Bug#861496: python-pysam: accesses network during build

[Andreas Tille]

Hi,

when using sbuild I was able to reproduce the issue which does not
happen in pbuilder :-(.  I'm going to exclude the said test and will
do a source only upload to make sure the issue will be really fixed.

Kind regards

Andreas.

-- 
http://fam-tille.de

Bug#861496: python-pysam: accesses network during build

[Santiago Vila]

Package: src:python-pysam
Version: 0.10.0+ds-1

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -A"
but it failed:


[...]
 debian/rules build-indep
dh build-indep --with python2,python3 --buildsystem=pybuild
   dh_testdir -i -O--buildsystem=pybuild
   dh_update_autotools_config -i -O--buildsystem=pybuild
   dh_auto_configure -i -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:184: python3.5 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None

[... snipped ...]

testParsing (tabix_test.VCFFromVCFTest_3) ... ok
testConnecting (tabix_test.VCFFromVCFTest_4) ... ok
testParsing (tabix_test.VCFFromVCFTest_4) ... ok
testConnecting (tabix_test.VCFFromVCFTest_5) ... ok
testParsing (tabix_test.VCFFromVCFTest_5) ... ok
testConnecting (tabix_test.VCFFromVCFTest_6) ... ok
testParsing (tabix_test.VCFFromVCFTest_6) ... ok
testConnecting (tabix_test.VCFFromVCFTest_7) ... ok
testParsing (tabix_test.VCFFromVCFTest_7) ... ok
testConnecting (tabix_test.VCFFromVCFTest_8) ... ok
testParsing (tabix_test.VCFFromVCFTest_8) ... ok
testConnecting (tabix_test.VCFFromVCFTest_9) ... ok
testParsing (tabix_test.VCFFromVCFTest_9) ... ok
testConnecting (tabix_test.VCFFromVCFTest_issue85) ... ok
testParsing (tabix_test.VCFFromVCFTest_issue85) ... ok
testConnecting (tabix_test.VCFFromVCFTest_vcf_v42) ... ok
testParsing (tabix_test.VCFFromVCFTest_vcf_v42) ... ok
test_samtools_python.test_idxstats_parse_split_lines ... ok
test_samtools_python.test_bedcov_split_lines ... ok
test_samtools_python.test_idxstats_parse ... ok
test_samtools_python.test_bedcov ... ok

==
ERROR: testFTPView (faidx_test.TestRemoteFileFTP)
--
Traceback (most recent call last):
  File "/<>/python-pysam-0.10.0+ds/tests/faidx_test.py", line 229, in 
testFTPView
with pysam.Fastafile(self.url) as f:
  File "pysam/libcfaidx.pyx", line 114, in pysam.libcfaidx.FastaFile.__cinit__ 
(pysam/libcfaidx.c:2349)
  File "pysam/libcfaidx.pyx", line 155, in pysam.libcfaidx.FastaFile._open 
(pysam/libcfaidx.c:3205)
OSError: could not open file 
`ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa`

--
Ran 918 tests in 1230.931s

FAILED (errors=1)
(0, 0)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd 
/<>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build; python3.5 -m 
nose 
dh_auto_test: pybuild --test -i python{version} -p 3.5 returned exit code 13
debian/rules:38: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25
make[1]: Leaving directory '/<>/python-pysam-0.10.0+ds'
debian/rules:32: recipe for target 'build-indep' failed
make: *** [build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2


Maybe this usually works because the ftp server is usually up,
but in either case, packages must not try network access during build.

Thanks.