[Debian-med-packaging] Bug#845737: snakemake: FTBFS randomly (sbuild hangs)

[Santiago Vila]

Package: src:snakemake
Version: 3.7.1+dfsg-1
Severity: serious

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --with python3,sphinxdoc --buildsystem=pybuild --parallel
   dh_testdir -i -O--buildsystem=pybuild -O--parallel
   dh_update_autotools_config -i -O--buildsystem=pybuild -O--parallel
   dh_auto_configure -i -O--buildsystem=pybuild -O--parallel
I: pybuild base:184: python3.5 setup.py config 
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/snakemake-3.7.1+dfsg'
dh_auto_build
I: pybuild base:184: /usr/bin/python3 setup.py build 
running build
running build_py

[... snipped ...]

	wildcards: sample=a
Subsequent jobs will be added dynamically depending on the output of this rule
rule random_clusters:
	input: c.init
	output: c_clusters/cluster_{*} (dynamic)
	wildcards: sample=c
Subsequent jobs will be added dynamically depending on the output of this rule
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
Dynamically updating jobs
4 of 11 steps (36%) done
rule concatenate_clusters:
	input: b_clusters/cluster_0, b_clusters/cluster_2, b_clusters/cluster_1
	output: b_final
	wildcards: sample=b
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
5 of 11 steps (45%) done
Dynamically updating jobs
6 of 10 steps (60%) done
rule concatenate_clusters:
	input: c_clusters/cluster_1, c_clusters/cluster_2, c_clusters/cluster_0
	output: c_final
	wildcards: sample=c
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
7 of 10 steps (70%) done
Dynamically updating jobs
8 of 9 steps (89%) done
rule concatenate_clusters:
	input: a_clusters/cluster_0, a_clusters/cluster_1, a_clusters/cluster_2
	output: a_final
	wildcards: sample=a
/bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory
9 of 9 steps (100%) done
localrule all:
	input: a_final, b_final, c_final
10 of 9 steps (111%) done
E: Build killed with signal TERM after 60 minutes of inactivity
--------------------------------------------------------------------------------

This happens randomly. Sometimes it fails, sometimes it does not.
When it fails, it does in this way, and sbuild has to terminate the process.

I attach four different build logs.

Thanks.
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