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Re: python-biopython: FTBFS: Test DSSP generation from MMCIF with non-standard residues.

Took some time to find out what is going on, but found the problem. I'll be working on it. 

(Problem is a test file used by biopython)

-maarten

Op 01-01-2023 om 20:21 schreef Nilesh Patra:

Hi Maarten,

This seems to stem from your latest upload of dssp. Could you consider taking
a look at this one?

Thanks,
Nilesh

On Sun, 1 Jan 2023 15:20:12 +0100 Lucas Nussbaum <lucas@debian.org> wrote:

Source: python-biopython
Version: 1.80+dfsg-4
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas@debian.org
Usertags: ftbfs-20230101 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):

make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p Tests_avoid
for avoid in  PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth mmtf mmtf_online  BioSQL_MySQLdb BioSQL_psycopg2   \
	    ; do \
     mv Tests/test_${avoid}.py Tests_avoid ; \
done
mv: cannot stat 'Tests/test_NACCESS_tool.py': No such file or directory
# For the doc package we need a clean testsuite without all the remaining files.  So keep a clean copy here
mkdir -p debian/tmp_tests
cp -a Tests debian/tmp_tests
# remove duplicated file
rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz
# We also keep the tests we need to avoid for later inspection
cp -a Tests_avoid debian/tmp_tests
# in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir
# to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set
LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
	--test-args='set -e; \
                              mkdir -p {build_dir}/home; \
                              mkdir -p {build_dir}/Doc/examples; \
                              cp -a Doc/Tutorial.tex {build_dir}/Doc; \
                              cp -a Doc/Tutorial {build_dir}/Doc; \
                              cp -a Doc/examples {build_dir}/Doc; \
                              cp -a Tests {build_dir}; \
                              cd {build_dir}/Tests; \
                              env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline'
	pybuild --test -i python{version} -p "3.11 3.10" --test --system=custom "--test-args=set -e; \\\
                              mkdir -p {build_dir}/home; \\\
                              mkdir -p {build_dir}/Doc/examples; \\\
                              cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\
                              cp -a Doc/Tutorial {build_dir}/Doc; \\\
                              cp -a Doc/examples {build_dir}/Doc; \\\
                              cp -a Tests {build_dir}; \\\
                              cd {build_dir}/Tests; \\\
                              env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline"
I: pybuild base:240: set -e; \
                              mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home; \
                              mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples; \
                              cp -a Doc/Tutorial.tex /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
                              cp -a Doc/Tutorial /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
                              cp -a Doc/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
                              cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; \
                              cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests; \
                              env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home python3.11 run_tests.py --offline
test_Ace ... ok


--
Maarten L. Hekkelman
http://www.hekkelman.com/
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