Your message dated Wed, 16 Apr 2025 20:59:07 +0000 with message-id <e1u59qd-00fatb...@fasolo.debian.org> and subject line Bug#1103330: fixed in sra-sdk 3.2.1+dfsg-4 has caused the Debian Bug report #1103330, regarding sra-sdk: FTBFS with the nocheck build profile to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1103330: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103330 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:sra-sdk Version: 3.2.1+dfsg-3 Severity: important Tags: trixie sid ftbfs User: debian...@lists.debian.org Usertags: ftbfs-nocheck-profile Dear maintainer: During a rebuild of all packages in unstable using the nocheck build profile, your package failed to build: -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem=cmake \ --with python3,javahelper,jh_maven_repo_helper debian/rules override_dh_auto_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_clean rm -rf ngs/ngs-java/x86_64-linux-gnu rm -rf ngs/ngs-bam/x86_64-linux-gnu rm -f ngs/ngs-bam/Makefile.config rm -f ngs/ngs-bam/Makefile.config.install.linux.x86_64.prl rm -f ngs/ngs-bam/Makefile.config.linux.x86_64 [... snipped ...] -rwxr-xr-x 1 buildd buildd 807504 Apr 16 11:11 abi-load.3.2.1 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 align-cache -> align-cache.3 lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 align-cache.3 -> align-cache.3.2.1 -rwxr-xr-x 1 buildd buildd 249680 Apr 16 11:11 align-cache.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 align-info -> align-info.3 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 align-info.3 -> align-info.3.2.1 -rwxr-xr-x 1 buildd buildd 97320 Apr 16 11:11 align-info.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 bam-load -> bam-load.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 bam-load.3 -> bam-load.3.2.1 -rwxr-xr-x 1 buildd buildd 14124856 Apr 16 11:11 bam-load.3.2.1 lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 cache-mgr -> cache-mgr.3 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 cache-mgr.3 -> cache-mgr.3.2.1 -rwxr-xr-x 1 buildd buildd 124728 Apr 16 11:11 cache-mgr.3.2.1 lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 ccextract -> ccextract.3 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 ccextract.3 -> ccextract.3.2.1 -rwxr-xr-x 1 buildd buildd 272968 Apr 16 11:11 ccextract.3.2.1 lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 cg-load -> cg-load.3 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 cg-load.3 -> cg-load.3.2.1 -rwxr-xr-x 1 buildd buildd 657864 Apr 16 11:11 cg-load.3.2.1 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 check-corrupt -> check-corrupt.3 lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 check-corrupt.3 -> check-corrupt.3.2.1 -rwxr-xr-x 1 buildd buildd 247200 Apr 16 11:11 check-corrupt.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 check-redact -> check-redact.3 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 check-redact.3 -> check-redact.3.2.1 -rwxr-xr-x 1 buildd buildd 97880 Apr 16 11:11 check-redact.3.2.1 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 compute-coverage -> compute-coverage.3 lrwxrwxrwx 1 buildd buildd 22 Apr 16 11:15 compute-coverage-ngs -> compute-coverage-ngs.3 lrwxrwxrwx 1 buildd buildd 26 Apr 16 11:15 compute-coverage-ngs.3 -> compute-coverage-ngs.3.2.1 -rwxr-xr-x 1 buildd buildd 2224928 Apr 16 11:14 compute-coverage-ngs.3.2.1 lrwxrwxrwx 1 buildd buildd 22 Apr 16 11:15 compute-coverage.3 -> compute-coverage.3.2.1 -rwxr-xr-x 1 buildd buildd 131184 Apr 16 11:11 compute-coverage.3.2.1 lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 copycat -> copycat.3 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 copycat.3 -> copycat.3.2.1 -rwxr-xr-x 1 buildd buildd 484072 Apr 16 11:11 copycat.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 crc32sum -> crc32sum.