Package: src:bioperl Version: 1.7.8-3 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/202605/ 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:bioperl, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_configure -- /usr/bin/perl Makefile.PL INSTALLDIRS=vendor OPTIMIZE="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" LD="x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for BioPerl [... snipped ...] ok 19 ok 20 ok 21 ok 22 ok 23 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 24 ok 25 ok 26 ok 27 ok 28 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 29 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' ok 30 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' ok 31 ok 32 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' ok 33 ok 34 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 35 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' ok 36 ok 37 ok 38 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 39 ok 40 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 41 - An object of class 'Bio::Annotation::Relation' isa 'Bio::Annotation::Relation' ok 42 ok 43 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 44 - An object of class 'Bio::Annotation::Relation' isa 'Bio::Annotation::Relation' ok 45 ok 46 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 47 ok 48 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 49 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 50 ok 51 ok 52 ok 53 - An object of class 'Bio::Seq' isa 'Bio::SeqI' ok 54 ok 55 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 56 - An object of class 'Bio::Annotation::Relation' isa 'Bio::Annotation::Relation' ok 57 ok 58 - An object of class 'Bio::Tree::AnnotatableNode' isa 'Bio::Tree::AnnotatableNode' ok 59 ok 60 ok 61 ok 62 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 63 - An object of class 'Bio::Tree::AnnotatableNode' isa 'Bio::Tree::AnnotatableNode' ok 64 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 65 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' ok 66 ok 67 ok 68 ok 69 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 70 - An object of class 'Bio::Tree::AnnotatableNode' isa 'Bio::Tree::AnnotatableNode' ok 71 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 72 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' ok 73 ok 74 ok 75 ok 76 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 77 ok 78 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 91 ok 92 - An object of class 'Bio::Tree::AnnotatableNode' isa 'Bio::Tree::AnnotatableNode' ok 93 ok 94 ok 95 ok 96 ok 97 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 98 ok t/Tree/TreeIO/tabtree.t ............. 1..24 ok 1 - use Bio::TreeIO; ok 2 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' ok 18 - Leaf nodes ok 19 - All nodes ok 20 ok 21 ok 22 ok 23 ok 24 ok t/Tree/TreeStatistics.t ............. 1..44 ok 1 - use Bio::TreeIO; ok 2 - use Bio::Tree::Statistics; ok 3 - cherries ok 4 - cherries # Subtest: transfer-bootstrap-expectation (experimental) 1..15 ok 1 - Testing TBE for node ok 2 - Testing TBE for node N7 ok 3 - Testing TBE for node N3 ok 4 - Testing TBE for node N1 ok 5 - Testing TBE for node N2 ok 6 - Testing TBE for node N6 ok 7 - Testing TBE for node N4 ok 8 - Testing TBE for node N5 ok 9 - Testing TBE for node N14 ok 10 - Testing TBE for node N10 ok 11 - Testing TBE for node N8 ok 12 - Testing TBE for node N9 ok 13 - Testing TBE for node N13 ok 14 - Testing TBE for node N11 ok 15 - Testing TBE for node N12 ok 5 - transfer-bootstrap-expectation (experimental) # Subtest: assess_bootstrap 1..15 ok 1 - Testing bootstrap for node ok 2 - Testing bootstrap for node N7 ok 3 - Testing bootstrap for node N3 ok 4 - Testing bootstrap for node N1 ok 5 - Testing bootstrap for node N2 ok 6 - Testing bootstrap for node N6 ok 7 - Testing bootstrap for node N4 ok 8 - Testing bootstrap for node N5 ok 9 - Testing bootstrap for node N14 ok 10 - Testing bootstrap for node N10 ok 11 - Testing bootstrap for node N8 ok 12 - Testing bootstrap for node N9 ok 13 - Testing bootstrap for node N13 ok 14 - Testing bootstrap for node N11 ok 15 - Testing bootstrap for node N12 ok 6 - assess_bootstrap ok 7 - read traits ok 8 - Add traits in second column and ignore missing ok 9 - Add traits in third column ok 10 - parsimony score ok 11 - subtree parsimony score ok 12 - ps value ok 13 - fitch_down ok 14 - ps value after fitch_down ok 15 - persistence of a leaf ok 16 - persistence of an internal node value ok 17 - persistence of an internal node value ok 18 - persistence of an internal node value ok 19 - leaf node: number of