Summary
Bugs of task
bio-dev
Total bugs:
170
Open bugs:
113
Fixed bugs:
57
Links to other tasks
Legend
Severity | Dependent | Suggested |
critical |
0 |
0 |
grave |
0 |
0 |
serious |
5 |
5 |
important |
19 |
5 |
normal |
20 |
5 |
minor |
33 |
6 |
wishlist |
12 |
3 |
|
Summary bugs page of task Biology development
Immediately looking into bugs of the dependencies of this task is advised (810)*
Open bugs in dependent packages
5 serious, 19 important, 20 normal, 33 minor, 12 wishlist
|
865130 |
reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' |
ftbfs, upstream |
|
1044647 |
fermi-lite: Fails to build source after successful build |
ftbfs, sid, trixie |
1049564 |
fermi-lite: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
|
929564 |
gatb-core-testdata: broken symlink: /usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit |
|
983926 |
gatb-core: ftbfs with -march=x86-64-v2 |
|
|
638753 |
libhdf5-serial-1.8.7: threadsafe memory leaks |
moreinfo |
715959 |
[Mayhem] Bug report on hdf5-tools: gif2h5 crashes with exit status 139 |
|
716008 |
[Mayhem] Bug report on hdf5-tools: h5copy crashes with exit status 139 |
|
716010 |
[Mayhem] Bug report on hdf5-tools: h5diff crashes with exit status 139 |
|
716011 |
[Mayhem] Bug report on hdf5-tools: h5dump crashes with exit status 139 |
|
716012 |
[Mayhem] Bug report on hdf5-tools: h5import crashes with exit status 139 |
|
740613 |
libhdf5-7: Please include support for compression with libaec |
|
748587 |
Duplicate and conflicting definitions of variable FILENAME |
upstream |
839784 |
libhdf5-dev: pkg-config file references ONLY the C library |
|
915807 |
hdf5: CVE-2017-17507 |
security, upstream |
958174 |
hdf5: please add the hdf5plugins |
|
968559 |
libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing |
moreinfo |
1023446 |
libhdf5-openmpi-dev: h5pcc configured as static build |
|
1023820 |
hdf5: Dependencies not tight enough |
|
1031726 |
hdf5: CVE-2022-26061 CVE-2022-25972 CVE-2022-25942 |
security, upstream |
1034807 |
hdf5: CVE-2018-11205 |
security, upstream |
1034838 |
hdf5: CVE-2019-8396 CVE-2019-8398 |
security |
1040862 |
hdf5: S3 VFD pulls in networking dependencies (libcurl), please package it as a VFD plugin |
|
1052250 |
pkg-config file incorrect for static linking |
|
1063856 |
hdf5: new upstream release |
|
1067758 |
Please provide a nojava build profile |
|
1067789 |
hdf5: diff for NMU version 1.10.10+repack-3.2 |
patch, pending |
1067950 |
hdf5: diff for NMU version 1.10.10+repack-3.3 |
patch, pending |
|
948463 |
libai-fann-perl: Integer overflow leading to heap buffer overflow |
|
|
599961 |
libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined |
|
|
1015473 |
libbpp-core: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1015475 |
libbpp-phyl: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1015474 |
libbpp-popgen: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1015476 |
libbpp-qt: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1015477 |
libbpp-raa: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1015478 |
libbpp-seq: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1015479 |
libbpp-seq-omics: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1039562 |
libchado-perl: fails to access database during installation |
wontfix |
1047661 |
libchado-perl: Fails to build source after successful build |
ftbfs, sid, trixie |
1049705 |
libchado-perl: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
|
1048817 |
libcifpp: Fails to build source after successful build |
ftbfs, sid, trixie |
1063191 |
libcifpp-data: Incorrect URL in update-libcifpp-data script |
patch |
1068860 |
[INTL:sv] Swedish strings for libcifpp debconf |
l10n, patch |
|
1015484 |
libedlib: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1057518 |
libgoby-java: FTBFS with default Java 21 |
ftbfs |
|
1015504 |
libmuscle: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1015505 |
libncl: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1046388 |
libpdb-redo: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1046372 |
librcsb-core-wrapper: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1047025 |
librostlab: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1067961 |
python3-sbml5 depends on swig |
|
|
1048497 |
libslow5lib: Fails to build source after successful build |
ftbfs, sid, trixie |
1049769 |
libslow5lib: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
1069771 |
libslow5lib FTBFS on big endian architectures |
ftbfs |
|
1015525 |
libssw: ftbfs with LTO (link time optimization) enabled |
experimental, sid, trixie |
|
1068925 |
macromoleculebuilder: FTBFS on armhf (error: inconsistent deduction for auto return type: 'long int' and then 'long long int') |
ftbfs |
|
1046152 |
mcl: Fails to build source after successful build |