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 crc32sum.3 -> crc32sum.3.2.1 -rwxr-xr-x 1 buildd buildd 79432 Apr 16 11:11 crc32sum.3.2.1 lrwxrwxrwx 1 buildd buildd 22 Apr 16 11:15 dump-blob-boundaries -> dump-blob-boundaries.3 lrwxrwxrwx 1 buildd buildd 26 Apr 16 11:15 dump-blob-boundaries.3 -> dump-blob-boundaries.3.2.1 -rwxr-xr-x 1 buildd buildd 31600 Apr 16 11:11 dump-blob-boundaries.3.2.1 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 dump-ref-fasta -> dump-ref-fasta.3 lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 dump-ref-fasta.3 -> dump-ref-fasta.3.2.1 -rwxr-xr-x 1 buildd buildd 2098080 Apr 16 11:14 dump-ref-fasta.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 fastconv -> fastconv.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 fastconv.3 -> fastconv.3.2.1 -rwxr-xr-x 1 buildd buildd 5042992 Apr 16 11:11 fastconv.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 fasterq-dump -> fasterq-dump.3 -rwxr-xr-x 1 buildd buildd 1016680 Apr 16 11:11 fasterq-dump-orig.3.2.1 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 fasterq-dump.3 -> fasterq-dump.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 fasterq-dump.3.2.1 -> sratools.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 fastq-dump -> fastq-dump.3 -rwxr-xr-x 1 buildd buildd 349696 Apr 16 11:11 fastq-dump-orig.3.2.1 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 fastq-dump.3 -> fastq-dump.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 fastq-dump.3.2.1 -> sratools.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 fastq-load -> fastq-load.3 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 fastq-load.3 -> fastq-load.3.2.1 -rwxr-xr-x 1 buildd buildd 859400 Apr 16 11:11 fastq-load.3.2.1 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 general-loader -> general-loader.3 lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 general-loader.3 -> general-loader.3.2.1 -rwxr-xr-x 1 buildd buildd 1646960 Apr 16 11:11 general-loader.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 helicos-load -> helicos-load.3 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 helicos-load.3 -> helicos-load.3.2.1 -rwxr-xr-x 1 buildd buildd 769640 Apr 16 11:11 helicos-load.3.2.1 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 illumina-dump -> illumina-dump.3 lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 illumina-dump.3 -> illumina-dump.3.2.1 -rwxr-xr-x 1 buildd buildd 255616 Apr 16 11:11 illumina-dump.3.2.1 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 illumina-load -> illumina-load.3 lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 illumina-load.3 -> illumina-load.3.2.1 -rwxr-xr-x 1 buildd buildd 819896 Apr 16 11:11 illumina-load.3.2.1 lrwxrwxrwx 1 buildd buildd 5 Apr 16 11:15 kar -> kar.3 lrwxrwxrwx 1 buildd buildd 6 Apr 16 11:15 kar+ -> kar+.3 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 kar+.3 -> kar+.3.2.1 -rwxr-xr-x 1 buildd buildd 237544 Apr 16 11:11 kar+.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 kar+meta -> kar+meta.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 kar+meta.3 -> kar+meta.3.2.1 -rwxr-xr-x 1 buildd buildd 159056 Apr 16 11:11 kar+meta.3.2.1 lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 kar.3 -> kar.3.2.1 -rwxr-xr-x 1 buildd buildd 190712 Apr 16 11:11 kar.3.2.1 lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 kdb-index -> kdb-index.3 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 kdb-index.3 -> kdb-index.3.2.1 -rwxr-xr-x 1 buildd buildd 78448 Apr 16 11:11 kdb-index.3.2.1 lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 kdbmeta -> kdbmeta.3 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 kdbmeta.3 -> kdbmeta.3.2.1 -rwxr-xr-x 1 buildd buildd 123624 Apr 16 11:11 kdbmeta.3.2.1 lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 latf-load -> latf-load.3 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 latf-load.3 -> latf-load.3.2.1 -rwxr-xr-x 1 buildd buildd 508272 Apr 16 11:12 latf-load.3.2.1 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 make-read-filter -> make-read-filter.3 lrwxrwxrwx 1 buildd buildd 22 Apr 16 11:15 make-read-filter.3 -> make-read-filter.3.2.1 -rwxr-xr-x 1 buildd buildd 158768 Apr 16 11:11 make-read-filter.3.2.1 lrwxrwxrwx 1 buildd buildd 7 Apr 16 11:15 md5cp -> md5cp.3 lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 md5cp.3 -> md5cp.3.2.1 -rwxr-xr-x 1 buildd buildd 89720 Apr 16 11:11 md5cp.