[Debian-med-packaging] Bug#1066569: python-bx: FTBFS: src/pwm_utils.c:11:27: error: implicit declaration of function ‘strlen’ [-Werror=implicit-function-declaration]
Lucas Nussbaum
lucas at debian.org
Wed Mar 13 11:56:01 GMT 2024
Source: python-bx
Version: 0.11.0-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20240313 ftbfs-trixie ftbfs-impfuncdef
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
This is most likely caused by a change in dpkg 1.22.6, that enabled
-Werror=implicit-function-declaration. For more information, see
https://wiki.debian.org/qa.debian.org/FTBFS#A2024-03-13_-Werror.3Dimplicit-function-declaration
Relevant part (hopefully):
> x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.12 -c src/pwm_utils.c -o build/temp.linux-x86_64-cpython-312/src/pwm_utils.o
> src/pwm_utils.c: In function ‘main’:
> src/pwm_utils.c:11:27: error: implicit declaration of function ‘strlen’ [-Werror=implicit-function-declaration]
> 11 | int string_size = strlen(argv[1]);
> | ^~~~~~
> src/pwm_utils.c:5:1: note: include ‘<string.h>’ or provide a declaration of ‘strlen’
> 4 | #include <strings.h>
> +++ |+#include <string.h>
> 5 |
> src/pwm_utils.c:11:27: warning: incompatible implicit declaration of built-in function ‘strlen’ [-Wbuiltin-declaration-mismatch]
> 11 | int string_size = strlen(argv[1]);
> | ^~~~~~
> src/pwm_utils.c:11:27: note: include ‘<string.h>’ or provide a declaration of ‘strlen’
> src/pwm_utils.c:12:29: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 12 | if (strlen(argv[2]) != string_size) {
> | ^~
> cc1: some warnings being treated as errors
> error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
>
> ERROR Backend subprocess exited when trying to invoke build_wheel
> E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_bx-python
> I: pybuild plugin_pyproject:129: Building wheel for python3.11 with "build" module
> I: pybuild base:305: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_bx-python
> * Building wheel...
> running bdist_wheel
> running build
> running build_py
> creating build/lib.linux-x86_64-cpython-311
> copying lib/psyco_full.py -> build/lib.linux-x86_64-cpython-311
> creating build/lib.linux-x86_64-cpython-311/bx_extras
> copying lib/bx_extras/pyparsing.py -> build/lib.linux-x86_64-cpython-311/bx_extras
> copying lib/bx_extras/__init__.py -> build/lib.linux-x86_64-cpython-311/bx_extras
> copying lib/bx_extras/stats.py -> build/lib.linux-x86_64-cpython-311/bx_extras
> copying lib/bx_extras/lrucache.py -> build/lib.linux-x86_64-cpython-311/bx_extras
> copying lib/bx_extras/fpconst_tests.py -> build/lib.linux-x86_64-cpython-311/bx_extras
> copying lib/bx_extras/fpconst.py -> build/lib.linux-x86_64-cpython-311/bx_extras
> copying lib/bx_extras/pstat.py -> build/lib.linux-x86_64-cpython-311/bx_extras
> creating build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/seqmapping.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/bitset_builders.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/__init__.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/seqmapping_tests.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/binned_array_tests.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/binned_array.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/wiggle.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/interval_index_file.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/bitset_tests.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/interval_index_file_tests.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/gene_reader.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/wiggle_tests.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/bitset_utils.py -> build/lib.linux-x86_64-cpython-311/bx
> copying lib/bx/filter.py -> build/lib.linux-x86_64-cpython-311/bx
> creating build/lib.linux-x86_64-cpython-311/bx/intervals
> copying lib/bx/intervals/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/intervals
> copying lib/bx/intervals/random_intervals.py -> build/lib.linux-x86_64-cpython-311/bx/intervals
> copying lib/bx/intervals/intersection_tests.py -> build/lib.linux-x86_64-cpython-311/bx/intervals
> copying lib/bx/intervals/io.py -> build/lib.linux-x86_64-cpython-311/bx/intervals
> copying lib/bx/intervals/cluster_tests.py -> build/lib.linux-x86_64-cpython-311/bx/intervals
