Summary
Bugs of task
bio-dev
Total bugs:
163
Open bugs:
135
Fixed bugs:
28
Links to other tasks
Legend
Severity | Dependent | Suggested |
critical |
0 |
0 |
grave |
0 |
0 |
serious |
0 |
2 |
important |
18 |
2 |
normal |
23 |
11 |
minor |
60 |
9 |
wishlist |
9 |
1 |
|
Summary bugs page of task Biology development
Immediately looking into bugs of the dependencies of this task is advised (729)*
Open bugs in dependent packages
18 important, 23 normal, 60 minor, 9 wishlist
|
865130 |
reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' |
ftbfs, upstream |
1043881 |
bamtools: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1043774 |
bio-tradis: Fails to build source after successful build |
ftbfs, sid, trixie |
|
749736 |
biococoa: GCC warnings that may lead to runtime issues with new GNUstep libraries |
bookworm, bullseye, buster, jessie, sid, stretch, trixie |
|
1043996 |
biosquid: Fails to build source after successful build |
ftbfs, sid, trixie |
1049808 |
biosquid: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
|
1056799 |
cyvcf2: ftbfs with cython 3.0.x |
sid, trixie |
|
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 |
|
|
1046620 |
htseq: Fails to build source after successful build |
ftbfs, sid, trixie |
|
948463 |
libai-fann-perl: Integer overflow leading to heap buffer overflow |
|
|
1047073 |
libbio-asn1-entrezgene-perl: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1046631 |
libbio-samtools-perl: Fails to build source after successful build |
ftbfs, sid, trixie |
|
599961 |
libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined |
|
1047210 |
libbio-scf-perl: Fails to build source after successful build |
ftbfs, sid, trixie |
|
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 |
|
1015484 |
libedlib: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
1048671 |
libedlib: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1015486 |
libfastahack: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
|
1046227 |
libgo-perl: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1047938 |
libjloda-java: Fails to build source after successful build |
ftbfs, sid, trixie |
|
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 |
|
1046603 |
libpll: Fails to build source after successful build |
ftbfs, sid, trixie |
1049759 |
libpll: Fails to build binary packages again 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 |
|
1048643 |
librostlab-blast: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1047821 |
libseqlib: Fails to build source after successful build |
ftbfs, sid, trixie |
|
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 |
|
1015525 |
libssw: ftbfs with LTO (link time optimization) enabled |
experimental, sid, trixie |
|
1015526 |
libtabixpp: ftbfs with LTO (link time optimization) enabled |
sid, trixie |
1049726 |
libtabixpp: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
|
1057440 |
libvcflib: 1 |
|
|
1045603 |
libwfa2: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1046152 |
mcl: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1046060 |
minimap2: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1044055 |
mirtop: test failure with pandas 2.0 |
|
|
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 |
|
1056438 |
pyfai's autopkg tests fail with Python 3.12 |
sid, trixie |
|
1044064 |
pyranges: FTBFS with pandas 2.0 |
|
|
1044072 |
python-anndata: FTBFS with pandas 2.0 |
|
1056455 |
python-anndata's autopkg tests fail with Python 3.12 |
sid, trixie |
|
1044074 |
python-biom-format: FTBFS with pandas 2.0 |
|
|
1055709 |
python-bx ftbfs with Python 3.12 |
sid, trixie |
|
1053940 |
python-cooler: test failure with pandas 2.1 |
|
|
1056464 |
python-csb's autopkg tests fail with Python 3.12 |
sid, trixie |
|
1044056 |
python-nanoget: test failure with pandas 2.0 |
|
|
1046425 |
python-pairix: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1046452 |
python-pymummer: Fails to build source after successful build |
ftbfs, pending, sid, trixie |
|
1045607 |
python-pyspoa: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1046140 |
python-pyvcf: Fails to build source after successful build |
ftbfs, pending, sid, trixie |
|
1044065 |
python-skbio: FTBFS with pandas 2.0 |
|
1048510 |
python-skbio: Fails to build source after successful build |
ftbfs, sid, trixie |
1049511 |
python-skbio: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
1056047 |
