Package: src:unicycler Version: 0.5.1+dfsg-3 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:unicycler, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' find . -name __pycache__ -type d | xargs rm -rf make distclean make[2]: Entering directory '/<<PKGBUILDDIR>>' Platform: Linux Compiler: g++ 15.2.0 rm -f unicycler/src/minimap/index.o unicycler/src/minimap/kthread.o unicycler/src/minimap/bseq.o unicycler/src/minimap/sdust.o unicycler/src/minimap/map.o unicycler/src/minimap/misc.o unicycler/src/minimap/sketch.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/paf.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/semi_global_align.o unicycler/src/string_functions.o unicycler/src/kmers.o unicycler/src/random_alignments.o unicycler/src/overlap_align.o unicycler/src/consensus_align.o unicycler/src/ref_seqs.o unicycler/src/start_end_align.o unicycler/src/scoredalignment.o unicycler/src/miniasm_assembly.o unicycler/src/path_align.o unicycler/src/global_align.o unicycler/src/minimap_align.o rm -f unicycler/cpp_functions.so make[2]: Leaving directory '/<<PKGBUILDDIR>>' make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:384: python3.14 setup.py config running config I: pybuild base:384: python3.13 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<<PKGBUILDDIR>>' make make[2]: Entering directory '/<<PKGBUILDDIR>>' Platform: Linux Compiler: g++ 15.2.0 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/index.o unicycler/src/minimap/index.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/kthread.o unicycler/src/minimap/kthread.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/bseq.o unicycler/src/minimap/bseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/sdust.o unicycler/src/minimap/sdust.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/map.o unicycler/src/minimap/map.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/misc.o unicycler/src/minimap/misc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/minimap/sketch.o unicycler/src/minimap/sketch.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/dotter.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/hit.o unicycler/src/miniasm/hit.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sys.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asg.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sdict.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/miniasm/paf.o unicycler/src/miniasm/paf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/semi_global_align_exhaustive.o unicycler/src/semi_global_align_exhaustive.cpp In file included from unicycler/include/semi_global_align_exhaustive.h:17, from unicycler/src/semi_global_align_exhaustive.cpp:12: unicycler/include/scoredalignment.h:20:17: error: âseqanâ is not a namespace-name 20 | using namespace seqan; | ^~~~~ unicycler/include/scoredalignment.h:27:26: error: expected â)â before â<â token 27 | ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment, | ~ ^ | ) unicycler/include/scoredalignment.h:56:51: error: âScoreâ has not been declared 56 | int getCigarScore(CigarType type, int length, Score<int, Simple> & scoringScheme, | ^~~~~ unicycler/include/scoredalignment.h:56:56: error: expected â,â or â...â before â<â token 56 | int getCigarScore(CigarType type, int length, Score<int, Simple> & scoringScheme, | ^ unicycler/include/semi_global_align_exhaustive.h:20:17: error: âseqanâ is not a namespace-name 20 | using namespace seqan; | ^~~~~ In file included from unicycler/include/semi_global_align.h:24, from unicycler/src/semi_global_align_exhaustive.cpp:15: unicycler/include/random_alignments.h:21:17: error: âseqanâ is not a namespace-name 21 | using namespace seqan; | ^~~~~ unicycler/include/semi_global_align.h:29:17: error: âseqanâ is not a namespace-name 29 | using namespace seqan; | ^~~~~ unicycler/include/semi_global_align.h:34:9: error: âSeedâ does not name a type 34 | typedef Seed<Simple> TSeed; | ^~~~ unicycler/include/semi_global_align.h:35:9: error: âSeedSetâ does not name a type 35 | typedef SeedSet<TSeed> TSeedSet; | ^~~~~~~ unicycler/include/semi_global_align.h:140:29: error: âStringâ has not been declared 140 | String<TSeed> & seedChain, std::string & output, int maxLineNum, | ^~~~~~ unicycler/include/semi_global_align.h:140:35: error: expected â,â or â...