[Debian-med-packaging] Bug#1022427: obitools: FTBFS: TypeError: cannot use a string pattern on a bytes-like object
Lucas Nussbaum
lucas at debian.org
Sun Oct 23 14:38:46 BST 2022
Source: obitools
Version: 1.2.13+dfsg-4
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20221023 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --with python3 --buildsystem=pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:240: python3.10 setup.py config
> /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils.
> warnings.warn(
> /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
> warnings.warn("Setuptools is replacing distutils.")
> ['src/obitools/_obitools.pyx']
> ['src/obitools/tools/_solexapairend.pyx']
> ['src/obitools/format/_format.pyx']
> ['src/obitools/format/genericparser/_genericparser.pyx']
> ['src/obitools/fastq/_fastq.pyx']
> ['src/obitools/fasta/_fasta.pyx']
> ['src/obitools/utils/_utils.pyx']
> @@@@> ['src/obitools/align/_lcs.h']
> ['src/obitools/align/_lcs.pyx', 'src/obitools/align/_lcs.ext.2.c', 'src/obitools/align/_lcs.ext.1.c', 'src/obitools/align/_lcs.ext.4.c', 'src/obitools/align/_lcs.ext.3.c']
> ['src/obitools/align/_freeendgap.pyx']
> ['src/obitools/align/_nwsdnabyprot.pyx']
> ['src/obitools/align/_dynamic.pyx']
> ['src/obitools/align/_qsrassemble.pyx']
> ['src/obitools/align/_profilenws.pyx']
> ['src/obitools/align/_gprofilenws.pyx']
> ['src/obitools/align/_nws.pyx']
> ['src/obitools/align/_codonnws.pyx']
> ['src/obitools/align/_rassemble.pyx']
> ['src/obitools/align/_assemble.pyx']
> ['src/obitools/align/_qsassemble.pyx']
> ['src/obitools/align/_freeendgapfm.pyx']
> @@@@> ['src/obitools/align/_sse.h']
> ['src/obitools/align/_upperbond.pyx', 'src/obitools/align/_upperbond.ext.1.c']
> @@@@> ['src/obitools/word/_readindex.h']
> ['src/obitools/word/_readindex.pyx']
> ['src/obitools/word/_binary.pyx']
> ['src/obitools/profile/_profile.pyx']
> ['src/obitools/options/_bioseqfilter.pyx']
> ['src/obitools/options/_options.pyx']
> running config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:240: /usr/bin/python3 setup.py build
> /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils.
> warnings.warn(
> /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
> warnings.warn("Setuptools is replacing distutils.")
> ['src/obitools/_obitools.pyx']
> ['src/obitools/tools/_solexapairend.pyx']
> ['src/obitools/format/_format.pyx']
> ['src/obitools/format/genericparser/_genericparser.pyx']
> ['src/obitools/fastq/_fastq.pyx']
> ['src/obitools/fasta/_fasta.pyx']
> ['src/obitools/utils/_utils.pyx']
> @@@@> ['src/obitools/align/_lcs.h']
> ['src/obitools/align/_lcs.pyx', 'src/obitools/align/_lcs.ext.2.c', 'src/obitools/align/_lcs.ext.1.c', 'src/obitools/align/_lcs.ext.4.c', 'src/obitools/align/_lcs.ext.3.c']
> ['src/obitools/align/_freeendgap.pyx']
> ['src/obitools/align/_nwsdnabyprot.pyx']
> ['src/obitools/align/_dynamic.pyx']
> ['src/obitools/align/_qsrassemble.pyx']
> ['src/obitools/align/_profilenws.pyx']
> ['src/obitools/align/_gprofilenws.pyx']
> ['src/obitools/align/_nws.pyx']
> ['src/obitools/align/_codonnws.pyx']
> ['src/obitools/align/_rassemble.pyx']
> ['src/obitools/align/_assemble.pyx']
> ['src/obitools/align/_qsassemble.pyx']
> ['src/obitools/align/_freeendgapfm.pyx']
> @@@@> ['src/obitools/align/_sse.h']
> ['src/obitools/align/_upperbond.pyx', 'src/obitools/align/_upperbond.ext.1.c']
> @@@@> ['src/obitools/word/_readindex.h']
> ['src/obitools/word/_readindex.pyx']
> ['src/obitools/word/_binary.pyx']
> ['src/obitools/profile/_profile.pyx']
> ['src/obitools/options/_bioseqfilter.pyx']
> ['src/obitools/options/_options.pyx']
> running build
>
>
> Running obidistutils build process
>
>
> running littlebigman
> creating build
> creating build/temp.linux-x86_64-cpython-310
> building 'littlebigman' program
> creating build/temp.linux-x86_64-cpython-310/distutils.ext
> creating build/temp.linux-x86_64-cpython-310/distutils.ext/src
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c distutils.ext/src/littlebigman.c -o build/temp.linux-x86_64-cpython-310/distutils.ext/src/littlebigman.o -msse2
> distutils.ext/src/littlebigman.c: In function ‘main’:
> distutils.ext/src/littlebigman.c:20:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
> 20 | else
> | ^~~~
> distutils.ext/src/littlebigman.c:23:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
> 23 | return 0;
> | ^~~~~~
> x86_64-linux-gnu-gcc build/temp.linux-x86_64-cpython-310/distutils.ext/src/littlebigman.o -o build/temp.linux-x86_64-cpython-310/littlebigman
> Your CPU is in mode : b'-DLITTLE_END'
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/sample.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/fast.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/decorator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/collections.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/solexaPairEnd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/zipfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/SVGdraw.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/svg.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/gzip.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> copying src/obitools/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tagmatcher
> copying src/obitools/tagmatcher/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tagmatcher
> copying src/obitools/tagmatcher/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tagmatcher
> copying src/obitools/tagmatcher/options.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tagmatcher
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/interactive
> copying src/obitools/interactive/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/interactive
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tools
> copying src/obitools/tools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tools
> copying src/obitools/tools/solexapairend.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tools
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/unit
