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.
snakemake_3.7.1+dfsg-1_amd64-20161116T014246Z.gz
Description: application/gzip
snakemake_3.7.1+dfsg-1_amd64-20161123T013257Z.gz
Description: application/gzip
snakemake_3.7.1+dfsg-1_amd64-20161123T013456Z.gz
Description: application/gzip
snakemake_3.7.1+dfsg-1_amd64-20161125T220118Z.gz
Description: application/gzip