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 meta-cmp -> meta-cmp.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 meta-cmp.3 -> meta-cmp.3.2.1 -rwxr-xr-x 1 buildd buildd 82024 Apr 16 11:11 meta-cmp.3.2.1 lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 meta-copy -> meta-copy.3 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 meta-copy.3 -> meta-copy.3.2.1 -rwxr-xr-x 1 buildd buildd 81952 Apr 16 11:11 meta-copy.3.2.1 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 meta-repair -> meta-repair.3 lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 meta-repair.3 -> meta-repair.3.2.1 -rwxr-xr-x 1 buildd buildd 136048 Apr 16 11:11 meta-repair.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 ngs-pileup -> ngs-pileup.3 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 ngs-pileup.3 -> ngs-pileup.3.2.1 -rwxr-xr-x 1 buildd buildd 2608704 Apr 16 11:14 ngs-pileup.3.2.1 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 pacbio-correct -> pacbio-correct.3 lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 pacbio-correct.3 -> pacbio-correct.3.2.1 -rwxr-xr-x 1 buildd buildd 76024 Apr 16 11:11 pacbio-correct.3.2.1 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 pacbio-load -> pacbio-load.3 lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 pacbio-load.3 -> pacbio-load.3.2.1 -rwxr-xr-x 1 buildd buildd 476952 Apr 16 11:11 pacbio-load.3.2.1 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 pacbio-loadxml -> pacbio-loadxml.3 lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 pacbio-loadxml.3 -> pacbio-loadxml.3.2.1 -rwxr-xr-x 1 buildd buildd 757368 Apr 16 11:11 pacbio-loadxml.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 pileup-stats -> pileup-stats.3 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 pileup-stats.3 -> pileup-stats.3.2.1 -rwxr-xr-x 1 buildd buildd 2848488 Apr 16 11:14 pileup-stats.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 prefetch -> prefetch.3 -rwxr-xr-x 1 buildd buildd 479464 Apr 16 11:11 prefetch-orig.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 prefetch.3 -> prefetch.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 prefetch.3.2.1 -> sratools.3.2.1 lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 rcexplain -> rcexplain.3 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 rcexplain.3 -> rcexplain.3.2.1 -rwxr-xr-x 1 buildd buildd 67456 Apr 16 11:11 rcexplain.3.2.1 lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 read-filter-redact -> read-filter-redact.3 lrwxrwxrwx 1 buildd buildd 24 Apr 16 11:15 read-filter-redact.3 -> read-filter-redact.3.2.1 -rwxr-xr-x 1 buildd buildd 111192 Apr 16 11:11 read-filter-redact.3.2.1 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 ref-variation -> ref-variation.3 lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 ref-variation.3 -> ref-variation.3.2.1 -rwxr-xr-x 1 buildd buildd 3020016 Apr 16 11:14 ref-variation.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 rowwritetest -> rowwritetest.3 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 rowwritetest.3 -> rowwritetest.3.2.1 -rwxr-xr-x 1 buildd buildd 88592 Apr 16 11:11 rowwritetest.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sam-dump -> sam-dump.3 -rwxr-xr-x 1 buildd buildd 834512 Apr 16 11:11 sam-dump-orig.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sam-dump.3 -> sam-dump.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sam-dump.3.2.1 -> sratools.3.2.1 lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 samview -> samview.