> creating build/lib.linux-x86_64-cpython-311/bx/intseq
> copying lib/bx/intseq/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/intseq
> creating build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/lav.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/epo.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/lav_tests.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/score_tests.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/axt.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/score.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/epo_tests.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/maf.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/maf_tests.py -> build/lib.linux-x86_64-cpython-311/bx/align
> copying lib/bx/align/core.py -> build/lib.linux-x86_64-cpython-311/bx/align
> creating build/lib.linux-x86_64-cpython-311/bx/tabular
> copying lib/bx/tabular/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/tabular
> copying lib/bx/tabular/io.py -> build/lib.linux-x86_64-cpython-311/bx/tabular
> creating build/lib.linux-x86_64-cpython-311/bx/bbi
> copying lib/bx/bbi/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/bbi
> copying lib/bx/bbi/bigwig_tests.py -> build/lib.linux-x86_64-cpython-311/bx/bbi
> creating build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/pwm_score_maf.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/maf_select_motifs.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/position_weight_matrix.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/pwm_tests.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/pwm_score_positions.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.linux-x86_64-cpython-311/bx/pwm
> creating build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/fasta.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/nib_tests.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/qdna_tests.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/seq.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/twobit.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/nib.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/twobit_tests.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/seq_tests.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/qdna.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/fasta_tests.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> copying lib/bx/seq/core.py -> build/lib.linux-x86_64-cpython-311/bx/seq
> creating build/lib.linux-x86_64-cpython-311/bx/phylo
> copying lib/bx/phylo/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/phylo
> copying lib/bx/phylo/phast.py -> build/lib.linux-x86_64-cpython-311/bx/phylo
> copying lib/bx/phylo/newick_tests.py -> build/lib.linux-x86_64-cpython-311/bx/phylo
> copying lib/bx/phylo/phast_tests.py -> build/lib.linux-x86_64-cpython-311/bx/phylo
> copying lib/bx/phylo/newick.py -> build/lib.linux-x86_64-cpython-311/bx/phylo
> creating build/lib.linux-x86_64-cpython-311/bx/arrays
> copying lib/bx/arrays/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/arrays
> copying lib/bx/arrays/array_tree_tests.py -> build/lib.linux-x86_64-cpython-311/bx/arrays
> creating build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/seeklzop.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/cdb_tests.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/seeklzop_tests.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/seekbzip2.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/bgzf_tests.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/binary_file.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/seekbzip2_tests.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/readlengths.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/cdb.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/filecache.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> copying lib/bx/misc/filecache_tests.py -> build/lib.linux-x86_64-cpython-311/bx/misc
> creating build/lib.linux-x86_64-cpython-311/bx/motif
> copying lib/bx/motif/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/motif
> copying lib/bx/motif/pwm.py -> build/lib.linux-x86_64-cpython-311/bx/motif
> copying lib/bx/motif/pwm_tests.py -> build/lib.linux-x86_64-cpython-311/bx/motif