â before â<â token 140 | String<TSeed> & seedChain, std::string & output, int maxLineNum, | ^ unicycler/include/semi_global_align.h:164:34: error: âStringâ was not declared in this scope; did you mean âseqan2::Stringâ? 164 | long long getMaxSeedChainGapArea(String<TSeed> & seedChain, int readLen, int trimmedRefLen); | ^~~~~~ | seqan2::String In file included from /usr/include/seqan/sequence.h:105, from unicycler/include/semi_global_align_exhaustive.h:16: /usr/include/seqan/sequence/string_base.h:290:7: note: âseqan2::Stringâ declared here 290 | class String; | ^~~~~~ unicycler/include/semi_global_align.h:164:41: error: âTSeedâ was not declared in this scope 164 | long long getMaxSeedChainGapArea(String<TSeed> & seedChain, int readLen, int trimmedRefLen); | ^~~~~ unicycler/include/semi_global_align.h:164:50: error: âseedChainâ was not declared in this scope 164 | long long getMaxSeedChainGapArea(String<TSeed> & seedChain, int readLen, int trimmedRefLen); | ^~~~~~~~~ unicycler/include/semi_global_align.h:164:61: error: expected primary-expression before âintâ 164 | long long getMaxSeedChainGapArea(String<TSeed> & seedChain, int readLen, int trimmedRefLen); | ^~~ unicycler/include/semi_global_align.h:164:74: error: expected primary-expression before âintâ 164 | long long getMaxSeedChainGapArea(String<TSeed> & seedChain, int readLen, int trimmedRefLen); | ^~~ unicycler/include/semi_global_align.h:164:91: error: expression list treated as compound expression in initializer [-fpermissive] 164 | long long getMaxSeedChainGapArea(String<TSeed> & seedChain, int readLen, int trimmedRefLen); | ^ unicycler/src/semi_global_align_exhaustive.cpp: In function âScoredAlignment* semiGlobalAlignmentExhaustive(std::string, std::string, int, int, int, int)â: unicycler/src/semi_global_align_exhaustive.cpp:45:5: error: âDna5Stringâ was not declared in this scope; did you mean âseqan2::Dna5Stringâ? 45 | Dna5String sequenceH(s1); | ^~~~~~~~~~ | seqan2::Dna5String In file included from /usr/include/seqan/sequence.h:112: /usr/include/seqan/sequence/sequence_shortcuts.h:119:36: note: âseqan2::Dna5Stringâ declared here 119 | typedef String<Dna5, Alloc<void> > Dna5String; | ^~~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:46:15: error: expected â;â before âsequenceVâ 46 | Dna5String sequenceV(s2); | ^~~~~~~~~~ | ; unicycler/src/semi_global_align_exhaustive.cpp:48:5: error: âAlignâ was not declared in this scope; did you mean âseqan2::Alignâ? 48 | Align<Dna5String, ArrayGaps> alignment; | ^~~~~ | seqan2::Align In file included from /usr/include/seqan/file.h:65, from /usr/include/seqan/stream.h:62, from /usr/include/seqan/score.h:43, from /usr/include/seqan/graph_align.h:45, from /usr/include/seqan/align.h:59, from unicycler/include/scoredalignment.h:18: /usr/include/seqan/file/file_forwards.h:46:7: note: âseqan2::Alignâ declared here 46 | class Align; | ^~~~~ unicycler/src/semi_global_align_exhaustive.cpp:48:23: error: âArrayGapsâ was not declared in this scope; did you mean âseqan2::ArrayGapsâ? 48 | Align<Dna5String, ArrayGaps> alignment; | ^~~~~~~~~ | seqan2::ArrayGaps In file included from /usr/include/seqan/index.h:137, from /usr/include/seqan/seeds.h:51, from unicycler/include/semi_global_align.h:16: /usr/include/seqan/index/index_esa_base.h:263:29: note: âseqan2::ArrayGapsâ declared here 263 | typedef Tag<ArrayGaps_> ArrayGaps; | ^~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:48:34: error: âalignmentâ was not declared in this scope; did you mean âseqan2::alignmentâ? 48 | Align<Dna5String, ArrayGaps> alignment; | ^~~~~~~~~ | seqan2::alignment In file included from /usr/include/seqan/index.h:138: /usr/include/seqan/index/index_esa_stree.h:1193:5: note: âseqan2::alignmentâ declared here 1193 | alignment(Iter< Index< StringSet<TString, Owner<ConcatDirect<TConcSpec> > >, TIndexSpec >, VSTree<TSpec> > &it) | ^~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:49:12: error: ârowsâ was not declared in this scope; did you mean âseqan2::rowsâ? 49 | resize(rows(alignment), 2); | ^~~~ | seqan2::rows In file included from /usr/include/seqan/align.h:97: /usr/include/seqan/align/align_base.h:341:1: note: âseqan2::rowsâ declared here 341 | rows(Align<TSource, TSpec> const & me) | ^~~~ unicycler/src/semi_global_align_exhaustive.cpp:49:5: error: âresizeâ was not declared in this scope; did you mean âseqan2::resizeâ? 