Your message dated Tue, 12 Sep 2023 19:08:21 +0000 with message-id <e1qg8kh-00euly...@fasolo.debian.org> and subject line Bug#1006336: fixed in trinityrnaseq 2.15.1+dfsg-1 has caused the Debian Bug report #1006336, regarding trinityrnaseq: autopkgtest regression in testing: segmentation fault 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.) -- 1006336: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006336 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: trinityrnaseq Version: 2.13.2+dfsg-3 Severity: serious Dear maintainer, Somewhere around the end of January 2022, the autopkgtest of you package started to fail on amd64. Paul https://ci.debian.net/data/autopkgtest/testing/amd64/t/trinityrnaseq/19291359/log.gz All commands completed successfully. :-) ** Harvesting all assembled transcripts into a single multi-fasta file... Thursday, February 17, 2022: 04:50:39 CMD: find /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/Trinity.tmp * [Thu Feb 17 04:50:39 2022] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa 2 Error encountered:: <!---- CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa 2 2>tmp.5696.1645073439.stderr Errmsg: CMD: salmon --no-version-check index -t Trinity.tmp.fasta -i Trinity.tmp.fasta.salmon.idx -k 25 -p 2 > _salmon.7661.stderr 2>&1 CMD: salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.idx -l U -r /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa -o salmon_outdir -p 2 --minAssignedFrags 1 --validateMappings > _salmon.7661.stderr 2>&1 Error, cmd: salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.idx -l U -r /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa -o salmon_outdir -p 2 --minAssignedFrags 1 --validateMappings > _salmon.7661.stderr 2>&1 failed with msg: ### salmon (selective-alignment-based) v1.6.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { Trinity.tmp.fasta.salmon.idx } ### [ libType ] => { U } ### [ unmatedReads ] => { /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa } ### [ output ] => { salmon_outdir } ### [ threads ] => { 2 } ### [ minAssignedFrags ] => { 1 } ### [ validateMappings ] => { } Logs will be written to salmon_outdir/logs [2022-02-17 04:50:39.427] [jointLog] [info] setting maxHashResizeThreads to 2 ----------------------------------------- | Loading contig table | Time = 192.25 us ----------------------------------------- size = 637 ----------------------------------------- | Loading contig offsets | Time = 33.61 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 11.282 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 122.06 us ----------------------------------------- size = 246121 Number of ones: 636 Number of ones per inventory item: 512 Inventory entries filled: 2 [2022-02-17 04:50:39.427] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2022-02-17 04:50:39.427] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2022-02-17 04:50:39.427] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. [2022-02-17 04:50:39.427] [jointLog] [info] parsing read library format [2022-02-17 04:50:39.427] [jointLog] [info] There is 1 library. [2022-02-17 04:50:39.427] [jointLog] [info] Loading pufferfish index [2022-02-17 04:50:39.427] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig boundaries | Time = 618.3 us ----------------------------------------- size = 246121 ----------------------------------------- | Loading sequence | Time = 49.733 us ----------------------------------------- size = 230857 ----------------------------------------- | Loading positions | Time = 398.03 us ----------------------------------------- size = 254072 ----------------------------------------- | Loading reference sequence | Time = 48.899 us ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 17.842 us ----------------------------------------- [2022-02-17 04:50:39.429] [jointLog] [info] done Segmentation fault Error, cmd: salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.idx -l U -r /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa -o salmon_outdir -p 2 --minAssignedFrags 1 --validateMappings > _salmon.7661.stderr 2>&1 died with ret (35584) at /usr/lib/trinityrnaseq/PerlLib/Process_cmd.pm line 19. Process_cmd::process_cmd("salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.i"...) called at /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl line 40 eval {...