Your message dated Thu, 14 Mar 2024 12:10:19 +0000
with message-id <e1rkjud-00bozw...@fasolo.debian.org>
and subject line Bug#1066569: fixed in python-bx 0.11.0-3
has caused the Debian Bug report #1066569,
regarding python-bx: FTBFS: src/pwm_utils.c:11:27: error: implicit declaration
of function ‘strlen’ [-Werror=implicit-function-declaration]
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1066569: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066569
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: python-bx
Version: 0.11.0-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@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=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&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 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.
--- End Message ---
--- Begin Message ---
Source: python-bx
Source-Version: 0.11.0-3
Done: Michael R. Crusoe <cru...@debian.org>
We believe that the bug you reported is fixed in the latest version of
python-bx, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1066...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <cru...@debian.org> (supplier of updated python-bx package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 14 Mar 2024 12:40:18 +0100
Source: python-bx
Architecture: source
Version: 0.11.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <cru...@debian.org>
Closes: 1066569
Changes:
python-bx (0.11.0-3) unstable; urgency=medium
.
* Added patch to correct an include. Closes: #1066569
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