49 | resize(rows(alignment), 2); | ^~~~~~ | seqan2::resize In file included from /usr/include/seqan/index.h:169: /usr/include/seqan/index/index_fm_compressed_sa.h:456:1: note: âseqan2::resizeâ declared here 456 | resize(CompressedSA<TText, TSpec, TConfig> & compressedSA, TSize size, Tag<TExpand> tag) | ^~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:50:18: error: ârowâ was not declared in this scope; did you mean âseqan2::rowâ? 50 | assignSource(row(alignment, 0), sequenceH); | ^~~ | seqan2::row /usr/include/seqan/align/align_base.h:372:1: note: âseqan2::rowâ declared here 372 | row(Align<TSource, TSpec> const & me, | ^~~ unicycler/src/semi_global_align_exhaustive.cpp:50:37: error: âsequenceHâ was not declared in this scope 50 | assignSource(row(alignment, 0), sequenceH); | ^~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:50:5: error: âassignSourceâ was not declared in this scope; did you mean âseqan2::assignSourceâ? 50 | assignSource(row(alignment, 0), sequenceH); | ^~~~~~~~~~~~ | seqan2::assignSource In file included from /usr/include/seqan/align.h:89: /usr/include/seqan/align/gaps_anchor.h:672:1: note: âseqan2::assignSourceâ declared here 672 | assignSource(Gaps<TSequence, AnchorGaps<TGapAnchor> > & gaps, TSequence2 const & source) | ^~~~~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:51:37: error: âsequenceVâ was not declared in this scope 51 | assignSource(row(alignment, 1), sequenceV); | ^~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:52:5: error: âScoreâ was not declared in this scope; did you mean âseqan2::Scoreâ? 52 | Score<int, Simple> scoringScheme(matchScore, mismatchScore, gapExtensionScore, gapOpenScore); | ^~~~~ | seqan2::Score In file included from /usr/include/seqan/score.h:45: /usr/include/seqan/score/score_base.h:68:7: note: âseqan2::Scoreâ declared here 68 | class Score; | ^~~~~ unicycler/src/semi_global_align_exhaustive.cpp:52:11: error: expected primary-expression before âintâ 52 | Score<int, Simple> scoringScheme(matchScore, mismatchScore, gapExtensionScore, gapOpenScore); | ^~~ unicycler/src/semi_global_align_exhaustive.cpp:54:5: error: âAlignConfigâ was not declared in this scope; did you mean âseqan2::AlignConfigâ? 54 | AlignConfig<true, true, true, true> alignConfig; | ^~~~~~~~~~~ | seqan2::AlignConfig In file included from /usr/include/seqan/align.h:70: /usr/include/seqan/align/align_config.h:93:7: note: âseqan2::AlignConfigâ declared here 93 | class AlignConfig | ^~~~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:54:41: error: âalignConfigâ was not declared in this scope 54 | AlignConfig<true, true, true, true> alignConfig; | ^~~~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:56:36: error: âscoringSchemeâ was not declared in this scope; did you mean âseqan2::scoringSchemeâ? 56 | globalAlignment(alignment, scoringScheme, alignConfig); | ^~~~~~~~~~~~~ | 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) | ^~~~~~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:56:9: error: âglobalAlignmentâ was not declared in this scope; did you mean âseqan2::globalAlignmentâ? 56 | globalAlignment(alignment, scoringScheme, alignConfig); | ^~~~~~~~~~~~~~~ | seqan2::globalAlignment In file included from /usr/include/seqan/align.h:218: /usr/include/seqan/align/global_alignment_specialized.h:121:5: note: âseqan2::globalAlignmentâ declared here 121 | int globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH, | ^~~~~~~~~~~~~~~ unicycler/src/semi_global_align_exhaustive.cpp:66:67: error: âscoringSchemeâ was not declared in this scope; did you mean âseqan2::scoringSchemeâ? 66 | 0, startTime, 0, true, true, true, scoringScheme); | ^~~~~~~~~~~~~ | seqan2::scoringScheme /usr/include/seqan/find/find_score.h:180:1: note: âseqan2::scoringSchemeâ declared here 180 | scoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me) | ^~~~~~~~~~~~~ make[2]: *** [Makefile:120: unicycler/src/semi_global_align_exhaustive.o] Error 1 make[2]: Leaving directory '/<<PKGBUILDDIR>>' make[1]: *** [debian/rules:30: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:23: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
