On 3/26/19 9:46 PM, Lucas Nussbaum wrote: > Source: cnvkit > Version: 0.9.5-2 > Severity: serious > Tags: buster sid > User: debian...@lists.debian.org > Usertags: qa-ftbfs-20190325 qa-ftbfs > Justification: FTBFS in buster on amd64 > > Hi, > > During a rebuild of all packages in buster (in a buster chroot, not a > sid chroot), your package failed to build on amd64.
I just did a try on buster. It succeeded first time, not on a second rebuild (with same error). I fixed and tested on buster with new patch d/patches/controldir. Git is up-to-date and in UNRELEASED state. As we are in freeze, should we ask release team to unblock transition and then push to unstable? Though not a bug issue, bug could be forwarded upstream as it raises an error to use an existing dir. Olivier > > Relevant part (hopefully): >> make[2]: Entering directory '/<<PKGBUILDDIR>>/test' >> python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv >> picard/p2-5_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv >> picard/p2-9_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv >> picard/p2-20_5.antitargetcoverage.csv -d build/ >> python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/ >> python3 ../cnvkit.py import-picard picard/p2-5_5.antitargetcoverage.csv -d >> build/ >> python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ >> WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' >> WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' >> WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' >> Created directory build/ >> Traceback (most recent call last): >> File "../cnvkit.py", line 13, in <module> >> args.func(args) >> File "/<<PKGBUILDDIR>>/cnvlib/commands.py", line 1368, in >> _cmd_import_picard >> os.mkdir(args.output_dir) >> FileExistsError: [Errno 17] File exists: 'build/' >> Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions >> Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions >> make[2]: *** [Makefile:58: build/p2-5_5.targetcoverage.cnn] Error 1 > The full build log is available from: > http://qa-logs.debian.net/2019/03/25/cnvkit_0.9.5-2_testing.log > > A list of current common problems and possible solutions is available at > http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! > > About the archive rebuild: The rebuild was done on EC2 VM instances from > Amazon Web Services, using a clean, minimal and up-to-date chroot. Every > failed build was retried once to eliminate random failures. > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438