> copying src/obitools/unit/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/unit
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/unit/obitools
> copying src/obitools/unit/obitools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/unit/obitools
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/statistics
> copying src/obitools/statistics/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/statistics
> copying src/obitools/statistics/hypergeometric.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/statistics
> copying src/obitools/statistics/noncentralhypergeo.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/statistics
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format
> copying src/obitools/format/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format
> copying src/obitools/format/options.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/genericparser
> copying src/obitools/format/genericparser/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/genericparser
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/sequence
> copying src/obitools/format/sequence/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/sequence
> copying src/obitools/format/sequence/fastq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/sequence
> copying src/obitools/format/sequence/fnaqual.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/sequence
> copying src/obitools/format/sequence/embl.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/sequence
> copying src/obitools/format/sequence/tagmatcher.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/sequence
> copying src/obitools/format/sequence/genbank.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/sequence
> copying src/obitools/format/sequence/fasta.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/sequence
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/ontology
> copying src/obitools/format/ontology/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/ontology
> copying src/obitools/format/ontology/go_obo.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/ontology
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/sequenceencoder
> copying src/obitools/sequenceencoder/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/sequenceencoder
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fastq
> copying src/obitools/fastq/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fastq
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/eutils
> copying src/obitools/eutils/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/eutils
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/carto
> copying src/obitools/carto/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/carto
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/dnahash
> copying src/obitools/dnahash/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/dnahash
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecotag
> copying src/obitools/ecotag/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecotag
> copying src/obitools/ecotag/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecotag
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/goa
> copying src/obitools/goa/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/goa
> copying src/obitools/goa/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/goa
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/location
> copying src/obitools/location/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/location
> copying src/obitools/location/feature.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/location
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/metabarcoding
> copying src/obitools/metabarcoding/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/metabarcoding
> copying src/obitools/metabarcoding/options.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/metabarcoding
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fasta
> copying src/obitools/fasta/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fasta
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/table
> copying src/obitools/table/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/table
> copying src/obitools/table/csv.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/table
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/utils
> copying src/obitools/utils/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/utils
> copying src/obitools/utils/iterator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/utils
> copying src/obitools/utils/crc64.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/utils
> copying src/obitools/utils/bioseq.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/utils
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/distances
> copying src/obitools/distances/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/distances
> copying src/obitools/distances/observed.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/distances
> copying src/obitools/distances/phylip.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/distances
> copying src/obitools/distances/r.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/distances
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/alignment
> copying src/obitools/alignment/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/alignment
> copying src/obitools/alignment/ace.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/alignment
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/phylogeny
> copying src/obitools/phylogeny/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/phylogeny
> copying src/obitools/phylogeny/newick.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/phylogeny
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/solexa
> copying src/obitools/solexa/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/solexa
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align
> copying src/obitools/align/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align
