Closed tillea closed 8 months ago
Hi, the Debian packaged pysam received a bug report about build failures with Python3.12. You can find a full build log in our CI. It starts with
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 -fwrapv -O2 -g -O2 -ffile-prefix- map=/builds/med-team/python-pysam/debian/output/source_dir=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/builds/med-team/ python-pysam/debian/output/source_dir/pysam -I/usr/include -I/builds/med-team/python-pysam/debian/output/source_dir/samtools -I/builds/med-team/python-pysam/debian/output/source_dir/samtools/lz4 -I/builds/med-team/python- pysam/debian/output/source_dir/bcftools -I/builds/med-team/python-pysam/debian/output/source_dir -I/usr/include/python3.12 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-312/pysam/libchtslib.o -Wno-unused -Wno- strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libchtslib.c: In function ‘__pyx_f_5pysam_10libchtslib_set_verbosity’: pysam/libchtslib.c:1387:32: error: ‘_PyCFrame’ has no member named ‘use_tracing’ 1387 | (unlikely((tstate)->cframe->use_tracing) &&\ | ^~ pysam/libchtslib.c:958:43: note: in definition of macro ‘unlikely’ 958 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ pysam/libchtslib.c:1426:15: note: in expansion of macro ‘__Pyx_IsTracing’ 1426 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~
It would be great if you could adapt pysam to Python3.12. Kind regards, Andreas.
I've received a hint that when building with cython 3.0.6 the failure above is vanishing. Thus I'm closing this issue.
Duplicate of Debian’s previous report, #1242.
Hi, the Debian packaged pysam received a bug report about build failures with Python3.12. You can find a full build log in our CI. It starts with
It would be great if you could adapt pysam to Python3.12. Kind regards, Andreas.