> creating build/lib.linux-x86_64-cpython-311/bx/cookbook
> copying lib/bx/cookbook/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/cookbook
> copying lib/bx/cookbook/doc_optparse.py -> build/lib.linux-x86_64-cpython-311/bx/cookbook
> copying lib/bx/cookbook/progress_bar.py -> build/lib.linux-x86_64-cpython-311/bx/cookbook
> copying lib/bx/cookbook/attribute.py -> build/lib.linux-x86_64-cpython-311/bx/cookbook
> copying lib/bx/cookbook/argparse.py -> build/lib.linux-x86_64-cpython-311/bx/cookbook
> creating build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/base_coverage.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/subtract.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/merge.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/find_clusters.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/coverage.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/intersect.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/quicksect.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/join.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/concat.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> copying lib/bx/intervals/operations/complement.py -> build/lib.linux-x86_64-cpython-311/bx/intervals/operations
> creating build/lib.linux-x86_64-cpython-311/bx/align/sitemask
> copying lib/bx/align/sitemask/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/align/sitemask
> copying lib/bx/align/sitemask/quality.py -> build/lib.linux-x86_64-cpython-311/bx/align/sitemask
> copying lib/bx/align/sitemask/cpg.py -> build/lib.linux-x86_64-cpython-311/bx/align/sitemask
> copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.linux-x86_64-cpython-311/bx/align/sitemask
> copying lib/bx/align/sitemask/core.py -> build/lib.linux-x86_64-cpython-311/bx/align/sitemask
> creating build/lib.linux-x86_64-cpython-311/bx/align/tools
> copying lib/bx/align/tools/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/align/tools
> copying lib/bx/align/tools/chop.py -> build/lib.linux-x86_64-cpython-311/bx/align/tools
> copying lib/bx/align/tools/tile.py -> build/lib.linux-x86_64-cpython-311/bx/align/tools
> copying lib/bx/align/tools/fuse.py -> build/lib.linux-x86_64-cpython-311/bx/align/tools
> copying lib/bx/align/tools/thread.py -> build/lib.linux-x86_64-cpython-311/bx/align/tools
> creating build/lib.linux-x86_64-cpython-311/bx/motif/io
> copying lib/bx/motif/io/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/motif/io
> copying lib/bx/motif/io/transfac_tests.py -> build/lib.linux-x86_64-cpython-311/bx/motif/io
> copying lib/bx/motif/io/transfac.py -> build/lib.linux-x86_64-cpython-311/bx/motif/io
> creating build/lib.linux-x86_64-cpython-311/bx/motif/logo
> copying lib/bx/motif/logo/__init__.py -> build/lib.linux-x86_64-cpython-311/bx/motif/logo
> copying lib/bx/motif/logo/template.ps -> build/lib.linux-x86_64-cpython-311/bx/motif/logo
> running build_ext
> building 'bx.bitset' extension
> creating build/temp.linux-x86_64-cpython-311
> creating build/temp.linux-x86_64-cpython-311/lib
> creating build/temp.linux-x86_64-cpython-311/lib/bx
> creating build/temp.linux-x86_64-cpython-311/src
> creating build/temp.linux-x86_64-cpython-311/src/kent
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.11 -c lib/bx/bitset.c -o build/temp.linux-x86_64-cpython-311/lib/bx/bitset.o
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.11 -c src/binBits.c -o build/temp.linux-x86_64-cpython-311/src/binBits.o
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.11 -c src/kent/bits.c -o build/temp.linux-x86_64-cpython-311/src/kent/bits.o
> src/kent/bits.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=]
> 9 | static char const rcsid[] = "$Id: bits.c,v 1.20 2008/03/25 16:32:31 angie Exp $";
> | ^~~~~
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.11 -c src/kent/common.c -o build/temp.linux-x86_64-cpython-311/src/kent/common.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/lib/bx/bitset.o build/temp.linux-x86_64-cpython-311/src/binBits.o build/temp.linux-x86_64-cpython-311/src/kent/bits.o build/temp.linux-x86_64-cpython-311/src/kent/common.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/bx/bitset.cpython-311-x86_64-linux-gnu.so
> building 'bx.intervals.intersection' extension