> copying src/obitools/align/ssearch.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align
> copying src/obitools/align/homopolymere.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/parallel
> copying src/obitools/parallel/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/parallel
> copying src/obitools/parallel/jobqueue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/parallel
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph
> copying src/obitools/graph/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph
> copying src/obitools/graph/dag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph
> copying src/obitools/graph/tree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph
> copying src/obitools/graph/rootedtree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph/algorithms
> copying src/obitools/graph/algorithms/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph/algorithms
> copying src/obitools/graph/algorithms/compact.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph/algorithms
> copying src/obitools/graph/algorithms/clique.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph/algorithms
> copying src/obitools/graph/algorithms/component.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph/algorithms
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph/layout
> copying src/obitools/graph/layout/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph/layout
> copying src/obitools/graph/layout/radialtree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/graph/layout
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecobarcode
> copying src/obitools/ecobarcode/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecobarcode
> copying src/obitools/ecobarcode/rawdata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecobarcode
> copying src/obitools/ecobarcode/taxonomy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecobarcode
> copying src/obitools/ecobarcode/options.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecobarcode
> copying src/obitools/ecobarcode/databases.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecobarcode
> copying src/obitools/ecobarcode/ecotag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecobarcode
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/thermo
> copying src/obitools/thermo/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/thermo
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb
> copying src/obitools/seqdb/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb
> copying src/obitools/seqdb/dnaparser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/blastdb
> copying src/obitools/seqdb/blastdb/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/blastdb
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/embl
> copying src/obitools/seqdb/embl/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/embl
> copying src/obitools/seqdb/embl/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/embl
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/genbank
> copying src/obitools/seqdb/genbank/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/genbank
> copying src/obitools/seqdb/genbank/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/genbank
> copying src/obitools/seqdb/genbank/ncbi.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/seqdb/genbank
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/word
> copying src/obitools/word/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/word
> copying src/obitools/word/options.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/word
> copying src/obitools/word/predicate.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/word
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecopcr
> copying src/obitools/ecopcr/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecopcr
> copying src/obitools/ecopcr/taxonomy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecopcr
> copying src/obitools/ecopcr/options.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecopcr
> copying src/obitools/ecopcr/annotation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecopcr
> copying src/obitools/ecopcr/sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/ecopcr
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/profile
> copying src/obitools/profile/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/profile
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/options
> copying src/obitools/options/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/options
> copying src/obitools/options/bioseqfilter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/options
> copying src/obitools/options/bioseqedittag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/options
> copying src/obitools/options/bioseqcutter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/options
> copying src/obitools/options/taxonomyfilter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/options
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/blast
> copying src/obitools/blast/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/blast
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/barcodecoverage
> copying src/obitools/barcodecoverage/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/barcodecoverage
> copying src/obitools/barcodecoverage/drawBcTree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/barcodecoverage
> copying src/obitools/barcodecoverage/findErrors.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/barcodecoverage
> copying src/obitools/barcodecoverage/calcBc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/barcodecoverage
> copying src/obitools/barcodecoverage/readFiles.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/barcodecoverage
> copying src/obitools/barcodecoverage/writeBcTree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/barcodecoverage
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obischemas
> copying src/obitools/obischemas/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obischemas
