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

[Lucas Nussbaum]

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.

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.