Your message dated Thu, 28 Mar 2019 11:03:50 +0000
with message-id <[email protected]>
and subject line Bug#925568: fixed in cnvkit 0.9.5-3
has caused the Debian Bug report #925568,
regarding cnvkit: FTBFS: FileExistsError: [Errno 17] File exists: 'build/'
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.
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--
925568: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925568
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: cnvkit
Version: 0.9.5-2
Severity: serious
Tags: buster sid
User: [email protected]
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.
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.
--- End Message ---
--- Begin Message ---
Source: cnvkit
Source-Version: 0.9.5-3
We believe that the bug you reported is fixed in the latest version of
cnvkit, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <[email protected]> (supplier of updated cnvkit 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 27 Mar 2019 08:00:39 +0000
Source: cnvkit
Binary: cnvkit
Architecture: source amd64
Version: 0.9.5-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Olivier Sallou <[email protected]>
Description:
cnvkit - Copy number variant detection from targeted DNA sequencing
Closes: 925568
Changes:
cnvkit (0.9.5-3) unstable; urgency=medium
.
* Fix buster rebuilds (Closes: #925568)
d/patches/controldir.patch
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