> copying src/obitools/obischemas/options.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obischemas
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obischemas/kb
> copying src/obitools/obischemas/kb/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obischemas/kb
> copying src/obitools/obischemas/kb/extern.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obischemas/kb
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fnaqual
> copying src/obitools/fnaqual/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fnaqual
> copying src/obitools/fnaqual/quality.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fnaqual
> copying src/obitools/fnaqual/fasta.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fnaqual
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tree
> copying src/obitools/tree/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tree
> copying src/obitools/tree/dot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tree
> copying src/obitools/tree/layout.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tree
> copying src/obitools/tree/newick.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tree
> copying src/obitools/tree/unrooted.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tree
> copying src/obitools/tree/svg.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tree
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obo
> copying src/obitools/obo/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obo
> copying src/obitools/obo/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obo
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obo/go
> copying src/obitools/obo/go/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obo/go
> copying src/obitools/obo/go/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/obo/go
> running build_ext
> obitools._obitools src/obitools/_obitools.pyx ok
> obitools.tools._solexapairend src/obitools/tools/_solexapairend.pyx ok
> obitools.format._format src/obitools/format/_format.pyx ok
> obitools.format.genericparser._genericparser src/obitools/format/genericparser/_genericparser.pyx ok
> obitools.fastq._fastq src/obitools/fastq/_fastq.pyx ok
> obitools.fasta._fasta src/obitools/fasta/_fasta.pyx ok
> obitools.utils._utils src/obitools/utils/_utils.pyx ok
> obitools.align._lcs src/obitools/align/_lcs.pyx ok
> obitools.align._lcs src/obitools/align/_lcs.ext.2.c ok
> obitools.align._lcs src/obitools/align/_lcs.ext.1.c ok
> obitools.align._lcs src/obitools/align/_lcs.ext.4.c ok
> obitools.align._lcs src/obitools/align/_lcs.ext.3.c ok
> obitools.align._freeendgap src/obitools/align/_freeendgap.pyx ok
> obitools.align._nwsdnabyprot src/obitools/align/_nwsdnabyprot.pyx ok
> obitools.align._dynamic src/obitools/align/_dynamic.pyx ok
> obitools.align._qsrassemble src/obitools/align/_qsrassemble.pyx ok
> obitools.align._profilenws src/obitools/align/_profilenws.pyx ok
> obitools.align._gprofilenws src/obitools/align/_gprofilenws.pyx ok
> obitools.align._nws src/obitools/align/_nws.pyx ok
> obitools.align._codonnws src/obitools/align/_codonnws.pyx ok
> obitools.align._rassemble src/obitools/align/_rassemble.pyx ok
> obitools.align._assemble src/obitools/align/_assemble.pyx ok
> obitools.align._qsassemble src/obitools/align/_qsassemble.pyx ok
> obitools.align._freeendgapfm src/obitools/align/_freeendgapfm.pyx ok
> obitools.align._upperbond src/obitools/align/_upperbond.pyx ok
> obitools.align._upperbond src/obitools/align/_upperbond.ext.1.c ok
> obitools.word._readindex src/obitools/word/_readindex.pyx ok
> obitools.word._binary src/obitools/word/_binary.pyx ok
> obitools.profile._profile src/obitools/profile/_profile.pyx ok
> obitools.options._bioseqfilter src/obitools/options/_bioseqfilter.pyx ok
> obitools.options._options src/obitools/options/_options.pyx ok
> #####> ['src/obitools/_obitools.pyx']
> cythoning src/obitools/_obitools.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/_obitools.c
> creating build/temp.linux-x86_64-cpython-310/pyrex
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools
> building 'obitools._obitools' extension
> creating build/temp.linux-x86_64-cpython-310/build
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/_obitools.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/_obitools.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/_obitools.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/_obitools.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/tools/_solexapairend.pyx']
> cythoning src/obitools/tools/_solexapairend.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/tools/_solexapairend.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/tools
> building 'obitools.tools._solexapairend' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/tools
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/tools/_solexapairend.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/tools/_solexapairend.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/tools/_solexapairend.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/tools/_solexapairend.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/format/_format.pyx']
> cythoning src/obitools/format/_format.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/_format.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/format
> building 'obitools.format._format' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/format
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/_format.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/_format.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/_format.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/_format.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/format/genericparser/_genericparser.pyx']
> cythoning src/obitools/format/genericparser/_genericparser.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/genericparser/_genericparser.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/genericparser
> building 'obitools.format.genericparser._genericparser' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/genericparser
