[Debian-med-packaging] Bug#925568: Bug#925568: cnvkit: FTBFS: FileExistsError: [Errno 17] File exists: 'build/'

[Olivier Sallou]

On 3/26/19 9:46 PM, Lucas Nussbaum wrote:
> Source: cnvkit
> Version: 0.9.5-2
> Severity: serious
> Tags: buster sid
> User: debian-qa at 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.
>
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-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

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