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.