clusters = 0 ok 20 - number of clusters ok 21 - number of clusters ok 22 - number of clusters ok 23 - number of leaves in phylotype ok 24 - number of leaves in phylotype ok 25 - number of leaves in phylotype ok 26 - number of leaves in phylotype ok 27 - phylotype length ok 28 - phylotype length ok 29 - phylotype length ok 30 - phylotype length ok 31 - phylotype length ok 32 - sum of leaf distances ok 33 - sum of leaf distances ok 34 - sum of leaf distances ok 35 - sum of leaf distances ok 36 - sum of leaf distances ok 37 - genetic diversity ok 38 - separation ok 39 - association index ok 40 - subtree association index ok 41 - monophyletic clade size ok 42 - monophyletic clade size ok 43 - monophyletic clade size ok 44 - monophyletic clade size ok Test Summary Report ------------------- t/Align/AlignStats.t (Wstat: 65280 (exited 255) Tests: 43 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 45 tests but ran 43. t/Align/SimpleAlign.t (Wstat: 65280 (exited 255) Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 206 tests but ran 5. t/LocalDB/Fasta.t (Wstat: 6400 (exited 25) Tests: 102 Failed: 0) Non-zero exit status: 25 Parse errors: Bad plan. You planned 109 tests but ran 102. t/Ontology/OntologyEngine.t (Wstat: 65280 (exited 255) Tests: 7 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 7. t/Root/IO.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 154 tests but ran 1. t/Root/RootI.t (Wstat: 65280 (exited 255) Tests: 3 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 43 tests but ran 3. t/SearchIO/blast.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 1389 tests but ran 1. t/SearchIO/infernal.t (Wstat: 6400 (exited 25) Tests: 110 Failed: 0) Non-zero exit status: 25 Parse errors: Bad plan. You planned 496 tests but ran 110. t/SearchIO/psl.t (Wstat: 65280 (exited 255) Tests: 52 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 53 tests but ran 52. t/Seq/LocatableSeq.t (Wstat: 65280 (exited 255) Tests: 26 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 119 tests but ran 26. t/Seq/PrimaryQual.t (Wstat: 7424 (exited 29) Tests: 25 Failed: 0) Non-zero exit status: 29 Parse errors: Bad plan. You planned 70 tests but ran 25. t/Seq/PrimarySeq.t (Wstat: 65280 (exited 255) Tests: 50 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 312 tests but ran 50. t/Seq/Quality.t (Wstat: 65280 (exited 255) Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 85 tests but ran 1. t/Seq/SimulatedRead.t (Wstat: 65280 (exited 255) Tests: 158 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 194 tests but ran 158. t/SeqFeature/Generic.t (Wstat: 65280 (exited 255) Tests: 331 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 364 tests but ran 331. t/SeqIO/fasta.t (Wstat: 65280 (exited 255) Tests: 18 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 22 tests but ran 18. t/SeqIO/fastq.t (Wstat: 6400 (exited 25) Tests: 128 Failed: 0) Non-zero exit status: 25 Parse errors: Bad plan. You planned 149 tests but ran 128. t/SeqIO/msout.t (Wstat: 65280 (exited 255) Tests: 88 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 165 tests but ran 88. t/SeqIO/SeqIO.t (Wstat: 2304 (exited 9) Tests: 54 Failed: 0) Non-zero exit status: 9 Parse errors: Bad plan. You planned 58 tests but ran 54. t/SeqIO/Splicedseq.t (Wstat: 6400 (exited 25) Tests: 16 Failed: 0) Non-zero exit status: 25 Parse errors: Bad plan. You planned 27 tests but ran 16. t/SeqIO/swiss.t (Wstat: 6400 (exited 25) Tests: 242 Failed: 0) Non-zero exit status: 25 Parse errors: Bad plan. You planned 247 tests but ran 242. t/SeqTools/Backtranslate.t (Wstat: 65280 (exited 255) Tests: 7 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 8 tests but ran 7. t/SeqTools/GuessSeqFormat.t (Wstat: 65280 (exited 255) Tests: 12 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 105 tests but ran 12. t/SeqTools/SeqPattern.t (Wstat: 65280 (exited 255) Tests: 11 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 28 tests but ran 11. t/SeqTools/SeqUtils.t (Wstat: 512 (exited 2) Tests: 37 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 133 tests but ran 37. t/Tools/PrositeScan.t (Wstat: 65280 (exited 255) Tests: 3 Failed: 1) Failed test: 3 Non-zero exit status: 255 Files=211, Tests=11707, 48 wallclock secs ( 0.66 usr 0.28 sys + 38.84 cusr 8.27 csys = 48.05 CPU) Result: FAIL Failed 26/211 test programs. 1/11707 subtests failed. make[1]: *** [Makefile:3272: test_dynamic] Error 255 make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_test: error: make -j2 test TEST_VERBOSE=1 returned exit code 2 make: *** [debian/rules:8: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