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/genericparser/_genericparser.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/genericparser/_genericparser.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/format/genericparser/_genericparser.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/format/genericparser/_genericparser.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/fastq/_fastq.pyx']
> cythoning src/obitools/fastq/_fastq.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/fastq/_fastq.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/fastq
> building 'obitools.fastq._fastq' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/fastq
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/fastq/_fastq.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/fastq/_fastq.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/fastq/_fastq.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fastq/_fastq.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/fasta/_fasta.pyx']
> cythoning src/obitools/fasta/_fasta.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/fasta/_fasta.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/fasta
> building 'obitools.fasta._fasta' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/fasta
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/fasta/_fasta.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/fasta/_fasta.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/fasta/_fasta.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/fasta/_fasta.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/utils/_utils.pyx']
> cythoning src/obitools/utils/_utils.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils
> building 'obitools.utils._utils' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.o
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.c: In function ‘__pyx_f_8obitools_5utils_6_utils_progressBar’:
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.c:3852:57: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
> 3852 | ((void)fprintf(stderr, ((char *)"\r%s %5.1f %% |%.*s%c%.*s] remain : %d days %02d:%02d:%02d"), ((char *)__pyx_t_13), (__pyx_v_percent * 100.0), __pyx_v_fraction, __pyx_v_diese, (__pyx_v_wheel[__pyx_v_arrow]), (50 - __pyx_v_fraction), __pyx_v_spaces, __pyx_v_days, __pyx_v_hour, __pyx_v_minu, __pyx_v_sec));
> | ~~^~ ~~~~~~~~~~~~~~~~
> | | |
> | int long long unsigned int
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.c:3852:63: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 8 has type ‘long long unsigned int’ [-Wformat=]
> 3852 | ((void)fprintf(stderr, ((char *)"\r%s %5.1f %% |%.*s%c%.*s] remain : %d days %02d:%02d:%02d"), ((char *)__pyx_t_13), (__pyx_v_percent * 100.0), __pyx_v_fraction, __pyx_v_diese, (__pyx_v_wheel[__pyx_v_arrow]), (50 - __pyx_v_fraction), __pyx_v_spaces, __pyx_v_days, __pyx_v_hour, __pyx_v_minu, __pyx_v_sec));
> | ~~^~ ~~~~~~~~~~~~~~~~~~~~~~~
> | | |
> | int long long unsigned int
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.c:3893:57: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
> 3893 | ((void)fprintf(stderr, ((char *)"\r%s %5.1f %% |%.*s%c%.*s] remain : %02d:%02d:%02d"), ((char *)__pyx_t_13), (__pyx_v_percent * 100.), __pyx_v_fraction, __pyx_v_diese, (__pyx_v_wheel[__pyx_v_arrow]), (50 - __pyx_v_fraction), __pyx_v_spaces, __pyx_v_hour, __pyx_v_minu, __pyx_v_sec));
> | ~~^~ ~~~~~~~~~~~~~~~~
> | | |
> | int long long unsigned int
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.c:3893:63: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 8 has type ‘long long unsigned int’ [-Wformat=]
> 3893 | ((void)fprintf(stderr, ((char *)"\r%s %5.1f %% |%.*s%c%.*s] remain : %02d:%02d:%02d"), ((char *)__pyx_t_13), (__pyx_v_percent * 100.), __pyx_v_fraction, __pyx_v_diese, (__pyx_v_wheel[__pyx_v_arrow]), (50 - __pyx_v_fraction), __pyx_v_spaces, __pyx_v_hour, __pyx_v_minu, __pyx_v_sec));
> | ~~^~ ~~~~~~~~~~~~~~~~~~~~~~~
> | | |
> | int long long unsigned int
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/utils/_utils.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/utils/_utils.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_lcs.pyx', 'src/obitools/align/_lcs.ext.2.c', 'src/obitools/align/_lcs.ext.1.c', 'src/obitools/align/_lcs.ext.4.c', 'src/obitools/align/_lcs.ext.3.c']
> cythoning src/obitools/align/_lcs.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_lcs.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/align
> building 'obitools.align._lcs' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align
> creating build/temp.linux-x86_64-cpython-310/src
> creating build/temp.linux-x86_64-cpython-310/src/obitools
> creating build/temp.linux-x86_64-cpython-310/src/obitools/align
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/obitools/align -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_lcs.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_lcs.o -msse2
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/obitools/align -I/usr/include/python3.10 -c src/obitools/align/_lcs.ext.1.c -o build/temp.linux-x86_64-cpython-310/src/obitools/align/_lcs.ext.1.o -msse2
> src/obitools/align/_lcs.ext.1.c: In function ‘simpleLCS’:
> src/obitools/align/_lcs.ext.1.c:159:25: warning: ‘pl’ may be used uninitialized [-Wmaybe-uninitialized]
> 159 | if(lpath) *lpath=pl;
> | ~~~~~~^~~
> src/obitools/align/_lcs.ext.1.c:103:17: note: ‘pl’ was declared here
> 103 | int32_t pl,pu,pd;
> | ^~
> src/obitools/align/_lcs.ext.1.c:166:16: warning: ‘sl’ may be used uninitialized [-Wmaybe-uninitialized]
> 166 | return lcs;
> | ^~~
> src/obitools/align/_lcs.ext.1.c:102:17: note: ‘sl’ was declared here
> 102 | int32_t sl,su,sd;
> | ^~
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/obitools/align -I/usr/include/python3.10 -c src/obitools/align/_lcs.ext.2.c -o build/temp.linux-x86_64-cpython-310/src/obitools/align/_lcs.ext.2.o -msse2
> In file included from src/obitools/align/_lcs.ext.2.c:34:
> src/obitools/align/_lcs_fast.h:8:14: warning: ‘printreg’ defined but not used [-Wunused-function]
> 8 | static void printreg(VTYPE r)
> | ^~~~~~~~
> In file included from /usr/lib/gcc/x86_64-linux-gnu/12/include/xmmintrin.h:1316,
> from src/obitools/align/_sse.h:5,
> from src/obitools/align/_lcs.h:1,
> from src/obitools/align/_lcs.ext.2.c:1:
> In function ‘_mm_extract_epi16’,
> inlined from ‘fastLCSScore16’ at src/obitools/align/_lcs_fast.h:400:39:
> /usr/lib/gcc/x86_64-linux-gnu/12/include/emmintrin.h:1390:27: warning: ‘scurrent’ may be used uninitialized [-Wmaybe-uninitialized]
> 1390 | return (unsigned short) __builtin_ia32_vec_ext_v8hi ((__v8hi)__A, __N);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> src/obitools/align/_lcs_fast.h: In function ‘fastLCSScore16’:
> src/obitools/align/_lcs_fast.h:132:16: note: ‘scurrent’ was declared here
> 132 | VTYPE scurrent;
> | ^~~~~~~~
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/obitools/align -I/usr/include/python3.10 -c src/obitools/align/_lcs.ext.3.c -o build/temp.linux-x86_64-cpython-310/src/obitools/align/_lcs.ext.3.o -msse2
> In file included from src/obitools/align/_lcs.ext.3.c:34:
> src/obitools/align/_lcs_fast.h:8:14: warning: ‘printreg’ defined but not used [-Wunused-function]
> 8 | static void printreg(VTYPE r)
> | ^~~~~~~~
> In file included from /usr/lib/gcc/x86_64-linux-gnu/12/include/xmmintrin.h:1316,
> from src/obitools/align/_sse.h:5,
> from src/obitools/align/_lcs.h:1,
> from src/obitools/align/_lcs.ext.3.c:1:
> In function ‘_mm_extract_epi16’,
> inlined from ‘_s2_extract_epi8’ at src/obitools/align/_sse.h:77:12,
> inlined from ‘fastLCSScore8’ at src/obitools/align/_lcs_fast.h:400:39:
> /usr/lib/gcc/x86_64-linux-gnu/12/include/emmintrin.h:1390:27: warning: ‘scurrent’ may be used uninitialized [-Wmaybe-uninitialized]
> 1390 | return (unsigned short) __builtin_ia32_vec_ext_v8hi ((__v8hi)__A, __N);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> src/obitools/align/_lcs_fast.h: In function ‘fastLCSScore8’:
> src/obitools/align/_lcs_fast.h:132:16: note: ‘scurrent’ was declared here
> 132 | VTYPE scurrent;
> | ^~~~~~~~
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/obitools/align -I/usr/include/python3.10 -c src/obitools/align/_lcs.ext.4.c -o build/temp.linux-x86_64-cpython-310/src/obitools/align/_lcs.ext.4.o -msse2
> src/obitools/align/_lcs.ext.4.c: In function ‘buildTable’:
> src/obitools/align/_lcs.ext.4.c:96:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
> 96 | if (zero.c[0]+zero.c[1]+zero.c[2]+zero.c[3]==0)
> | ^
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_lcs.o build/temp.linux-x86_64-cpython-310/src/obitools/align/_lcs.ext.1.o build/temp.linux-x86_64-cpython-310/src/obitools/align/_lcs.ext.2.o build/temp.linux-x86_64-cpython-310/src/obitools/align/_lcs.ext.3.o build/temp.linux-x86_64-cpython-310/src/obitools/align/_lcs.ext.4.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_lcs.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_freeendgap.pyx']
> cythoning src/obitools/align/_freeendgap.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_freeendgap.c
> building 'obitools.align._freeendgap' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_freeendgap.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_freeendgap.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_freeendgap.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_freeendgap.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_nwsdnabyprot.pyx']
> cythoning src/obitools/align/_nwsdnabyprot.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nwsdnabyprot.c
> building 'obitools.align._nwsdnabyprot' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nwsdnabyprot.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nwsdnabyprot.o
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nwsdnabyprot.c: In function ‘__pyx_f_8obitools_5align_13_nwsdnabyprot_12NWSDNAByProt_doAlignment’:
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nwsdnabyprot.c:4966:29: warning: ‘__pyx_v_smatrix’ may be used uninitialized [-Wmaybe-uninitialized]
> 4966 | __pyx_r = (__pyx_v_smatrix[__pyx_v_idx]).score;
> | ^
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nwsdnabyprot.c:3985:67: note: ‘__pyx_v_smatrix’ was declared here
> 3985 | struct __pyx_t_8obitools_5align_13_nwsdnabyprot_CodonAlignCell *__pyx_v_smatrix;
> | ^~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nwsdnabyprot.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_nwsdnabyprot.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_dynamic.pyx']
> cythoning src/obitools/align/_dynamic.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_dynamic.c
> building 'obitools.align._dynamic' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_dynamic.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_dynamic.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_dynamic.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_dynamic.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_qsrassemble.pyx']
> cythoning src/obitools/align/_qsrassemble.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_qsrassemble.c
> building 'obitools.align._qsrassemble' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_qsrassemble.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_qsrassemble.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_qsrassemble.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_qsrassemble.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_profilenws.pyx']
> cythoning src/obitools/align/_profilenws.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_profilenws.c
> building 'obitools.align._profilenws' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_profilenws.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_profilenws.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_profilenws.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_profilenws.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_gprofilenws.pyx']
> cythoning src/obitools/align/_gprofilenws.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_gprofilenws.c