ftbfs, sid, trixie |
|
225651 |
ncbi-tools-x11: want Cn3D++ |
|
|
1046095 |
nim-hts: Fails to build source after successful build |
ftbfs, sid, trixie |
1049588 |
nim-hts: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
|
1061814 |
openmm fails its autopkg tests with Python 3.12 |
ftbfs, patch, sid, trixie |
1065911 |
openmm: Please drop dependencies on python3-distutils |
|
|
1068052 |
openms: FTBFS on armel,armhf (error: âQOpenGLFunctions_2_0â does not name a type) |
ftbfs |
|
1061938 |
pyfai: Segfault when closing a dialg |
|
|
1064147 |
ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO |
fixed-upstream, ftbfs, sid |
|
1067989 |
python3-cobra: Please replace python3-appdirs dependency with platformdirs |
sid, trixie |
|
1058479 |
python-cogent: please (temporarily) drop python3-numba dependencies |
wontfix |
|
1069359 |
python-cooler: FTBFS on arm64: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpi8kk3ih0/tmp_sf3nv42.multi.cool' |
ftbfs, sid, trixie |
|
1058482 |
python-loompy: please (temporarily) drop python3-numba dependencies |
|
|
1068960 |
python-pybedtools: FTBFS: testsuite error: 14 failed, 491 passed, 2 deselected, 3 xfailed |
ftbfs |
|
1045607 |
python-pyspoa: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1046218 |
python-streamz: Fails to build source after successful build |
ftbfs, sid, trixie |
|
983517 |
pytorch: Build documentation |
|
1056388 |
FTBFS with fmtlib 10 |
fixed-upstream, ftbfs |
1057644 |
pytorch: build for all supported Python versions |
wontfix |
|
1069509 |
r-cran-metamix: FTBFS on armhf: tests fail |
ftbfs, sid, trixie |
|
927955 |
python-rdkit: missing module pyAvalonTools |
|
964773 |
rdkit: Please build rdkit with inchi support |
wontfix |
983040 |
rdkit: doesn't ship with inchi support enabled |
wontfix |
983077 |
rdkit doesn't ship with inchi support enabled |
wontfix |
1064311 |
rdkit: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1045897 |
reprof: Fails to build source after successful build |
ftbfs, sid, trixie |
1049597 |
reprof: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
|
1045625 |
ruby-crb-blast: Fails to build source after successful build |
ftbfs, sid, trixie |
|
917851 |
seqan2 2.4.0+dfsg-9: FTBFS, alignment problem |
ftbfs |
1047218 |
seqan2: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1048951 |
seqan3: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1069370 |
shasta: FTBFS: dpkg-shlibdeps: error: cannot continue due to the error above |
ftbfs, sid, trixie |
|
1053411 |
sra-sdk: FTBFS with re2 >= 20230601 (which requires abseil) |
upstream |
Open bugs in suggested packages
5 serious, 5 important, 5 normal, 6 minor, 3 wishlist
|
1049876 |
bbhash: FTBFS on 32 bit architectures |
ftbfs, sid, trixie |
|
928076 |
bcbio: Workflows not ready for non-developers to depend on. |
|
1018312 |
bcbio: build-depends on python3-nose or uses it for autopkgtest |
|
|
1022772 |
btllib: fails to build on 32-bit archs |
wontfix |
1032358 |
btllib: Depends on libsdsl-dev, breaking installability when not needed |
patch, pending |
1058455 |
btllib: add build support for loongarch64 |
patch |
|
1043870 |
concurrentqueue: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1045042 |
ctdconverter: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1069261 |
cwlformat: fails with newer ruamel.yaml |
patch, sid, trixie |
|
1049797 |
freecontact: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
1069552 |
freecontact: FTBFS on armel: make[1]: *** [Makefile:469: all-recursive] Error 1 |
ftbfs, sid, trixie |
|
1063953 |
intake: autopkgtest regression with pytest 8 |
|
1064752 |
intake: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13 |
ftbfs, sid, trixie |
1067969 |
python3-intake: Please replace python3-appdirs dependency with platformdirs |
sid, trixie |
|
934619 |
libmaus2 FTBFS (mostly 32bit): error: no matching function for call |
fixed-upstream, ftbfs, help, upstream |
1069691 |
libmaus2: FTBFS on arm64: what(): AutoArray<unsigned long,alloc_type_memalign_cacheline> failed to allocate 1398102 elements (11184816 bytes) |
ftbfs |
|
1060444 |
python3-networkx: postinst warning |
|
|
1046648 |
python-ncls: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1035277 |
python-seqcluster: please add autopkgtests (to add coverage for python3-numpy) |
|
|
1065945 |
q2-emperor: Please drop dependencies on python3-distutils |
|
|
1065946 |
q2-sample-classifier: Please drop dependencies on python3-distutils |
|
|
1065333 |
q2-types: test data heavily outweighs actual code |
|
|
1066085 |
q2cli: please make the build reproducible |
patch, pending |
|
1068006 |
qiime: Please replace python3-appdirs dependency with platformdirs |
sid, trixie |
Done bugs
|
1061931 |
biosquid: NMU diff for 64-bit time_t transition |
patch |
|
1067499 |
libconsensuscore-dev: ships /usr/include/meson.build |