} called at /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl line 39 main::run_cmd_capture_stderr("salmon --no-version-check quant -i Trinity.tmp.fasta.salmon.i"..., "_salmon.7661.stderr") called at /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl line 27 ---> Error, cmd: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/trinity_out_dir/both.fa 2 2>tmp.5696.1645073439.stderr died with ret 65280 at /usr/lib/trinityrnaseq/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x56312e81af88)) called at /usr/lib/trinityrnaseq/Trinity line 4127 main::salmon_expr_filtering("Trinity.tmp.fasta", "/tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinity"..., "/tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinity"...) called at /usr/lib/trinityrnaseq/Trinity line 1460 make[1]: *** [Makefile:2: test] Error 255 make[1]: Leaving directory '/tmp/autopkgtest-lxc.ayemar40/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline' make: *** [Makefile:18: test] Error 2
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--- Begin Message ---Source: trinityrnaseq Source-Version: 2.15.1+dfsg-1 Done: Michael R. Crusoe <cru...@debian.org> We believe that the bug you reported is fixed in the latest version of trinityrnaseq, 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 1006...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael R. Crusoe <cru...@debian.org> (supplier of updated trinityrnaseq 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: Tue, 12 Sep 2023 17:12:30 +0200 Source: trinityrnaseq Architecture: source Version: 2.15.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <cru...@debian.org> Closes: 1004773 1006336 Changes: trinityrnaseq (2.15.1+dfsg-1) unstable; urgency=medium . [ Michael R. Crusoe ] * d/watch: update for GitHub API breakage . [ Andreas Tille ] * Standards-Version: 4.6.2 (routine-update) . [ Michael R. Crusoe ] * d/control: update homepage * d/control: remove unused test-deps * d/source/lintian-overrides: note that we clean up the config.{log,status} automatically. * d/patches/R_4.2_fix: fix for R 4.2.x+. Closes: #1006336, #1004773 Checksums-Sha1: b85a25f43fa002c684fe19b894768b619e898ab3 2321 trinityrnaseq_2.15.1+dfsg-1.dsc 0857b38a12ed7b84799ff870397a752991b8d618 307318092 trinityrnaseq_2.15.1+dfsg.orig.tar.xz 5b659b883d9f773f0fe36c4381e85a5c2cee2ad7 39144 trinityrnaseq_2.15.1+dfsg-1.debian.tar.xz 2800a1c1cde54b36b49f754cb872362c12415e31 14570 trinityrnaseq_2.15.1+dfsg-1_source.buildinfo Checksums-Sha256: 23118c6ad566f3e0c45e4f8a21c3b3b8c5053c7cee618864e1be35caf9d6d6ac 2321 trinityrnaseq_2.15.1+dfsg-1.dsc b4892295ab2e92cf77b3f1022dac79945238436a81210538446e88b93e71c362 307318092 trinityrnaseq_2.15.1+dfsg.orig.tar.xz d415c0e6d5ee17c75eeccc24c24efb73e62f0314abf28bc03ce602075905332a 39144 trinityrnaseq_2.15.1+dfsg-1.debian.tar.xz 14ab5f9b254f1c93164311bfa4ae01fad1aead082c484e63427511929cfad00d 14570 trinityrnaseq_2.15.1+dfsg-1_source.buildinfo Files: b1ff11b5e062a611ad861ee0b075ecfc 2321 science optional trinityrnaseq_2.15.1+dfsg-1.dsc 5c0c9a8ab99b6f2593bea6029d56dfa3 307318092 science optional trinityrnaseq_2.15.1+dfsg.orig.tar.xz db7f6938c2dc4c31d29c9243de15ca70 39144 science optional trinityrnaseq_2.15.1+dfsg-1.debian.tar.xz 793b22a97a5d84f983a66312c992e7d3 14570 science optional trinityrnaseq_2.15.1+dfsg-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmUAgScACgkQPCZ2P2xn 5uIHTQ//YCFTAi5DDyAetT28J/Y7su6ssdLcsvAddbPdR6LRMZ9cGpsonA67zxa2 zDvA/moWNXBkJnkXnTsYlcuoGsWpEBI5N1bbLHPFBqYb+okyHYaEu3qII7w+dEpu 7+33CdAM7C7lPizEujGrF/HrIDM+N0ccLyuCvJdvqWwl8djxS+GKBRL9iiR/8shU OYDnufJXwxIQ9xWE8L2vwyfRA9oWsofDcKAqWqHEMaOCcKJSNAgiokXMOgbzdWRm OakbqZLRFYvshMWCwybPy1g1lgH6f+3iksNXNku6XdHbiC0aB8d6sPOJ8dwnYsiF GnussVBMWHpn4QVDa8bnzf8djZf/jaak7a+tDzULUXdSodM+XRBfDo0txFTsN/qY iYMBQ7aGzlOXgKg4wdDH1AVds1SzVvGfy7/YaB2HIuSpZaBLr8Hk5XQHmspZ6ehi ozUkEIGFFqzUlp6803nfoWhc+zjlCqErolanB8MpaWG530W7fjqkuwS/7igU4fvU PSr9KBZ+LV9bS9w1CvzZyZmBC8ko3Nev605uJwPjBIS9wsrM5nwk9EcOyYOtAout cATq4PCAwvn59iqU8Qu+DXPQ4gqYc7JeP6U1CjalMbZJIBxFiyV6xTGe83zlV+n5 yqVu6Kra7ByEaV89v7ZiFLXkYyEJjzkf/Z2FZjElVXwJ3y4xGaw= =/e2O -----END PGP SIGNATURE-----
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