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 samview-util -> samview-util.3 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 samview-util.3 -> samview-util.3.2.1 -rwxr-xr-x 1 buildd buildd 64176 Apr 16 11:11 samview-util.3.2.1 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 samview.3 -> samview.3.2.1 -rwxr-xr-x 1 buildd buildd 305696 Apr 16 11:11 samview.3.2.1 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 schema-replace -> schema-replace.3 lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 schema-replace.3 -> schema-replace.3.2.1 -rwxr-xr-x 1 buildd buildd 82928 Apr 16 11:11 schema-replace.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sff-dump -> sff-dump.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sff-dump.3 -> sff-dump.3.2.1 -rwxr-xr-x 1 buildd buildd 234512 Apr 16 11:11 sff-dump.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sff-load -> sff-load.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sff-load.3 -> sff-load.3.2.1 -rwxr-xr-x 1 buildd buildd 818504 Apr 16 11:11 sff-load.3.2.1 lrwxrwxrwx 1 buildd buildd 7 Apr 16 11:15 sharq -> sharq.3 lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 sharq.3 -> sharq.3.2.1 -rwxr-xr-x 1 buildd buildd 44902232 Apr 16 11:13 sharq.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sortreadtest -> sortreadtest.3 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 sortreadtest.3 -> sortreadtest.3.2.1 -rwxr-xr-x 1 buildd buildd 79784 Apr 16 11:11 sortreadtest.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sra-info -> sra-info.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sra-info.3 -> sra-info.3.2.1 -rwxr-xr-x 1 buildd buildd 2904864 Apr 16 11:11 sra-info.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 sra-pileup -> sra-pileup.3 -rwxr-xr-x 1 buildd buildd 443160 Apr 16 11:11 sra-pileup-orig.3.2.1 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 sra-pileup.3 -> sra-pileup.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sra-pileup.3.2.1 -> sratools.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 sra-search -> sra-search.3 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 sra-search.3 -> sra-search.3.2.1 -rwxr-xr-x 1 buildd buildd 4340304 Apr 16 11:14 sra-search.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sra-sort -> sra-sort.3 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 sra-sort-cg -> sra-sort-cg.3 lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 sra-sort-cg.3 -> sra-sort-cg.3.2.1 -rwxr-xr-x 1 buildd buildd 808784 Apr 16 11:11 sra-sort-cg.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sra-sort.3 -> sra-sort.3.2.1 -rwxr-xr-x 1 buildd buildd 808816 Apr 16 11:11 sra-sort.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sra-stat -> sra-stat.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sra-stat.3 -> sra-stat.3.2.1 -rwxr-xr-x 1 buildd buildd 347472 Apr 16 11:11 sra-stat.3.2.1 lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 srapath -> srapath.3 -rwxr-xr-x 1 buildd buildd 256120 Apr 16 11:11 srapath-orig.3.2.1 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 srapath.3 -> srapath.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 srapath.3.2.1 -> sratools.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sratools -> sratools.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sratools.3 -> sratools.3.2.1 -rwxr-xr-x 1 buildd buildd 5471720 Apr 16 11:11 sratools.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 srf-load -> srf-load.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 srf-load.3 -> srf-load.3.2.1 -rwxr-xr-x 1 buildd buildd 999560 Apr 16 11:11 srf-load.3.2.1 lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 test-download -> test-download.3 lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 test-download.3 -> test-download.3.2.1 -rwxr-xr-x 1 buildd buildd 93648 Apr 16 11:11 test-download.3.2.1 lrwxrwxrwx 1 buildd buildd 24 Apr 16 11:15 test-read-write-cursor -> test-read-write-cursor.3 lrwxrwxrwx 1 buildd buildd 28 Apr 16 11:15 test-read-write-cursor.3 -> test-read-write-cursor.3.2.1 -rwxr-xr-x 1 buildd buildd 75488 Apr 16 11:11 test-read-write-cursor.