Bug#959587: Info received (Bug#959587: python-biopython: FTBFS: AssertionError: False is not true)
The small patch on this pull request ought to solve the immediate Debian testing issue for biopython: https://github.com/biopython/biopython/pull/2890 Peter On Wed, May 6, 2020 at 3:06 PM Debian Bug Tracking System < ow...@bugs.debian.org> wrote: > Thank you for the additional information you have supplied regarding > this Bug report. > > This is an automatically generated reply to let you know your message > has been received. > > Your message is being forwarded to the package maintainers and other > interested parties for their attention; they will reply in due course. > > Your message has been sent to the package maintainer(s): > Debian Med Packaging Team > > If you wish to submit further information on this problem, please > send it to 959...@bugs.debian.org. > > Please do not send mail to ow...@bugs.debian.org unless you wish > to report a problem with the Bug-tracking system. > > -- > 959587: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959587 > Debian Bug Tracking System > Contact ow...@bugs.debian.org with problems >
Bug#959587: python-biopython: FTBFS: AssertionError: False is not true
Control: forwarded -1 https://github.com/biopython/biopython/issues/2863
Bug#959587: python-biopython: FTBFS: AssertionError: False is not true
Thanks for the heads up, logged as: On Tue, May 5, 2020 at 7:40 PM Andreas Tille wrote: > Control: tags -1 upstream > Control: forwarded -1 Peter Cock > > Hi Peter, > > with the upload of ncbi-blast+ version 2.10 Biopython test is running > into failures (see > >https://bugs.debian.org/959587#10 > > ) > > Could you please adjust the Biopython test suite accordingly? > > Kind regards > > Andreas. > > On Tue, May 05, 2020 at 11:38:23AM -0400, Aaron M. Ucko wrote: > > > > > Since there is a strong relation in time with your upload and this > > > FTBFS of biopython do you think that this could be connected: > > > > Yes, per https://www.ncbi.nlm.nih.gov/books/NBK131777/, the upgrade to > > 2.10.0 changed the default database version (controlled by makeblastdb's > > -blastdb_version flag) from 4 to 5, causing some output files to change > > names (and formats): > > > > *.nsd -> *.nnd > > *.nsi -> *.nni > > *.psd -> *.pnd > > *.psi -> *.pni > > > > Thanks for checking! > > -- > http://fam-tille.de >
Bug#959587: python-biopython: FTBFS: AssertionError: False is not true
Thanks for the heads up, logged as: https://github.com/biopython/biopython/issues/2863 Peter On Tue, May 5, 2020 at 7:40 PM Andreas Tille wrote: > Control: tags -1 upstream > Control: forwarded -1 Peter Cock > > Hi Peter, > > with the upload of ncbi-blast+ version 2.10 Biopython test is running > into failures (see > >https://bugs.debian.org/959587#10 > > ) > > Could you please adjust the Biopython test suite accordingly? > > Kind regards > > Andreas. > > On Tue, May 05, 2020 at 11:38:23AM -0400, Aaron M. Ucko wrote: > > > > > Since there is a strong relation in time with your upload and this > > > FTBFS of biopython do you think that this could be connected: > > > > Yes, per https://www.ncbi.nlm.nih.gov/books/NBK131777/, the upgrade to > > 2.10.0 changed the default database version (controlled by makeblastdb's > > -blastdb_version flag) from 4 to 5, causing some output files to change > > names (and formats): > > > > *.nsd -> *.nnd > > *.nsi -> *.nni > > *.psd -> *.pnd > > *.psi -> *.pni > > > > Thanks for checking! > > -- > http://fam-tille.de >
Bug#959587: python-biopython: FTBFS: AssertionError: False is not true
Control: tags -1 upstream Control: forwarded -1 Peter Cock Hi Peter, with the upload of ncbi-blast+ version 2.10 Biopython test is running into failures (see https://bugs.debian.org/959587#10 ) Could you please adjust the Biopython test suite accordingly? Kind regards Andreas. On Tue, May 05, 2020 at 11:38:23AM -0400, Aaron M. Ucko wrote: > > > Since there is a strong relation in time with your upload and this > > FTBFS of biopython do you think that this could be connected: > > Yes, per https://www.ncbi.nlm.nih.gov/books/NBK131777/, the upgrade to > 2.10.0 changed the default database version (controlled by makeblastdb's > -blastdb_version flag) from 4 to 5, causing some output files to change > names (and formats): > > *.nsd -> *.nnd > *.nsi -> *.nni > *.psd -> *.pnd > *.psi -> *.pni > > Thanks for checking! -- http://fam-tille.de
Bug#959587: python-biopython: FTBFS: AssertionError: False is not true
Andreas Tille writes: > I've checked ncbi-blast+ and your last upload does not seem to be > pushed. AFAICT, it's all properly at https://salsa.debian.org/med-team/ncbi-blastplus. > Since there is a strong relation in time with your upload and this > FTBFS of biopython do you think that this could be connected: Yes, per https://www.ncbi.nlm.nih.gov/books/NBK131777/, the upgrade to 2.10.0 changed the default database version (controlled by makeblastdb's -blastdb_version flag) from 4 to 5, causing some output files to change names (and formats): *.nsd -> *.nnd *.nsi -> *.nni *.psd -> *.pnd *.psi -> *.pni Thanks for checking! BTW, python-biopython's build dependency on emboss reminded me that emboss-data is still probably overkill for emboss(-lib)'s needs and could stand to be split up (#682042). -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
Bug#959587: python-biopython: FTBFS: AssertionError: False is not true
Hi Aaron,
I've checked ncbi-blast+ and your last upload does not seem to be
pushed.