> building 'obitools.align._gprofilenws' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_gprofilenws.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_gprofilenws.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_gprofilenws.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_gprofilenws.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_nws.pyx']
> cythoning src/obitools/align/_nws.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nws.c
> building 'obitools.align._nws' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nws.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nws.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_nws.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_nws.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_codonnws.pyx']
> cythoning src/obitools/align/_codonnws.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_codonnws.c
> building 'obitools.align._codonnws' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_codonnws.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_codonnws.o
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_codonnws.c: In function ‘__pyx_f_8obitools_5align_9_codonnws_8CodonNWS_backtrack’:
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_codonnws.c:26568:104: warning: ‘__pyx_v_p’ may be used uninitialized [-Wmaybe-uninitialized]
> 26568 | (__pyx_v_self->__pyx_base.__pyx_base.path->path[__pyx_v_self->__pyx_base.__pyx_base.path->length]) = __pyx_v_p;
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_codonnws.c:26178:7: note: ‘__pyx_v_p’ was declared here
> 26178 | int __pyx_v_p;
> | ^~~~~~~~~
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_codonnws.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_codonnws.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_rassemble.pyx']
> cythoning src/obitools/align/_rassemble.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_rassemble.c
> building 'obitools.align._rassemble' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_rassemble.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_rassemble.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_rassemble.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_rassemble.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_assemble.pyx']
> cythoning src/obitools/align/_assemble.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_assemble.c
> building 'obitools.align._assemble' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_assemble.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_assemble.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_assemble.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_assemble.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_qsassemble.pyx']
> cythoning src/obitools/align/_qsassemble.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_qsassemble.c
> building 'obitools.align._qsassemble' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_qsassemble.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_qsassemble.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_qsassemble.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_qsassemble.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_freeendgapfm.pyx']
> cythoning src/obitools/align/_freeendgapfm.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_freeendgapfm.c
> building 'obitools.align._freeendgapfm' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_freeendgapfm.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_freeendgapfm.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_freeendgapfm.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_freeendgapfm.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/align/_upperbond.pyx', 'src/obitools/align/_upperbond.ext.1.c']
> cythoning src/obitools/align/_upperbond.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_upperbond.c
> building 'obitools.align._upperbond' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/obitools/align -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_upperbond.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_upperbond.o -msse2
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/obitools/align -I/usr/include/python3.10 -c src/obitools/align/_upperbond.ext.1.c -o build/temp.linux-x86_64-cpython-310/src/obitools/align/_upperbond.ext.1.o -msse2
> src/obitools/align/_upperbond.ext.1.c: In function ‘buildTable’:
> src/obitools/align/_upperbond.ext.1.c:96:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
> 96 | if (zero.c[0]+zero.c[1]+zero.c[2]+zero.c[3]==0)
> | ^
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/align/_upperbond.o build/temp.linux-x86_64-cpython-310/src/obitools/align/_upperbond.ext.1.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/align/_upperbond.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/word/_readindex.pyx']
> cythoning src/obitools/word/_readindex.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/word
> building 'obitools.word._readindex' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/word
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/obitools/word -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.o -msse2
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c: In function ‘__pyx_pf_8obitools_4word_10_readindex_9ReadIndex_10indexWords’:
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c:6289:3: warning: implicit declaration of function ‘heapsort’ [-Wimplicit-function-declaration]
> 6289 | heapsort(__pyx_v_self->_wordlist, __pyx_v_i, (sizeof(pobinuc)), __pyx_f_8obitools_4word_10_readindex_cmpwords);
> | ^~~~~~~~
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c: In function ‘__pyx_gb_8obitools_4word_10_readindex_9ReadIndex_14generator’:
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c:6558:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 6558 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
> | ^
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c: In function ‘__pyx_gb_8obitools_4word_10_readindex_9ReadIndex_17generator1’:
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c:6756:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 6756 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
> | ^
> In function ‘__pyx_pf_8obitools_4word_10_readindex_9ReadIndex_8load’,
> inlined from ‘__pyx_pw_8obitools_4word_10_readindex_9ReadIndex_9load’ at build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c:4505:13:
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c:5718:10: warning: pointer ‘__pyx_v_f’ may be used after ‘fclose’ [-Wuse-after-free]
> 5718 | (void)(fclose(__pyx_v_f));
> | ~^~~~~~~~~~~~~~~~~~
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.c:5585:10: note: call to ‘fclose’ here
> 5585 | (void)(fclose(__pyx_v_f));
> | ~^~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_readindex.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/word/_readindex.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/word/_binary.pyx']
> cythoning src/obitools/word/_binary.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_binary.c
> building 'obitools.word._binary' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_binary.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_binary.o
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_binary.c: In function ‘__pyx_f_8obitools_4word_7_binary_bin2str’:
> build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_binary.c:1818:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 1818 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
> | ^
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/word/_binary.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/word/_binary.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/profile/_profile.pyx']
> cythoning src/obitools/profile/_profile.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/profile/_profile.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/profile
> building 'obitools.profile._profile' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/profile
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/profile/_profile.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/profile/_profile.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/profile/_profile.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/profile/_profile.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/options/_bioseqfilter.pyx']
> cythoning src/obitools/options/_bioseqfilter.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/options/_bioseqfilter.c
> creating build/temp.linux-x86_64-cpython-310/pyrex/obitools/options
> building 'obitools.options._bioseqfilter' extension
> creating build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/options
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/options/_bioseqfilter.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/options/_bioseqfilter.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/options/_bioseqfilter.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/options/_bioseqfilter.cpython-310-x86_64-linux-gnu.so
> #####> ['src/obitools/options/_options.pyx']
> cythoning src/obitools/options/_options.pyx to build/temp.linux-x86_64-cpython-310/pyrex/obitools/options/_options.c
> building 'obitools.options._options' extension
> x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c build/temp.linux-x86_64-cpython-310/pyrex/obitools/options/_options.c -o build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/options/_options.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/build/temp.linux-x86_64-cpython-310/pyrex/obitools/options/_options.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_obitools/build/obitools/options/_options.cpython-310-x86_64-linux-gnu.so
> running build_scripts
> creating build/scripts-3.10
> creating build/raw_scripts
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/setup.py", line 50, in <module>
> setup(name=PACKAGE,
> File "/<<PKGBUILDDIR>>/distutils.ext/obidistutils/core.py", line 202, in setup
> ori_setup(**attrs)
> File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 87, in setup
> return distutils.core.setup(**attrs)
> File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 185, in setup
> return run_commands(dist)
> File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands
> dist.run_commands()
> File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 968, in run_commands
> self.run_command(cmd)
> File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1217, in run_command
> super().run_command(command)
> File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 987, in run_command
> cmd_obj.run()
> File "/<<PKGBUILDDIR>>/distutils.ext/obidistutils/command/build.py", line 45, in run
> ori_build.run(self)
> File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build.py", line 132, in run
> self.run_command(cmd_name)
> File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 319, in run_command
> self.distribution.run_command(command)
> File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1217, in run_command
> super().run_command(command)
> File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 987, in run_command
> cmd_obj.run()
> File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_scripts.py", line 57, in run
> self.copy_scripts()
> File "/<<PKGBUILDDIR>>/distutils.ext/obidistutils/command/build_scripts.py", line 57, in copy_scripts
> match = first_line_re.match(first_line)
> TypeError: cannot use a string pattern on a bytes-like object
> E: pybuild pybuild:379: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build
> dh_auto_build: error: pybuild --build -i python{version} -p 3.10 returned exit code 13
> make: *** [debian/rules:15: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2022/10/23/obitools_1.2.13+dfsg-4_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221023;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221023&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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