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 test-sra -> test-sra.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 test-sra.3 -> test-sra.3.2.1 -rwxr-xr-x 1 buildd buildd 343496 Apr 16 11:11 test-sra.3.2.1 lrwxrwxrwx 1 buildd buildd 8 Apr 16 11:15 testld -> testld.3 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 testld.3 -> testld.3.2.1 -rwxr-xr-x 1 buildd buildd 76472 Apr 16 11:11 testld.3.2.1 lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 txt2kdb -> txt2kdb.3 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 txt2kdb.3 -> txt2kdb.3.2.1 -rwxr-xr-x 1 buildd buildd 83256 Apr 16 11:11 txt2kdb.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 var-expand -> var-expand.3 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 var-expand.3 -> var-expand.3.2.1 -rwxr-xr-x 1 buildd buildd 2049376 Apr 16 11:14 var-expand.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 vdb-config -> vdb-config.3 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 vdb-config.3 -> vdb-config.3.2.1 -rwxr-xr-x 1 buildd buildd 2655424 Apr 16 11:13 vdb-config.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 vdb-copy -> vdb-copy.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-copy.3 -> vdb-copy.3.2.1 -rwxr-xr-x 1 buildd buildd 329728 Apr 16 11:11 vdb-copy.3.2.1 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 vdb-decrypt -> vdb-decrypt.3 lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 vdb-decrypt.3 -> vdb-decrypt.3.2.1 -rwxr-xr-x 1 buildd buildd 121584 Apr 16 11:11 vdb-decrypt.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 vdb-diff -> vdb-diff.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-diff.3 -> vdb-diff.3.2.1 -rwxr-xr-x 1 buildd buildd 155224 Apr 16 11:11 vdb-diff.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 vdb-dump -> vdb-dump.3 -rwxr-xr-x 1 buildd buildd 887840 Apr 16 11:11 vdb-dump-orig.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-dump.3 -> vdb-dump.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-dump.3.2.1 -> sratools.3.2.1 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 vdb-encrypt -> vdb-encrypt.3 lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 vdb-encrypt.3 -> vdb-encrypt.3.2.1 -rwxr-xr-x 1 buildd buildd 119960 Apr 16 11:11 vdb-encrypt.3.2.1 lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 vdb-lock -> vdb-lock.3 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-lock.3 -> vdb-lock.3.2.1 -rwxr-xr-x 1 buildd buildd 68336 Apr 16 11:11 vdb-lock.3.2.1 lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 vdb-sql -> vdb-sql.3 lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 vdb-sql.3 -> vdb-sql.3.2.1 -rwxr-xr-x 1 buildd buildd 5296480 Apr 16 11:11 vdb-sql.3.2.1 lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 vdb-unlock -> vdb-unlock.3 lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 vdb-unlock.3 -> vdb-unlock.3.2.1 -rwxr-xr-x 1 buildd buildd 68344 Apr 16 11:11 vdb-unlock.3.2.1 lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-validate -> vdb-validate.3 lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 vdb-validate.3 -> vdb-validate.3.2.1 -rwxr-xr-x 1 buildd buildd 261640 Apr 16 11:11 vdb-validate.3.2.1 cd debian/tmp/usr/bin && \ for bin in *-orig.* ; do \ base=${bin%-orig.*} && \ vbase=$(readlink "$(readlink $base)") && \ vdriver=$(readlink "$vbase") && \ mv -v $bin $base-orig && \ ln -snfv ${vdriver%%.[0-9]*} $vbase || exit $? ; \ done && \ for bin in *[a-z+] ; do \ bin2=$(readlink $bin) ; \ bin3=$(readlink "$bin2") ; \ case $bin2 in \ $bin.