Your message dated Thu, 30 Apr 2020 20:35:42 +0000 with message-id <e1jufui-0001fy...@fasolo.debian.org> and subject line Bug#958090: fixed in diamond-aligner 0.9.32-2 has caused the Debian Bug report #958090, regarding diamond-aligner 0.9.31-1 fails on architectures where char is unsigned 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.) -- 958090: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=958090 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: diamond-aligner Version: 0.9.31-1 Severity: serious Tags: ftbfs Control: affects -1 src:proteinortho https://ci.debian.net/data/autopkgtest/testing/arm64/p/proteinortho/4965864/log.gz https://buildd.debian.org/status/package.php?p=proteinortho&suite=sid ... make -j4 test make[1]: Entering directory '/<<PKGBUILDDIR>>' [TEST] Clean up all test files... [TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped) [TEST] Clean up all test files... [1/12] -p=blastp+ test: passed [2/12] -p=blastp+ synteny (PoFF) test: tput: No value for $TERM and no -T specified [STDERR] Error: wrong fromat... Please make sure you only provide *.blast-graph or *.proteinortho-graph files as input... Died at .//src/BUILD/Linux_aarch64/proteinortho_summary.pl line 117, <$FH> line 2. USAGE: proteinortho2html.pl <myproject.proteinortho> (<fasta1> <fasta2> ...) the first argument points to the proteinortho output (tsv)-file. Any further (optional) files should be fasta files, for conversion of the identifier to a proper gene name/ describtion. The HTML output is printed to stdout, use '>' to write the html output to a file. passed [3/12] -p=diamond test: Parameter-vector : (version=6.0.15,step=0,verbose=0,debug=1,exactstep3=0,synteny=0,duplication=2,cs=3,alpha=0.5,connectivity=0.1,cpus=4,evalue=1e-05,purity=1e-07,coverage=50,identity=25,blastmode=diamond,sim=0.95,report=3,keep=0,force=1,selfblast=0,twilight=0,singles=0,clean=0,blastOptions=,nograph=0,xml=0,desc=0,tmp_path=./proteinortho_cache_test_diamond/,blastversion=unknown,binpath=,makedb=diamond makedb --in,blast=,jobs_todo=10,project=test_diamond,po_path=.//src/BUILD/Linux_aarch64,run_id=,threads_per_process=1,useMcl=0,freemem=-1) [1;31m[Error][0m [1;33m diamond failed. The most likely errorsources of this are: - no space left on device error. - outdated diamond, please update diamond or consider another -p algorithm. - the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas' - maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for diamond? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'. [0m (If you cannot solve this error, please send a report to incoming+paulklemm-phd-proteinortho-7278443-iss...@incoming.gitlab.com including the parameter-vector above or visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes for more help. Further more all mails to lech...@staff.uni-marburg.de are welcome) Perl exited with active threads: 3 running and unjoined 0 finished and unjoined 0 running and detached Error, could not open file test_diamond.proteinortho.tsv: No such file or directory at ./src/chk_test.pl line 6. make[1]: *** [Makefile:253: test_step2] Error 2
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--- Begin Message ---Source: diamond-aligner Source-Version: 0.9.32-2 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of diamond-aligner, 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 958...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated diamond-aligner 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: SHA256 Format: 1.8 Date: Thu, 30 Apr 2020 21:43:33 +0200 Source: diamond-aligner Architecture: source Version: 0.9.32-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Closes: 958090 958515 Changes: diamond-aligner (0.9.32-2) unstable; urgency=medium . * Fixed different build issues Closes: #958515, #958090 * Upstream says diamond-aligner does not run on 32bit systems https://github.com/bbuchfink/diamond/issues/347#issuecomment-622051316 Checksums-Sha1: 1973d1e038a0d934e902775e7d456a2b595ae00e 2202 diamond-aligner_0.9.32-2.dsc e1a7c7a86f1ba85a8818e3e4c5c29b895242e62f 131260 diamond-aligner_0.9.32-2.debian.tar.xz ed9d0afd750d5d13809ce3d3c36b5a70539a28ca 6823 diamond-aligner_0.9.32-2_amd64.buildinfo Checksums-Sha256: da8eec3012c3c001633a9f744fbcbe57ee633f6a6ce43b0bc504c59176244537 2202 diamond-aligner_0.9.32-2.dsc c2fd3b38a8a7f2bbf49a1f540c83c1a84d6603ca97b17e8bb8227e7ecf2c3c2f 131260 diamond-aligner_0.9.32-2.debian.tar.xz 0876234037fac5f589249caa65c8fe6a2f4e4b0f2ec9390e982e472a22a69abb 6823 diamond-aligner_0.9.32-2_amd64.buildinfo Files: 769a315f5986f88d58b7c91b7298fe5f 2202 science optional diamond-aligner_0.9.32-2.dsc ae1353df8b261f1c334f94cffd162d90 131260 science optional diamond-aligner_0.9.32-2.debian.tar.xz 03feaffbf0da20107ad3c916e1313f65 6823 science optional diamond-aligner_0.9.32-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl6rLhsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGpzxAAi3tKZ2Ah74aHr9E8mvvewt0BCfZfuxt2 KT2hwUc7eSZ9DB/KQRId87i4ssgAstNiJ232gPks0ugNxqgHgIDhkJxPH27cy4y5 Cs0T1LbZXQEg+KJAw2H4IsFRx0hnxF/SK88gfLnPJAdScbso8VEsu1ksuqN2N0ND YHDMLdhkHSeExru8/QuJsBrxrR7PR7SQGqYkzwCidNJRBoK7Qu5w7iF6hiqANneH lZE59TMdyLouBqk3LC7AE+z3ccZx+QHrcCsmS9A/3Vyh1S6W+g/h2zVf1T6SUISc r6vMf8uYinOiSyyGsTBHVLGeChwsXgLnbUrCq+AYFCowUtpxu9++HRLpCbYpKed2 CDZ3oGzq6Q+cZ68krgfC8tCatLLtK1w/EU3aKngf0oWpPwJWS5FNlYugU8krB5gC VnkbvB7w+9wKrHIDkMqWXy+NwjBl0igeZLVLrdbS20/a75RlXUl3T2JAO/BydqEy ew/dylkiK6UJ9r7iLCIXwTsVUqjq2IETxdEcaefBJHANWdKzavpRaraMyTQTHGXS PbqAuS1I5BwQqWFR43BWUlmOkgVwQCMI4NksWre8HF9UoK4SFJMzk1JpeUX7M/lG 2wob4rPa7iKT+7D6229YsWqVVPMIziulrT+/lydzaWjm49mslsdpUsD5kYCPhgPf RdmUiN6zMZk= =x7XR -----END PGP SIGNATURE-----
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