Source: libbio-db-hts-perl Version: 3.01-1 X-Debbugs-CC: debian...@lists.debian.org Severity: serious User: debian...@lists.debian.org Usertags: regression
Dear maintainers, With a recent upload of libbio-db-hts-perl you added an autopkgtest to libbio-db-hts-perl, great. However, it fails. 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=libbio-db-hts-perl https://ci.debian.net/data/autopkgtest/testing/amd64/libb/libbio-db-hts-perl/3632505/log.gz 1..22 # Base class package "Bio::SeqFeature::Lite" is empty. # (Perhaps you need to 'use' the module which defines that package first, # or make that module available in @INC (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base). # at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm line 457. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm line 457. not ok 1 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Alignment.pm line 457. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Alignment.pm line 457. not ok 2 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Alignment.pm exited successfully ok 3 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Constants.pm exited successfully ok 4 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Faidx.pm exited successfully ok 5 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/FetchIterator.pm exited successfully ok 6 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Kseq/Record.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Kseq.pm line 71. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Kseq.pm line 71. not ok 7 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Kseq.pm exited successfully ok 8 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Pileup.pm exited successfully # Base class package "Bio::SeqFeature::Lite" is empty. # (Perhaps you need to 'use' the module which defines that package first, # or make that module available in @INC (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base). # at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm line 457. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/AlignWrapper.pm line 457. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/PileupWrapper.pm line 49. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/PileupWrapper.pm line 49. not ok 9 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/PileupWrapper.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56. not ok 10 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm exited successfully ok 11 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/ReadIterator.pm exited successfully # Name "Bio::DB::HTS::Segment::abs_ref" used only once: possible typo at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Segment.pm line 70. # Name "Bio::DB::HTS::Segment::ref" used only once: possible typo at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Segment.pm line 70. # Name "Bio::DB::HTS::Segment::sourceseq" used only once: possible typo at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Segment.pm line 70. ok 12 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Segment.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix/Iterator.pm line 21. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix/Iterator.pm line 21. not ok 13 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix/Iterator.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix.pm line 22. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix.pm line 22. not ok 14 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Tabix.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Query.pm line 56. # Compilation failed in require at /usr/share/perl/5.30/base.pm line 137. # ...propagated at /usr/share/perl/5.30/base.pm line 159. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Target.pm line 41. not ok 15 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/Target.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm line 3. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm line 3. not ok 16 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm line 3. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Header.pm line 3. # Compilation failed in require at /usr/share/perl/5.30/base.pm line 137. # ...propagated at /usr/share/perl/5.30/base.pm line 159. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/HeaderPtr.pm line 3. not ok 17 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/HeaderPtr.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Iterator.pm line 21. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Iterator.pm line 21. not ok 18 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Iterator.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm line 5. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm line 5. not ok 19 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm line 5. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/Row.pm line 5. # Compilation failed in require at /usr/share/perl/5.30/base.pm line 137. # ...propagated at /usr/share/perl/5.30/base.pm line 159. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/RowPtr.pm line 3. not ok 20 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF/RowPtr.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF.pm line 408. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF.pm line 408. not ok 21 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS/VCF.pm exited successfully # Can't locate Bio/SeqFeature/Lite.pm in @INC (you may need to install the Bio::SeqFeature::Lite module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. # BEGIN failed--compilation aborted at /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm line 1360. not ok 22 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.30/Bio/DB/HTS.pm exited successfully not ok 4 - all modules in libbio-db-hts-perl pass the syntax check Dubious, test returned 1 (wstat 256, 0x100) Failed 1/4 subtests
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