* ) rm -v $bin2 && mv -v $bin3 $bin || exit $? ;; \ esac ; \ done renamed 'fasterq-dump-orig.3.2.1' -> 'fasterq-dump-orig' 'fasterq-dump.3.2.1' -> 'sratools' renamed 'fastq-dump-orig.3.2.1' -> 'fastq-dump-orig' 'fastq-dump.3.2.1' -> 'sratools' renamed 'prefetch-orig.3.2.1' -> 'prefetch-orig' 'prefetch.3.2.1' -> 'sratools' renamed 'sam-dump-orig.3.2.1' -> 'sam-dump-orig' 'sam-dump.3.2.1' -> 'sratools' renamed 'sra-pileup-orig.3.2.1' -> 'sra-pileup-orig' 'sra-pileup.3.2.1' -> 'sratools' renamed 'srapath-orig.3.2.1' -> 'srapath-orig' 'srapath.3.2.1' -> 'sratools' renamed 'vdb-dump-orig.3.2.1' -> 'vdb-dump-orig' 'vdb-dump.3.2.1' -> 'sratools' removed 'abi-dump.3' renamed 'abi-dump.3.2.1' -> 'abi-dump' removed 'abi-load.3' renamed 'abi-load.3.2.1' -> 'abi-load' removed 'align-cache.3' renamed 'align-cache.3.2.1' -> 'align-cache' removed 'align-info.3' renamed 'align-info.3.2.1' -> 'align-info' removed 'bam-load.3' renamed 'bam-load.3.2.1' -> 'bam-load' removed 'cache-mgr.3' renamed 'cache-mgr.3.2.1' -> 'cache-mgr' removed 'ccextract.3' renamed 'ccextract.3.2.1' -> 'ccextract' removed 'cg-load.3' renamed 'cg-load.3.2.1' -> 'cg-load' removed 'check-corrupt.3' renamed 'check-corrupt.3.2.1' -> 'check-corrupt' removed 'check-redact.3' renamed 'check-redact.3.2.1' -> 'check-redact' removed 'compute-coverage.3' renamed 'compute-coverage.3.2.1' -> 'compute-coverage' removed 'compute-coverage-ngs.3' renamed 'compute-coverage-ngs.3.2.1' -> 'compute-coverage-ngs' removed 'copycat.3' renamed 'copycat.3.2.1' -> 'copycat' removed 'crc32sum.3' renamed 'crc32sum.3.2.1' -> 'crc32sum' removed 'dump-blob-boundaries.3' renamed 'dump-blob-boundaries.3.2.1' -> 'dump-blob-boundaries' removed 'dump-ref-fasta.3' renamed 'dump-ref-fasta.3.2.1' -> 'dump-ref-fasta' removed 'fastconv.3' renamed 'fastconv.3.2.1' -> 'fastconv' removed 'fasterq-dump.3' renamed 'fasterq-dump.3.2.1' -> 'fasterq-dump' removed 'fastq-dump.3' renamed 'fastq-dump.3.2.1' -> 'fastq-dump' removed 'fastq-load.3' renamed 'fastq-load.3.2.1' -> 'fastq-load' removed 'general-loader.3' renamed 'general-loader.3.2.1' -> 'general-loader' removed 'helicos-load.3' renamed 'helicos-load.3.2.1' -> 'helicos-load' removed 'illumina-dump.3' renamed 'illumina-dump.3.2.1' -> 'illumina-dump' removed 'illumina-load.3' renamed 'illumina-load.3.2.1' -> 'illumina-load' removed 'kar.3' renamed 'kar.3.2.1' -> 'kar' removed 'kar+.3' renamed 'kar+.3.2.1' -> 'kar+' removed 'kar+meta.3' renamed 'kar+meta.3.2.1' -> 'kar+meta' removed 'kdb-index.3' renamed 'kdb-index.3.2.1' -> 'kdb-index' removed 'kdbmeta.3' renamed 'kdbmeta.3.2.1' -> 'kdbmeta' removed 'latf-load.3' renamed 'latf-load.3.2.1' -> 'latf-load' removed 'make-read-filter.3' renamed 'make-read-filter.3.2.1' -> 'make-read-filter' removed 'md5cp.3' renamed 'md5cp.3.2.1' -> 'md5cp' removed 'meta-cmp.3' renamed 'meta-cmp.3.2.1' -> 'meta-cmp' removed 'meta-copy.3' renamed 'meta-copy.3.2.1' -> 'meta-copy' removed 'meta-repair.3' renamed 'meta-repair.3.2.1' -> 'meta-repair' removed 'ngs-pileup.3' renamed 'ngs-pileup.3.2.1' -> 'ngs-pileup' removed 'pacbio-correct.3' renamed 'pacbio-correct.3.2.1' -> 'pacbio-correct' removed 'pacbio-load.3' renamed 'pacbio-load.3.2.1' -> 'pacbio-load' removed 'pacbio-loadxml.3' renamed 'pacbio-loadxml.3.2.1' -> 'pacbio-loadxml' removed 'pileup-stats.3' renamed 'pileup-stats.3.2.1' -> 'pileup-stats' removed 'prefetch.3' renamed 'prefetch.3.2.1' -> 'prefetch' removed 'rcexplain.3' renamed 'rcexplain.3.2.1' -> 'rcexplain' removed 'read-filter-redact.3' renamed 'read-filter-redact.3.2.1' -> 'read-filter-redact' removed 'ref-variation.3' renamed 'ref-variation.3.2.1' -> 'ref-variation' removed 'rowwritetest.3' renamed 'rowwritetest.3.2.1' -> 'rowwritetest' removed 'sam-dump.3' renamed 'sam-dump.3.2.1' -> 'sam-dump' removed 'samview.3' renamed 'samview.3.2.1' -> 'samview' removed 'samview-util.3' renamed 'samview-util.3.2.1' -> 'samview-util' removed 'schema-replace.3' renamed 'schema-replace.3.2.1' -> 