Package: src:pyfastx
Version: 2.1.0-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --buildsystem pybuild --with python3
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py config
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:268: UserWarning:
Unknown distribution option: 'test_suite'
warnings.warn(msg)
running config
debian/rules execute_before_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# FIXME: we pull the zran files from indexed-gzip source package, which
# does not expose this file in its binary package, so this is vendored
# for the moment. Upstream originally vendored these files straight in
# src/, but stopped for whatever reason, possibly introduction of a
# library somewhere at some point. See #1038995 to track packaging.
cp --no-clobber debian/zran/* src/
cp: warning: behavior of -n is non-portable and may change in future; use
--update=none instead
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py build
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:268: UserWarning:
Unknown distribution option: 'test_suite'
warnings.warn(msg)
running build
running build_py
copying pyfastxcli.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build
running build_ext
building 'pyfastx' extension
creating build
creating build/temp.linux-x86_64-cpython-312
creating build/temp.linux-x86_64-cpython-312/build
creating build/temp.linux-x86_64-cpython-312/<<BUILDDIR>>
creating build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>
creating build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/fakeys.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fakeys.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/fasta.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fasta.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
/<<PKGBUILDDIR>>/src/fasta.c: In function ‘pyfastx_fasta_fetch’:
/<<PKGBUILDDIR>>/src/fasta.c:443:34: warning: comparison of integer expressions
of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long
int’} [-Wsign-compare]
443 | if (strlen(name) >= self->index->cache_name.m) {
| ^~
/<<PKGBUILDDIR>>/src/fasta.c: In function ‘pyfastx_fasta_composition’:
/<<PKGBUILDDIR>>/src/fasta.c:1058:13: warning: unused variable ‘i’
[-Wunused-variable]
1058 | int i;
| ^
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/fastq.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fastq.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/fastx.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fastx.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/fqkeys.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fqkeys.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/index.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/index.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/kseq.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/kseq.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/module.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/module.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
/<<PKGBUILDDIR>>/src/module.c: In function ‘pyfastx_reverse_complement’:
/<<PKGBUILDDIR>>/src/module.c:57:32: warning: passing argument 1 of
‘reverse_complement_seq’ discards ‘const’ qualifier from pointer target type
[-Wdiscarded-qualifiers]
57 | reverse_complement_seq(s);
| ^
In file included from /<<PKGBUILDDIR>>/src/fastq.h:8,
from /<<PKGBUILDDIR>>/src/module.c:3:
/<<PKGBUILDDIR>>/src/util.h:16:35: note: expected ‘char *’ but argument is of
type ‘const char *’
16 | void reverse_complement_seq(char *seq);
| ~~~~~~^~~
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/read.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/read.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/sequence.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/sequence.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
/<<PKGBUILDDIR>>/src/sequence.c: In function ‘pyfastx_sequence_get_fullseq’:
/<<PKGBUILDDIR>>/src/sequence.c:90:32: warning: comparison of integer
expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’
{aka ‘long int’} [-Wsign-compare]
90 | if (strlen(self->name) >= self->index->cache_name.m) {
| ^~
/<<PKGBUILDDIR>>/src/sequence.c: In function ‘pyfastx_sequence_subscript’:
/<<PKGBUILDDIR>>/src/sequence.c:431:20: warning: variable ‘slice_len’ set but
not used [-Wunused-but-set-variable]
431 | Py_ssize_t slice_len;
| ^~~~~~~~~
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/util.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/util.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/zran.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/zran.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -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/python3.12 -c /<<PKGBUILDDIR>>/src/zran_file_util.c -o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/zran_file_util.o -Wno-unused-result
-D_FILE_OFFSET_BITS=64 -D_LFS64_LARGEFILE -D_LARGEFILE64_SOURCE
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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-312/<<PKGBUILDDIR>>/src/fakeys.o build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fasta.o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fastq.o build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fastx.o build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/fqkeys.o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/index.o build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/kseq.o build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/module.o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/read.o build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/sequence.o build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/util.o
build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/zran.o build/temp.linux-x86_64-cpython-312/<<PKGBUILDDIR>>/src/zran_file_util.o -L/usr/lib/x86_64-linux-gnu -o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pyfastx.cpython-312-x86_64-linux-gnu.so -lsqlite3
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build;
python3.12 -m unittest discover -v
test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok
test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ...
ok
test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok
test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok
test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok
test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok
test_build (tests.test_fasta.FastaTest.test_build) ... ok
test_exception (tests.test_fasta.FastaTest.test_exception) ... ok
test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok
test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok
test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok
test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok
test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok
test_iter_upper_full_name
(tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok
test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok
test_module (tests.test_fasta.FastaTest.test_module) ... ERROR
test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok
test_repr (tests.test_fasta.FastaTest.test_repr) ... ok
test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok
test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok
test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok
test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok
test_build (tests.test_fastq.FastqTest.test_build) ... ok
test_exception (tests.test_fastq.FastqTest.test_exception) ... ok
test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok
test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok
test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok
test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok
test_negative (tests.test_fastq.FastqTest.test_negative) ... ok
test_platform (tests.test_fastq.FastqTest.test_platform) ... ok
test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok
test_repr (tests.test_fastq.FastqTest.test_repr) ... ok
test_exception (tests.test_fastx.FastxTest.test_exception) ... ok
test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok
test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok
test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok
test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok
test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok
test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok
test_read (tests.test_read.ReadTest.test_read) ... ok
test_read_description (tests.test_read.ReadTest.test_read_description) ... ok
test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok
test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok
test_repr (tests.test_read.ReadTest.test_repr) ... ok
test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok
test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok
test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok
test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok
test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok
test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok
test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok
test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok
test_seq_reverse_complement
(tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok
test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok
test_seq_by_index
(tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok
test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key)
... ok
======================================================================
ERROR: test_module (tests.test_fasta.FastaTest.test_module)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/tests/test_fasta.py",
line 56, in test_module
with open(join(root_dir, 'src', 'version.h')) as fh:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory:
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/tests/../src/version.h'
----------------------------------------------------------------------
Ran 56 tests in 3.388s
FAILED (errors=1)
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build; python3.12 -m unittest discover
-v
dh_auto_test: error: pybuild --test -i python{version} -p 3.12 returned exit
code 13
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202408/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large from AWS, using sbuild and a
reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
