: Parameter 'all_node_names' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1729:69: style: Parameter 'all_node_names' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:1753:63: style: Parameter 'imported' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1753:63: style: Parameter 'imported' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:1753:96: style: Parameter 'ignore_site' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1753:96: style: Parameter 'ignore_site' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:1776:51: style: Parameter 'iscompat' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1776:51: style: Parameter 'iscompat' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:1776:74: style: Parameter 'ipat' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1776:74: style: Parameter 'ipat' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:1830:103: style: Parameter 'all_node_names' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:1830:103: style: Parameter 'all_node_names' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:543:11: style: Variable 'pname' can be declared as const array [constVariable]
2.8 ClonalFrameML-1.12/src/main.cpp:543:11: style: Variable 'pname' can be declared with const [constVariable]
head ClonalFrameML-1.12/src/main.cpp:979:40: style: Parameter 'fa' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:979:40: style: Parameter 'fa' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/main.cpp:979:59: style: Parameter 'ctree' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/main.cpp:979:59: style: Parameter 'ctree' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/myutils/DNA.h:260:32: style: Parameter 'code' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/myutils/DNA.h:260:32: style: Parameter 'code' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/myutils/DNA.h:273:34: style: Parameter 'code' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/myutils/DNA.h:273:34: style: Parameter 'code' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/myutils/DNA.h:734:29: style: Parameter 'tri' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/myutils/DNA.h:734:29: style: Parameter 'tri' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/myutils/DNA.h:750:31: style: Parameter 'tri' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/myutils/DNA.h:750:31: style: Parameter 'tri' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/myutils/DNA.h:772:39: style: Parameter 'tri' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/myutils/DNA.h:772:39: style: Parameter 'tri' can be declared with const [constParameter]
head ClonalFrameML-1.12/src/myutils/argumentwizard.h:152:32: style: Parameter 'label' can be declared as reference to const [constParameter]
2.8 ClonalFrameML-1.12/src/myutils/argumentwizard.h:152:32: style: Parameter 'label' can be declared with const [constParameter]


DONE