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 <lu...@debian.org> wrote:
Source: python-biopython
Version: 1.80+dfsg-4
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@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/
