Package: src:pizzly Version: 0.37.3+ds-11 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202601/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:pizzly, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_clean rm -f debian/pizzly.1 make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/pizzly.substvars debian/files rm -fr -- debian/pizzly/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ [... snipped ...] | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:338:20: error: âseqanâ has not been declared 338 | int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector()); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:338:54: error: ârefâ was not declared in this scope; did you mean âstd::refâ? 338 | int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector()); | ^~~ | std::ref In file included from /usr/include/c++/15/string:54, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /<<PKGBUILDDIR>>/main.cpp:1: /usr/include/c++/15/bits/refwrap.h:448:5: note: âstd::refâ declared here 448 | ref(reference_wrapper<_Tp> __t) noexcept | ^~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:338:59: error: âseqanâ has not been declared 338 | int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector()); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:332:13: warning: unused variable âtseqâ [-Wunused-variable] 332 | auto& tseq = it.first; | ^~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function: /<<PKGBUILDDIR>>/FilterFusions.hpp:403:9: error: âseqanâ has not been declared 403 | seqan::CharString read(seq.c_str()); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:404:9: error: âseqanâ has not been declared 404 | seqan::CharString splitref(tsplit.first.c_str()); // inefficient, refactor at some point | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:405:9: error: âseqanâ has not been declared 405 | seqan::CharString saferef(tsafe.first.c_str()); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:407:9: error: âseqanâ has not been declared 407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight; | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:407:21: error: âseqanâ has not been declared 407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight; | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:407:40: error: âreadRowLeftâ was not declared in this scope 407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight; | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:407:53: error: âreadRowRightâ was not declared in this scope 407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight; | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:407:67: error: âsplitRowLeftâ was not declared in this scope 407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight; | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:407:81: error: âsafeRowRightâ was not declared in this scope 407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight; | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:408:9: error: âseqanâ has not been declared 408 | seqan::setSource(readRowLeft, read); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:409:9: error: âseqanâ has not been declared 409 | seqan::setSource(readRowRight, read); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:410:9: error: âseqanâ has not been declared 410 | seqan::setSource(splitRowLeft, splitref); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:410:40: error: âsplitrefâ was not declared in this scope; did you mean âsplitrecâ? 410 | seqan::setSource(splitRowLeft, splitref); | ^~~~~~~~ | splitrec /<<PKGBUILDDIR>>/FilterFusions.hpp:411:9: error: âseqanâ has not been declared 411 | seqan::setSource(safeRowRight, saferef); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:411:40: error: âsaferefâ was not declared in this scope 411 | seqan::setSource(safeRowRight, saferef); | ^~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:413:9: error: âseqanâ has not been declared 413 | seqan::Score<int, seqan::Simple> scoringScheme(0,-1,-1); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:413:22: error: expected primary-expression before âintâ 413 | seqan::Score<int, seqan::Simple> scoringScheme(0,-1,-1); | ^~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:414:9: error: âseqanâ has not been declared 414 | seqan::AlignConfig<false, true, true, false> config; | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:414:54: error: âconfigâ was not declared in this scope 414 | seqan::AlignConfig<false, true, true, false> config; | ^~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:415:26: error: âseqanâ has not been declared 415 | int splitScore = seqan::splitAlignment(readRowLeft, splitRowLeft, readRowRight, safeRowRight, scoringScheme, config); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:415:103: error: âscoringSchemeâ was not declared in this scope; did you mean âseqan2::scoringSchemeâ? 