> creating build/temp.linux-x86_64-cpython-311/lib/bx/intervals
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c lib/bx/intervals/intersection.c -o build/temp.linux-x86_64-cpython-311/lib/bx/intervals/intersection.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/lib/bx/intervals/intersection.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/bx/intervals/intersection.cpython-311-x86_64-linux-gnu.so
> building 'bx.align._core' extension
> creating build/temp.linux-x86_64-cpython-311/lib/bx/align
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c lib/bx/align/_core.c -o build/temp.linux-x86_64-cpython-311/lib/bx/align/_core.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/lib/bx/align/_core.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/bx/align/_core.cpython-311-x86_64-linux-gnu.so
> building 'bx.seq._nib' extension
> creating build/temp.linux-x86_64-cpython-311/lib/bx/seq
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c lib/bx/seq/_nib.c -o build/temp.linux-x86_64-cpython-311/lib/bx/seq/_nib.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/lib/bx/seq/_nib.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/bx/seq/_nib.cpython-311-x86_64-linux-gnu.so
> building 'bx.seq._twobit' extension
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c lib/bx/seq/_twobit.c -o build/temp.linux-x86_64-cpython-311/lib/bx/seq/_twobit.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/lib/bx/seq/_twobit.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/bx/seq/_twobit.cpython-311-x86_64-linux-gnu.so
> building 'bx._seqmapping' extension
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c lib/bx/_seqmapping.c -o build/temp.linux-x86_64-cpython-311/lib/bx/_seqmapping.o
> lib/bx/_seqmapping.c: In function ‘__pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_6translate’:
> lib/bx/_seqmapping.c:3590:3: warning: ‘PyObject_AsWriteBuffer’ is deprecated [-Wdeprecated-declarations]
> 3590 | __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 54, __pyx_L1_error)
> | ^~~~~~~~~
> In file included from /usr/include/python3.11/Python.h:100,
> from lib/bx/_seqmapping.c:29:
> /usr/include/python3.11/abstract.h:354:17: note: declared here
> 354 | PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj,
> | ^~~~~~~~~~~~~~~~~~~~~~
> lib/bx/_seqmapping.c: In function ‘__pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_8translate_list’:
> lib/bx/_seqmapping.c:3850:3: warning: ‘PyObject_AsWriteBuffer’ is deprecated [-Wdeprecated-declarations]
> 3850 | __pyx_t_7 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 77, __pyx_L1_error)
> | ^~~~~~~~~
> /usr/include/python3.11/abstract.h:354:17: note: declared here
> 354 | PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj,
> | ^~~~~~~~~~~~~~~~~~~~~~
> lib/bx/_seqmapping.c: In function ‘__pyx_pf_2bx_11_seqmapping_15IntToIntMapping_6translate’:
> lib/bx/_seqmapping.c:5288:3: warning: ‘PyObject_AsReadBuffer’ is deprecated [-Wdeprecated-declarations]
> 5288 | __pyx_t_1 = PyObject_AsReadBuffer(__pyx_v_src, ((void const **)(&__pyx_v_s_buf)), (&__pyx_v_s_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 134, __pyx_L1_error)
> | ^~~~~~~~~
> /usr/include/python3.11/abstract.h:343:17: note: declared here
> 343 | PyAPI_FUNC(int) PyObject_AsReadBuffer(PyObject *obj,
> | ^~~~~~~~~~~~~~~~~~~~~
> lib/bx/_seqmapping.c:5368:3: warning: ‘PyObject_AsWriteBuffer’ is deprecated [-Wdeprecated-declarations]
> 5368 | __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 139, __pyx_L1_error)
> | ^~~~~~~~~
> /usr/include/python3.11/abstract.h:354:17: note: declared here
> 354 | PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj,
> | ^~~~~~~~~~~~~~~~~~~~~~
> In function ‘__pyx_pf_2bx_11_seqmapping_15IntToIntMapping___cinit__’,
> inlined from ‘__pyx_pw_2bx_11_seqmapping_15IntToIntMapping_1__cinit__’ at lib/bx/_seqmapping.c:4790:13,
> inlined from ‘__pyx_tp_new_2bx_11_seqmapping_IntToIntMapping’ at lib/bx/_seqmapping.c:7626:7:
> lib/bx/_seqmapping.c:4828:33: warning: argument 1 value ‘18446744073709551612’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
> 4828 | __pyx_v_self->table = ((int *)malloc((__pyx_v_in_size * (sizeof(int)))));
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> In file included from /usr/include/python3.11/Python.h:23:
> /usr/include/stdlib.h: In function ‘__pyx_tp_new_2bx_11_seqmapping_IntToIntMapping’:
> /usr/include/stdlib.h:553:14: note: in a call to allocation function ‘malloc’ declared here
> 553 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
> | ^~~~~~
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/lib/bx/_seqmapping.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/bx/_seqmapping.cpython-311-x86_64-linux-gnu.so
> building 'bx.misc.bgzf' extension
> creating build/temp.linux-x86_64-cpython-311/lib/bx/misc
> creating build/temp.linux-x86_64-cpython-311/src/samtools
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/samtools -I/usr/include/python3.11 -c lib/bx/misc/bgzf.c -o build/temp.linux-x86_64-cpython-311/lib/bx/misc/bgzf.o
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/samtools -I/usr/include/python3.11 -c src/samtools/bgzf.c -o build/temp.linux-x86_64-cpython-311/src/samtools/bgzf.o
> src/samtools/bgzf.c: In function ‘cache_block’:
> src/samtools/bgzf.c:422:47: warning: comparison of integer expressions of different signedness: ‘khint_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
> 422 | if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) {
> | ^
> src/samtools/bgzf.c: In function ‘read_block’:
> src/samtools/bgzf.c:462:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
> 462 | if (count != sizeof(header)) {
> | ^~
> src/samtools/bgzf.c: In function ‘bgzf_close’:
> src/samtools/bgzf.c:603:29: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
> 603 | int count, block_length = deflate_block(fp, 0);
> | ^~~~~
> src/samtools/bgzf.c: In function ‘bgzf_check_EOF’:
> src/samtools/bgzf.c:662:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 662 | fread(buf, 1, 28, fp->file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/lib/bx/misc/bgzf.o build/temp.linux-x86_64-cpython-311/src/samtools/bgzf.o -L/usr/lib/x86_64-linux-gnu -lz -o build/lib.linux-x86_64-cpython-311/bx/misc/bgzf.cpython-311-x86_64-linux-gnu.so
> building 'bx.intervals.cluster' extension
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.11 -c lib/bx/intervals/cluster.c -o build/temp.linux-x86_64-cpython-311/lib/bx/intervals/cluster.o
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.11 -c src/cluster.c -o build/temp.linux-x86_64-cpython-311/src/cluster.o
> x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/lib/bx/intervals/cluster.o build/temp.linux-x86_64-cpython-311/src/cluster.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/bx/intervals/cluster.cpython-311-x86_64-linux-gnu.so
> building 'bx.pwm._position_weight_matrix' extension
> creating build/temp.linux-x86_64-cpython-311/lib/bx/pwm
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.11 -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.linux-x86_64-cpython-311/lib/bx/pwm/_position_weight_matrix.o
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.11 -c src/pwm_utils.c -o build/temp.linux-x86_64-cpython-311/src/pwm_utils.o
> src/pwm_utils.c: In function ‘main’:
> src/pwm_utils.c:11:27: error: implicit declaration of function ‘strlen’ [-Werror=implicit-function-declaration]
> 11 | int string_size = strlen(argv[1]);
> | ^~~~~~
> src/pwm_utils.c:5:1: note: include ‘<string.h>’ or provide a declaration of ‘strlen’
> 4 | #include <strings.h>
> +++ |+#include <string.h>
> 5 |
> src/pwm_utils.c:11:27: warning: incompatible implicit declaration of built-in function ‘strlen’ [-Wbuiltin-declaration-mismatch]
> 11 | int string_size = strlen(argv[1]);
> | ^~~~~~
> src/pwm_utils.c:11:27: note: include ‘<string.h>’ or provide a declaration of ‘strlen’
> src/pwm_utils.c:12:29: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 12 | if (strlen(argv[2]) != string_size) {
> | ^~
> cc1: some warnings being treated as errors
> error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
>
> ERROR Backend subprocess exited when trying to invoke build_wheel
> E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_bx-python
> dh_auto_build: error: pybuild --build -i python{version} -p "3.12 3.11" returned exit code 13
> make: *** [debian/rules:15: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/python-bx_0.11.0-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&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 mark 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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