|
|
1062588 |
ffindex: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1062403 |
freecontact: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1062071 |
genometools: NMU diff for 64-bit time_t transition |
patch |
|
1033703 |
gffread: autopkgtest regression: test dependency not in testing |
bookworm-ignore |
|
1064095 |
hdf5: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
1065331 |
libhdf5-103-1t64: depends on libcurl4 instead of libcurl4t64 |
|
1068320 |
hdf5: Needs to not depend on libopenmpi-dev for 32-bit systems |
|
|
1062344 |
htslib: NMU diff for 64-bit time_t transition |
patch |
|
1062229 |
libbigwig: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1065759 |
libbio-samtools-perl: FTBFS: lib/Bio/DB/Sam.xs:324:4: error: implicit declaration of function âbam_sort_coreâ; did you mean âbam_format1_coreâ? [-Werror=implicit-function-declaration] |
confirmed, ftbfs, help, patch |
|
1047210 |
libbio-scf-perl: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1062230 |
libbpp-core: NMU diff for 64-bit time_t transition |
patch |
|
1062234 |
libbpp-phyl: NMU diff for 64-bit time_t transition |
patch |
|
1062232 |
libbpp-phyl-omics: NMU diff for 64-bit time_t transition |
patch |
|
1062236 |
libbpp-popgen: NMU diff for 64-bit time_t transition |
patch |
|
1062237 |
libbpp-qt: NMU diff for 64-bit time_t transition |
patch |
|
1062240 |
libbpp-seq: NMU diff for 64-bit time_t transition |
patch |
|
1062239 |
libbpp-seq-omics: NMU diff for 64-bit time_t transition |
patch |
|
1062316 |
libgkarrays: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1068573 |
libmaus2: fix error caused by sysconf function |
|
|
1062416 |
libmems: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1066475 |
libpsortb: FTBFS: debug_funcs.c:320:38: error: implicit declaration of function âget_mtx_indexâ [-Werror=implicit-function-declaration] |
ftbfs, sid, trixie |
|
1062580 |
libpwiz: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1062602 |
librcsb-core-wrapper: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1062612 |
librostlab: NMU diff for 64-bit time_t transition |
patch |
|
1048643 |
librostlab-blast: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1062619 |
libsbml: NMU diff for 64-bit time_t transition |
patch |
1068105 |
drop the Python3-Version attribute |
ftbfs, patch, sid, trixie |
|
1063136 |
libslow5lib: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1063137 |
libtabixpp: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1066716 |
libtfbs-perl: FTBFS: ./lib/pwm_searchPFF.c:55:7: error: implicit declaration of function âannounceâ [-Werror=implicit-function-declaration] |
ftbfs, sid, trixie |
|
1062695 |
libvbz-hdf-plugin: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1045603 |
libwfa2: Fails to build source after successful build |
ftbfs, sid, trixie |
1062731 |
libwfa2: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1064245 |
ncbi-tools6: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1064503 |
Please pacakge new upstream release 3.2.1 |
|
|
1063095 |
openmm: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|
1044072 |
python-anndata: FTBFS with pandas 2.0 |
sid, trixie |
|
1068996 |
python3-bx: maf_word_frequency.py fails to run |
|
|
1067759 |
python-dnaio ftbfs on s390x |
ftbfs, sid, trixie |
|
1063974 |
python-gffutils: autopkgtest regression with pytest 8 |
|
|
1054591 |
python3-pyflow: ${VERSION} not expanded in package metadata, causing PEP-440 validation failures |
|
|
994423 |
pytorch: Baseline violation on armhf |
bookworm, bullseye, experimental, ftbfs, sid, trixie |
1050175 |
Missing symbol when importing torch |
sid, trixie |
1060097 |
pytorch: FBFS: /<<PKGBUILDDIR>>/aten/src/ATen/native/quantized/cpu/qlinear_prepack.cpp:249:103: error: cannot convert âdnnl::memory::data_typeâ to âconst ideep::dims&â {aka âconst std::vector<long int>&â} |
ftbfs |
1065941 |
pytorch: Please drop dependencies on python3-distutils |
ftbfs |
|
1034852 |
r-bioc-annotationhub: autopkgtest regression: download failed |
bookworm-ignore |
|
1039501 |
r-bioc-biomart: autopkgtest regression: Failure ('test_ensembl_ssl_settings.R:71') |
|
|
1025045 |
r-bioc-structuralvariantannotation: Test failures in autopkgtest |
bookworm-ignore, upstream |
|
1063431 |
src:r-cran-future.apply: fails to migrate to testing for too long: autopkgtest failure |
sid, trixie, upstream |
|
1069296 |
sbmltoolbox: Depends on pre-t64 libsbml5 |
|
|
1068010 |
snakemake: Please replace python3-appdirs dependency with platformdirs |
sid, trixie |
|
1040391 |
sra-toolkit: broken symlink: /usr/lib/debian-med/bin/kget -> ../../../bin/vdb-get |
|
1065961 |
sra-sdk: Please drop dependencies on python3-distutils |
ftbfs |
|
1063189 |
staden-io-lib: NMU diff for 64-bit time_t transition |
patch, sid, trixie |
|