415 | int splitScore = seqan::splitAlignment(readRowLeft, splitRowLeft, readRowRight, safeRowRight, scoringScheme, config); | ^~~~~~~~~~~~~ | seqan2::scoringScheme In file included from /usr/include/seqan/find.h:93, from /usr/include/seqan/index.h:46: /usr/include/seqan/find/find_score.h:180:1: note: âseqan2::scoringSchemeâ declared here 180 | scoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me) | ^~~~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:426:24: error: âseqanâ has not been declared 426 | splitPos = seqan::toSourcePosition(readRowLeft, seqan::clippedEndPosition(readRowLeft)); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:426:61: error: âseqanâ has not been declared 426 | splitPos = seqan::toSourcePosition(readRowLeft, seqan::clippedEndPosition(readRowLeft)); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:433:27: error: âseqanâ has not been declared 433 | int t2pos = seqan::toSourcePosition(safeRowRight, 0); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:434:27: error: âseqanâ has not been declared 434 | int t2clip= seqan::toSourcePosition(readRowRight, 0); //seqan::clippedBeginPosition(readRowRight)); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:436:39: error: âseqanâ has not been declared 436 | t2copy.pos = t2.pos - seqan::length(saferef) + t2pos + (seqan::length(splitref) - t2clip); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:436:73: error: âseqanâ has not been declared 436 | t2copy.pos = t2.pos - seqan::length(saferef) + t2pos + (seqan::length(splitref) - t2clip); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:438:39: error: âseqanâ has not been declared 438 | t2copy.pos = t2.pos + seqan::length(saferef) - t2pos -1; | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function: /<<PKGBUILDDIR>>/FilterFusions.hpp:709:25: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ExonModel>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 709 | for (int i = 0; i < trm.exons.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function: /<<PKGBUILDDIR>>/FilterFusions.hpp:738:25: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<ExonModel>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 738 | for (int i = 0; i < trm.exons.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function: /<<PKGBUILDDIR>>/FilterFusions.hpp:765:11: warning: unused variable âgapâ [-Wunused-variable] 765 | int gap = d2 - d1; | ^~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:781:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 781 | return std::move(ret); | ~~~~~~~~~^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:781:21: note: remove âstd::moveâ call /<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function: /<<PKGBUILDDIR>>/FilterFusions.hpp:872:42: error: request for member âfindâ in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ 872 | const auto & seq1 = trx.seqs.find(sp.tr1)->second; | ^~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:873:42: error: request for member âfindâ in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ 873 | const auto & seq2 = trx.seqs.find(sp.tr2)->second; | ^~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:883:33: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<int>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 883 | for (int i = 0; i < v.size(); i++) { | ~~^~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:907:145: error: âseqanâ has not been declared 907 | std::string fasta_name = sp.tr1 + "_0:" + std::to_string(tp1) + "_" + sp.tr2 + "_" + std::to_string(tp2) + ":" + std::to_string(seqan::length(seq2)); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:920:82: error: âseqanâ has not been declared 920 | << ", \"endPos\" : " << std::to_string((sp.dir1) ? tp1 : seqan::length(seq1)) << ", \"edit\" : " << std::to_string(ed1) | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:924:82: error: âseqanâ has not been declared 924 | << ", \"endPos\" : " << std::to_string((sp.dir2) ? tp2 : seqan::length(seq2)) << ", \"edit\" : " << std::to_string(ed2) | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:929:35: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<int>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 929 | for (int i = 0; i < readsInTr.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:940:29: error: âseqanâ has not been declared 940 | << seqan::prefix(seq1, tp1) | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:941:29: error: âseqanâ has not been declared 941 | << seqan::suffix(seq2, tp2) | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:867:17: warning: unused variable âsplit_readsâ [-Wunused-variable] 867 | int split_reads = spp.second; | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:961:33: error: âseqanâ has not been declared 961 | int rlen1 = seqan::length(fr.seq1); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:962:33: error: âseqanâ has not been declared 962 | int rlen2 = seqan::length(fr.seq2); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:964:50: error: request for member âfindâ in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ 964 | const auto & seq1 = trx.seqs.find(t1.tr)->second; | ^~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:965:50: error: request for member âfindâ in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ 965 | const auto & seq2 = trx.seqs.find(t2.tr)->second; | ^~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:971:72: error: âseqanâ has not been declared 971 | int tp1 = (t1strand) ? std::min(t1.pos+rlen1, (int)seqan::length(seq1)-1) : std::max(t1.pos-rlen1,0); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:972:72: error: âseqanâ has not