Source: obitools Version: 1.2.13+dfsg-4 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@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=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221023&fusertaguser=lu...@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.