'schema-replace' removed 'sff-dump.3' renamed 'sff-dump.3.2.1' -> 'sff-dump' removed 'sff-load.3' renamed 'sff-load.3.2.1' -> 'sff-load' removed 'sharq.3' renamed 'sharq.3.2.1' -> 'sharq' removed 'sortreadtest.3' renamed 'sortreadtest.3.2.1' -> 'sortreadtest' removed 'sra-info.3' renamed 'sra-info.3.2.1' -> 'sra-info' removed 'sra-pileup.3' renamed 'sra-pileup.3.2.1' -> 'sra-pileup' removed 'sra-search.3' renamed 'sra-search.3.2.1' -> 'sra-search' removed 'sra-sort.3' renamed 'sra-sort.3.2.1' -> 'sra-sort' removed 'sra-sort-cg.3' renamed 'sra-sort-cg.3.2.1' -> 'sra-sort-cg' removed 'sra-stat.3' renamed 'sra-stat.3.2.1' -> 'sra-stat' removed 'srapath.3' renamed 'srapath.3.2.1' -> 'srapath' removed 'sratools.3' renamed 'sratools.3.2.1' -> 'sratools' removed 'srf-load.3' renamed 'srf-load.3.2.1' -> 'srf-load' removed 'test-download.3' renamed 'test-download.3.2.1' -> 'test-download' removed 'test-read-write-cursor.3' renamed 'test-read-write-cursor.3.2.1' -> 'test-read-write-cursor' removed 'test-sra.3' renamed 'test-sra.3.2.1' -> 'test-sra' removed 'testld.3' renamed 'testld.3.2.1' -> 'testld' removed 'txt2kdb.3' renamed 'txt2kdb.3.2.1' -> 'txt2kdb' removed 'var-expand.3' renamed 'var-expand.3.2.1' -> 'var-expand' removed 'vdb-config.3' renamed 'vdb-config.3.2.1' -> 'vdb-config' removed 'vdb-copy.3' renamed 'vdb-copy.3.2.1' -> 'vdb-copy' removed 'vdb-decrypt.3' renamed 'vdb-decrypt.3.2.1' -> 'vdb-decrypt' removed 'vdb-diff.3' renamed 'vdb-diff.3.2.1' -> 'vdb-diff' removed 'vdb-dump.3' renamed 'vdb-dump.3.2.1' -> 'vdb-dump' removed 'vdb-encrypt.3' renamed 'vdb-encrypt.3.2.1' -> 'vdb-encrypt' removed 'vdb-lock.3' renamed 'vdb-lock.3.2.1' -> 'vdb-lock' removed 'vdb-sql.3' renamed 'vdb-sql.3.2.1' -> 'vdb-sql' removed 'vdb-unlock.3' renamed 'vdb-unlock.3.2.1' -> 'vdb-unlock' removed 'vdb-validate.3' renamed 'vdb-validate.3.2.1' -> 'vdb-validate' mkdir debian/tmp/usr/lib/sra-toolkit mv debian/tmp/usr/bin/sratools debian/tmp/usr/lib/sra-toolkit for x in debian/tmp/usr/bin/*-orig; do \ mv -v $x debian/tmp/usr/lib/sra-toolkit ; \ ln -snfv ../lib/sra-toolkit/sratools ${x%-orig} ; \ done renamed 'debian/tmp/usr/bin/fasterq-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/fasterq-dump-orig' 'debian/tmp/usr/bin/fasterq-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/fastq-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/fastq-dump-orig' 'debian/tmp/usr/bin/fastq-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/prefetch-orig' -> 'debian/tmp/usr/lib/sra-toolkit/prefetch-orig' 'debian/tmp/usr/bin/prefetch' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/sam-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/sam-dump-orig' 'debian/tmp/usr/bin/sam-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/sra-pileup-orig' -> 'debian/tmp/usr/lib/sra-toolkit/sra-pileup-orig' 'debian/tmp/usr/bin/sra-pileup' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/srapath-orig' -> 'debian/tmp/usr/lib/sra-toolkit/srapath-orig' 'debian/tmp/usr/bin/srapath' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/vdb-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/vdb-dump-orig' 'debian/tmp/usr/bin/vdb-dump' -> '../lib/sra-toolkit/sratools' dh_install # remove susipcious file which is not executable and conflicts with package magic rm -f debian/*/usr/bin/magic pybuild --install --name ngs -d ngs/ngs-python I: pybuild base:311: dh_auto_install --buildsystem=cmake --builddirectory=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ngs/build --destdir=/<<PKGBUILDDIR>>/debian/python3-ngs -- dh_auto_install: error: "debian/control" not found. Are you sure you are in the correct directory? Compilation failed in require at /usr/bin/dh_auto_install line 12. BEGIN failed--compilation aborted at /usr/bin/dh_auto_install line 12. E: pybuild pybuild:389: install: plugin cmake failed with: exit code=25: dh_auto_install --buildsystem=cmake --builddirectory=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ngs/build --destdir=/<<PKGBUILDDIR>>/debian/python3-ngs -- make[1]: *** [debian/rules:113: override_dh_install] Error 13 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:24: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- The above is just how the build ends and not necessarily the most relevant part. If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202504/ 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 could not 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:sra-sdk, so that this is still visible in the BTS web page for this package. Notes: * When a package is built with the nocheck profile, it means: - DEB_BUILD_OPTIONS=nocheck (the tests should be skipped during the build) - DEB_BUILD_PROFILES=nocheck (Build-Depends marked <!nocheck> are not installed) - The contents of the package is allowed to be different than normal * This category of bugs was going to be RC for trixie, but according to the Release Managers it's a little bit late in the release cycle to introduce a bunch of RC bugs of this type. * In addition to the above, this package also fails when using DEB_BUILD_OPTIONS=nocheck alone. In this mode: - DEB_BUILD_OPTIONS=nocheck (the tests should be skipped during the build) - Build-Depends marked <!nocheck> are installed as normal - The contents of the package should not change compared to a regular build Thanks.
--- End Message ---
--- Begin Message ---Source: sra-sdk Source-Version: 3.2.1+dfsg-4 Done: Aaron M. Ucko <u...@debian.org> We believe that the bug you reported is fixed in the latest version of sra-sdk, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1103...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Aaron M. Ucko <u...@debian.org> (supplier of updated sra-sdk package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 16 Apr 2025 15:44:48 -0400 Source: sra-sdk Architecture: source Version: 3.2.1+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Aaron M. Ucko <u...@debian.org> Closes: 1097930 1103330 Changes: sra-sdk (3.2.1+dfsg-4) unstable; urgency=medium . * debian/patches: Add two patches for GCC 15 support. (Closes: #1097930.) - fix_bm_for_gcc15.patch: BitMagic cherry-pick, location adjusted. - include_cstdint_for_gcc15.patch: Compensate for libstdc++ changes. * debian/rules: Explicitly direct pybuild to use distutils. It can otherwise misfire when bypassing the test suite, which includes a setup.py run. (Closes: #1103330.) Checksums-Sha1: 9bb1373692e5416ab7ff4ecdb96472a05e98688f 3003 sra-sdk_3.2.1+dfsg-4.dsc e84f2a990c66e8867b8acc6e097901129a731cc0 3795792 sra-sdk_3.2.1+dfsg-4.debian.tar.xz Checksums-Sha256: f928e99797f68e5a464ea3f3ee60716196b895f423722631a9391efbfe6b7c80 3003 sra-sdk_3.2.1+dfsg-4.dsc 9d5e6496c6ccc9526f92bc87837cde3c43f7ae93a473020853a925fda8c6a19a 3795792 sra-sdk_3.2.1+dfsg-4.debian.tar.xz Files: c222dfad9ddf169202bd7c93b27fb4d6 3003 science optional sra-sdk_3.2.1+dfsg-4.dsc c93869217cc2e8c70947a79164a326be 3795792 science optional sra-sdk_3.2.1+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmgACPsACgkQHnCRsfFK ZKKavxAAjZX6UV6fijbO1V8ttZrC/7ZHvvSh3cUvQBkBU295xF/b73w7I/S9lm0V BxlUtHWZNTGkUlYI9nA5jFp01BJFXM5xLI5URpaAhszxDLv/jLsy1D3WdRx19hac Xevep3sFZH4CLg66+wfUuu1Y9tTV9bgLC/28BDMcCc7ObaazSzfhGPHWRO/Bpil3 evqKmIvfzNeIJwHxIJpqycexxFy37VmbyHoQeRTn/jL/NiO5rZxEMnSL2yLuw322 ghy3vgPLjoRwwJrBCv3UzBwTLDYboSAhOLiIGeqQ0HKmCwOCkI/y+WwUAMwwSDEO mu2uqK8DyNv+Zfb4k6SwtX+QygTOwrLXzp+Yb1MyQ1faxfB24A5f5tJ3uAkp2SI9 h7pezc0gPU7eMtNaLvCzsmTxIGKaN+qRyHxbawNN9iesJoSN5THzV/BF6H2ZHr1N GkquSidOfeMxaiaWefieKW23Dx3Z8j4UmrZfgO+sUjhWscYw9MzrIalU5fhbVQ3x DchWwfJFJ5g2OHy8gmufZWAKaV/sr+Tak3clwJiLPpEV4gFAXS09HA8tV03E0EmI uIkRaCfoexLqQaugNtRH1M2mLPOLN7O1Q3v2cCpV4Yk436aG27G5lN5+CrPBDbLM 3Ly8Zuqxp8ThaGVTMI+g8fd5QKs0qlo24b2Nx7g0eGMhMl2fHLg= =hyud -----END PGP SIGNATURE-----
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