been declared 972 | int tp2 = (t2strand) ? std::min(t2.pos+rlen2, (int)seqan::length(seq2)-1) : std::max(t2.pos-rlen2,0); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1033:29: warning: loop variable âpâ creates a copy from type âconst std::pair<const SplitInfo, std::vector<std::pair<int, int> > >â [-Wrange-loop-construct] 1033 | for (const auto p : trfmap) { | ^ /<<PKGBUILDDIR>>/FilterFusions.hpp:1033:29: note: use reference type to prevent copying 1033 | for (const auto p : trfmap) { | ^ | & /<<PKGBUILDDIR>>/FilterFusions.hpp:1037:44: error: request for member âfindâ in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ 1037 | const auto & seq1 = trx.seqs.find(spi.tr1)->second; | ^~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1038:44: error: request for member âfindâ in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ 1038 | const auto & seq2 = trx.seqs.find(spi.tr2)->second; | ^~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1080:145: error: âseqanâ has not been declared 1080 | fasta_name = spi.tr1 + "_0:" + std::to_string(spi.pos1) + "_" + spi.tr2 + "_" + std::to_string(spi.pos2) + ":" + std::to_string(seqan::length(seq2)); | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1083:88: error: âseqanâ has not been declared 1083 | << ", \"endPos\" : " << std::to_string((spi.dir1) ? spi.pos1 : seqan::length(seq1)) | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1086:88: error: âseqanâ has not been declared 1086 | << ", \"endPos\" : " << std::to_string((spi.dir2) ? spi.pos2 : seqan::length(seq2)) | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1091:35: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<int>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 1091 | for (int i = 0; i < readsInTr.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1102:28: error: âseqanâ has not been declared 1102 | << seqan::prefix(seq1, spi.pos1) | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1103:28: error: âseqanâ has not been declared 1103 | << seqan::suffix(seq2, spi.pos2) | ^~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1115:31: warning: comparison of integer expressions of different signedness: âintâ and âstd::vector<int>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare] 1115 | for (int i = 0; i < v.size(); i++) { | ~~^~~~~~~~~~ /<<PKGBUILDDIR>>/FilterFusions.hpp:1112:18: warning: unused variable âfirstJsonReadâ [-Wunused-variable] 1112 | bool firstJsonRead = true; | ^~~~~~~~~~~~~ /<<PKGBUILDDIR>>/main.cpp: At global scope: /<<PKGBUILDDIR>>/main.cpp:11:1: error: âseqanâ does not name a type 11 | seqan::ArgumentParser::ParseResult | ^~~~~ /<<PKGBUILDDIR>>/main.cpp: In function âint main(int, const char**)â: /<<PKGBUILDDIR>>/main.cpp:79:5: error: âseqanâ has not been declared 79 | seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv); | ^~~~~ /<<PKGBUILDDIR>>/main.cpp:83:9: error: âresâ was not declared in this scope 83 | if (res != seqan::ArgumentParser::PARSE_OK) | ^~~ /<<PKGBUILDDIR>>/main.cpp:83:16: error: âseqanâ has not been declared 83 | if (res != seqan::ArgumentParser::PARSE_OK) | ^~~~~ /<<PKGBUILDDIR>>/main.cpp:84:23: error: âseqanâ has not been declared 84 | return res == seqan::ArgumentParser::PARSE_ERROR; | ^~~~~ /<<PKGBUILDDIR>>/main.cpp:111:31: error: âbeginâ was not declared in this scope 111 | for (const auto &it : trx.seqs) { | ^~~~ /<<PKGBUILDDIR>>/main.cpp:111:31: note: suggested alternatives: In file included from /usr/include/c++/15/string:55: /usr/include/c++/15/bits/range_access.h:120:37: note: âstd::beginâ 120 | template<typename _Tp> const _Tp* begin(const valarray<_Tp>&) noexcept; | ^~~~~ In file included from /usr/include/seqan/index/index_pizzachili.h:39, from /usr/include/seqan/index.h:194: /usr/include/seqan/index/index_pizzachili_string.h:460:1: note: âseqan2::beginâ 460 | begin( | ^~~~~ /<<PKGBUILDDIR>>/main.cpp:111:31: error: âendâ was not declared in this scope 111 | for (const auto &it : trx.seqs) { | ^~~~ /<<PKGBUILDDIR>>/main.cpp:111:31: note: suggested alternatives: /usr/include/c++/15/bits/range_access.h:122:37: note: âstd::endâ 122 | template<typename _Tp> const _Tp* end(const valarray<_Tp>&) noexcept; | ^~~ /usr/include/seqan/index/index_pizzachili_string.h:480:1: note: âseqan2::endâ 480 | end( | ^~~ /<<PKGBUILDDIR>>/main.cpp:126:43: error: request for member âsizeâ in âtrx.Transcriptome::seqsâ, which is of non-class type âintâ 126 | } else if (numTxpSeqFound != trx.seqs.size()) { | ^~~~ /<<PKGBUILDDIR>>/main.cpp:127:78: error: request for member âsizeâ in âtrx.Transcriptome::seqsâ, which is of non-class type âintâ 127 | std::cerr << "Warning: could not find annotations for " << (trx.seqs.size() - numTxpSeqFound) << " transcripts\n" << std::endl; | ^~~~ /<<PKGBUILDDIR>>/GeneModel.hpp: In function âStrandedness operator~(const Strandedness&)â: /<<PKGBUILDDIR>>/GeneModel.hpp:18:1: warning: control reaches end of non-void function [-Wreturn-type] 18 | } | ^ make[3]: *** [CMakeFiles/pizzly.dir/build.make:82: CMakeFiles/pizzly.dir/main.cpp.o] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/pizzly.dir/all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[1]: *** [Makefile:94: all] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2 make: *** [debian/rules:7: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