Since there is a strong relation in time with your upload and this
FTBFS of biopython do you think that this could be connected:
On Sun, May 03, 2020 at 02:43:59PM +0200, Lucas Nussbaum wrote:
> > ==
> > FAIL: test_fasta_db_nucl (test_NCBI_BLAST_tools.BlastDB)
> > Test makeblastdb wrapper with nucleotide database.
> > --
> > Traceback (most recent call last):
> > File
> > "/<>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py",
> > line 248, in test_fasta_db_nucl
> > self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsd"))
> > AssertionError: False is not true
> >
> > ==
> > FAIL: test_fasta_db_prot (test_NCBI_BLAST_tools.BlastDB)
> > Test makeblastdb wrapper with protein database.
> > --
> > Traceback (most recent call last):
> > File
> > "/<>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py",
> > line 213, in test_fasta_db_prot
> > self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psd"))
> > AssertionError: False is not true
> >
> > --
> > Ran 519 tests in 222.972 seconds
> >
> > FAILED (failures = 1)
Kind regards
Andreas.
--
http://fam-tille.de
Bug#959587: python-biopython: FTBFS: AssertionError: False is not true
Source: python-biopython
Version: 1.76+dfsg-1
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200501 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<>'
> 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
> # 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 3.8 --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:217: set -e; \
> mkdir -p
> /<>/.pybuild/cpython3_3.8/build/home; \
> mkdir -p
> /<>/.pybuild/cpython3_3.8/build/Doc/examples; \
> cp -a Doc/Tutorial.tex
> /<>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Doc/Tutorial
> /<>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Doc/examples
> /<>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Tests
> /<>/.pybuild/cpython3_3.8/build; \
> cd
> /<>/.pybuild/cpython3_3.8/build/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign
> EMBOSS_ROOT=/usr/lib/emboss
> HOME=/<>/.pybuild/cpython3_3.8/build/home python3.8 run_tests.py
> --offline
> x_order_2: colinear!
> x_order_2: colinear!
> test_Ace ... ok
> test_Affy ... ok
> test_AlignIO ... ok
> test_AlignIO_ClustalIO ... ok
> test_AlignIO_EmbossIO ... ok
> test_AlignIO_FastaIO ... ok
> test_AlignIO_MauveIO ... ok
> test_AlignIO_PhylipIO ... ok
> test_AlignIO_convert ... ok
> test_AlignInfo ... ok
> test_Application ... ok
> test_BWA_tool ... ok
> test_BioSQL_MySQLdb_online ... skipping. internet not available
> test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file
> biosql.ini missing (see biosql.ini.sample)
> test_BioSQL_mysql_connector_online ... skipping. internet not available
> test_BioSQL_psycopg2_online ... skipping. internet not available
> test_BioSQL_sqlite3 ... ok
> test_BioSQL_sqlite3_online ... skipping. internet not available
> test_Blast_Record ... ok
> test_CAPS ... ok
> test_CelFile ... ok
> test_Chi2 ... ok
> test_ClustalOmega_tool ... ok
> test_Clustalw_tool ... ok
> test_Cluster ... ok
> test_CodonTable ... ok
> test_ColorSpiral ... ok
> test_Compass ... ok
> test_Consensus ... ok
> test_Crystal ... ok
> test_DSSP_tool ... ok
> test_Dialign_tool ... ok
> test_EMBL_unittest ... ok
> test_Emboss ... ok
> test_EmbossPrimer ... ok
> test_Entrez ... ok
> test_Entrez_online ... skipping. internet not available
> test_Entrez_parser ... ok
> test_Enzyme ... ok
> test_ExPASy ... skipping. internet not available
> test_FSSP ... ok
> test_Fasttree_tool ... ok
> test_File ... ok
> test_GenBank ... ok
> test_GenomeDiagram ... ok
> test_GraphicsBitmaps ... ok
> test_GraphicsChromosome ... ok
>
