Hi, I need to admit that the package does not even build for me. I had to add a patch to fix the includes and my attempt to rebuild the package ends in:
... /usr/bin/ld: ./source/svm/svm.cpp:794: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:849: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:849: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:904: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:904: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:916: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:916: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: source/svm/svm.o: in function `SvmRfe::getOrderedFeatureList[abi:cxx11](SvmDataset&, OneVsOneMultiClassSvmTrainer&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&)': ./source/svm/svm.cpp:1028: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:1028: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:1034: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:1034: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:1037: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:1037: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:1039: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:1039: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:1041: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:1044: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:1049: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:1080: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:1081: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: source/svm/svm.o: in function `OneVsOneMultiClassSvmTrainer::trainOnKFolds(SmoTrainer&, KernelFunctionCache&, KFoldLabeledObservationsDivider&)': ./source/svm/svm.cpp:965: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:965: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.cpp:966: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:966: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: source/svm/svm.o: in function `MultiClassSVM::score(std::vector<LabeledObservation, std::allocator<LabeledObservation> > const&)': ./source/svm/svm.cpp:439: undefined reference to `MothurOut::mothurOut(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' /usr/bin/ld: ./source/svm/svm.cpp:439: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: source/svm/svm.o: in function `ParameterSetBuilder::ParameterSetBuilder(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<double, std::allocator<double> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::vector<double, std::allocator<double> > > > > const&)': ./source/svm/svm.hpp:278: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.hpp:283: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.hpp:299: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: ./source/svm/svm.hpp:303: undefined reference to `MothurOut::mothurOutEndLine()' /usr/bin/ld: source/svm/svm.o: in function `_GLOBAL__sub_I__ZN12OutputFilter5QUIETE': ./source/svm/svm.cpp:65: undefined reference to `MothurOut::getInstance()' collect2: error: ld returned 1 exit status Any idea what might be wrong here? Kind regards Andreas. On Sun, May 17, 2020 at 08:51:42PM +0200, Paul Gevers wrote: > Source: mothur > Version: 1.44.0-1 > X-Debbugs-CC: debian...@lists.debian.org > Severity: serious > User: debian...@lists.debian.org > Usertags: regression > > Dear maintainer(s), > > With a recent upload of mothur the autopkgtest of mothur fails in > testing when that autopkgtest is run with the binary packages of mothur > from unstable. It passes when run with only packages from testing. In > tabular form: > > pass fail > mothur from testing 1.44.0-1 > all others from testing from testing > > I copied some of the output at the bottom of this report. > > Currently this regression is blocking the migration to testing [1]. Can > you please investigate the situation and fix it? > > More information about this bug and the reason for filing it can be found on > https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation > > Paul > > [1] https://qa.debian.org/excuses.php?package=mothur > > https://ci.debian.net/data/autopkgtest/testing/amd64/m/mothur/5517339/log.gz > > autopkgtest [19:10:00]: test run-unit-test: [----------------------- > TERM environment variable not set. > unique.seqs(fasta=HA.fasta) > command > Linux version > > Using ReadLine > mothur v.1.44.0 > Last updated: 05/16/2020 > by > Patrick D. Schloss > > Department of Microbiology & Immunology > > University of Michigan > http://www.mothur.org > > When using, please cite: > Schloss, P.D., et al., Introducing mothur: Open-source, > platform-independent, community-supported software for describing and > comparing microbial communities. Appl Environ Microbiol, 2009. > 75(23):7537-41. > > Distributed under the GNU General Public License > > Type 'help()' for information on the commands that are available > > For questions and analysis support, please visit our forum at > https://forum.mothur.org > > Type 'quit()' to exit program > > [NOTE]: Setting random seed to 19760620. > > Batch Mode > > > mothur > unique.seqs(fasta=HA.fasta) > 599 259 > > Output File Names: > HA.names > HA.unique.fasta > > dist.seqs(fasta=HA.unique.fasta, countends=F, cutoff=0.01) > command > > mothur > dist.seqs(fasta=HA.unique.fasta, countends=F, cutoff=0.01) > > Using 2 processors. > > Sequence Time Num_Dists_Below_Cutoff > 0 0 0 > 200 0 3443 > 100 0 5025 > 258 0 15965 > 182 0 16617 > > It took 0 secs to find distances for 259 sequences. 32582 distances > below cutoff 0.01. > > > Output File Names: > HA.unique.dist > > cluster(method=furthest, column=HA.unique.dist, name=HA.names, > cutoff=0.01, precision=1000) > command > > mothur > cluster(method=furthest, column=HA.unique.dist, name=HA.names, > cutoff=0.01, precision=1000) > > Using 2 processors. > unique 154 211 18 2 6 0 4 2 > 0 2 0 0 0 1 0 0 0 0 > 2 0 1 0 0 0 0 0 0 0 > 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 1 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 1 > 0.001 155 161 28 5 3 4 2 4 0 > 0 1 0 1 0 1 0 0 0 0 > 2 0 0 1 0 0 0 0 0 0 > 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 1 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 1 > 0.002 206 56 9 8 2 0 4 2 2 > 0 0 0 0 0 2 0 0 0 0 > 1 1 0 0 0 0 0 1 0 0 > 0 1 0 > 0 0 0 0 0 0 0 1 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 1 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 1 > 0.003 236 26 4 2 1 1 0 2 2 > 1 0 0 0 0 1 1 0 0 0 > 0 0 0 1 1 0 0 0 0 0 > 0 1 0 > 0 0 0 0 0 1 0 0 0 0 > 0 0 0 1 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 1 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 1 > 0.004 270 15 3 0 1 0 0 1 1 > 0 0 0 0 0 1 0 0 0 0 > 0 0 0 1 1 0 0 0 0 0 > 0 0 0 > 0 0 0 0 0 1 1 0 0 0 > 0 0 0 0 0 0 0 0 1 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 1 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 1 > 0.005 272 7 2 0 0 0 0 1 1 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 1 0 0 0 0 0 > 0 0 0 > 0 0 0 0 0 0 0 2 0 0 > 0 0 0 0 0 0 0 0 0 1 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 1 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 1 > 0.006 274 5 1 0 0 0 0 0 1 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 > 0 0 0 0 0 0 0 0 1 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 1 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 1 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 1 > 0.007 274 5 1 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 > 0 0 0 0 0 0 0 0 1 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 1 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 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0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 1 > 0.009 592 3 2 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 1 > It took 0 seconds to cluster > > Output File Names: > HA.unique.fn.sabund > HA.unique.fn.rabund > HA.unique.fn.list > > summary.single(list=HA.unique.fn.list, calc=nseqs-sobs-chao, > label=unique-0.001-0.003-0.005-0.008) > command > > mothur > summary.single(list=HA.unique.fn.list, calc=nseqs-sobs-chao, > label=unique-0.001-0.003-0.005-0.008) > unique > 0.001 > 0.003 > 0.005 > 0.008 > > Output File Names: > HA.unique.fn.summary > > heatmap.bin(scale=linear, label=unique-0.001-0.003) > command > > mothur > heatmap.bin(scale=linear, label=unique-0.001-0.003) > Using HA.unique.fn.list as input file for the list parameter. > Segmentation fault > autopkgtest [19:10:00]: test run-unit-test: -----------------------] > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de