Package: src:snakemake Version: 3.9.0+dfsg-1 Severity: serious Dear maintainer:
I tried to build this package 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
dh_testdir -i -O--buildsystem=pybuild
dh_update_autotools_config -i -O--buildsystem=pybuild
dh_autoreconf -i -O--buildsystem=pybuild
dh_auto_configure -i -O--buildsystem=pybuild
I: pybuild base:184: python3.5 setup.py config
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/snakemake-3.9.0+dfsg'
dh_auto_build
I: pybuild base:184: /usr/bin/python3 setup.py build
running build
[... snipped ...]
2 four
2 one
2 three
2 two
9
snakemake.logging: INFO: rule one:
input: a
output: 1.a
wildcards: sample=a
snakemake.logging: INFO:
snakemake.logging: INFO: rule one:
input: b
output: 1.b
wildcards: sample=b
snakemake.logging: INFO:
snakemake.logging: INFO: 1 of 9 steps (11%) done
snakemake.logging: INFO: rule two:
input: 1.a
output: 2.a
wildcards: sample=a
snakemake.logging: INFO:
snakemake.logging: INFO: 2 of 9 steps (22%) done
snakemake.logging: INFO: rule two:
input: 1.b
output: 2.b
wildcards: sample=b
snakemake.logging: INFO:
snakemake.logging: WARNING: Removing temporary output file 1.a.
snakemake.logging: INFO: 3 of 9 steps (33%) done
snakemake.logging: ERROR: WorkflowError:
File 2.a seems to be a broken symlink.
snakemake.logging: WARNING: Waiting at most 3 seconds for missing files.
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 70 tests in 36.186s
FAILED (errors=1)
Error in job two while creating output file 2.b.
MissingOutputException in line 9 of
/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/test_symlink_temp/Snakefile:
Missing files after 3 seconds:
2.b
E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: cd
/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m
nose tests
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned
exit code 13
debian/rules:16: recipe for target 'build-indep' failed
make: *** [build-indep] Error 25
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
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This is just how the build ends. I attach three different build logs.
They happened while trying to build the package 100 times, so the failure
rate is about 3%. If you try to reproduce this, please try a lot of times.
Thanks.
snakemake_3.9.0+dfsg-1_amd64-20161219T213843Z.gz
Description: application/gzip
snakemake_3.9.0+dfsg-1_amd64-20161219T214637Z.gz
Description: application/gzip
snakemake_3.9.0+dfsg-1_amd64-20161219T215659Z.gz
Description: application/gzip