python-skbio ftbfs with Python 3.12 (and cython 3.0.5) |
sid, trixie |
1056873 |
python-skbio: ftbfs with cython 3.0.x |
sid, trixie |
|
1049145 |
python-sqt: 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 |
|
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 |
1055696 |
python3-rdkit: unusable with Python 3.12 |
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 |
|
1015667 |
spoa: ftbfs with LTO (link time optimization) enabled |
experimental, sid, trixie |
|
1040391 |
sra-toolkit: broken symlink: /usr/lib/debian-med/bin/kget -> ../../../bin/vdb-get |
|
1053411 |
sra-sdk: FTBFS with re2 >= 20230601 (which requires abseil) |
upstream |
Open bugs in suggested packages
2 serious, 2 important, 11 normal, 9 minor, 1 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 |
|
1032358 |
btllib: Depends on libsdsl-dev, breaking installability when not needed |
patch |
|
1043870 |
concurrentqueue: Fails to build source after successful build |
ftbfs, sid, trixie |
|
976506 |
conda-package-handling: FTBFS in bullseye (failing tests) |
bullseye, ftbfs, patch, pending, sid, trixie |
1052523 |
conda-package-handling: please remove extraneous dependency on python3-six |
|
|
1045042 |
ctdconverter: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1049797 |
freecontact: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
|
1044050 |
intake: FTBFS with pandas 2.0 |
|
1050623 |
intake: autopkgtest needs update for dask 2023.8.0 |
ftbfs, sid, trixie |
|
934619 |
libmaus2 FTBFS (mostly 32bit): error: no matching function for call |
fixed-upstream, ftbfs, help, upstream |
|
1049859 |
minimap: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
|
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) |
|
|
1045829 |
q2-demux: Fails to build source after successful build |
ftbfs, sid, trixie |
1053942 |
q2-demux: test failure with pandas 2.1 |
|
|
1044060 |
q2-quality-control: test failure with pandas 2.0 |
|
|
1048362 |
q2-taxa: Fails to build source after successful build |
ftbfs, sid, trixie |
1053943 |
q2-taxa: test failure with pandas 2.1 |
|
|
1053944 |
q2-types: test failure with pandas 2.1 |
|
|
1044068 |
q2templates: FTBFS with pandas 2.0 |
|
|
1024580 |
r-bioc-affxparser: FTBFS on hppa - cannot handle R_PARISC_PCREL17F |
ftbfs, patch |
|
1049550 |
terraphast: Fails to build binary packages again after successful build |
ftbfs, sid, trixie |
Done bugs
|
1043819 |
bbhash: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1033703 |
gffread: autopkgtest regression: test dependency not in testing |
bookworm-ignore |
|
972537 |
please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3 |
|
|
1055447 |
htsjdk: FTBFS: 35741 tests completed, 9 failed, 10 skipped |
ftbfs, sid |
|
1045612 |
libgoby-java: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1032532 |
libthread-pool: fails to compile on 32bit platforms |
patch |
|
1057253 |
libvcflib: add support for loongarch64 |
patch |
|
992180 |
openmm FTBFS on \!amd64/arm64/hurd-i386/i386/ppc64el |
ftbfs |
1054763 |
openmm: FTBFS: make[1]: *** [debian/rules:38: override_dh_auto_test] Error 2 |
ftbfs, sid, trixie |
|
1056323 |
python-biom-format: FTBFS with Python 3.12 (test failures) |
ftbfs, patch, sid, trixie |
|
1055708 |
python-biopython's autopkg tests fail with Python 3.12 |
sid, trixie |
|
1030885 |
python-cogent: FTBFS (some tests require more than one CPU) |
ftbfs, patch |
|
1044066 |
python-pyani: FTBFS with pandas 2.0 |
|
|
1054591 |
python3-pyflow: ${VERSION} not expanded in package metadata, causing PEP-440 validation failures |
|
|
1047165 |
python-pysam: Fails to build source after successful build |
ftbfs, sid, trixie |
1055505 |
python-pysam new upstream needed to build with Python 3.12 |
sid, trixie, upstream |
|
1056037 |
python-sqt ftbfs with Python 3.12 |
sid, trixie |
|
994423 |
pytorch: Baseline violation on armhf |
bookworm, bullseye, ftbfs, sid |
1050175 |
Missing symbol when importing torch |
|
|
1029700 |
q2-quality-control: tests fail with scipy 1.10 |
|
|
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 |
|
1054790 |
rdkit: FTBFS: make[1]: *** [debian/rules:88: override_dh_auto_configure] Error 2 |
ftbfs, sid, trixie |
|
1053509 |
shasta: autopkgtest regression on arm64: is memory suddenly not enough? |
|
|
1045316 |
snakemake: Fails to build source after successful build |
ftbfs, sid, trixie |
|
1031192 |
toil: FTBFS (The job JobClass is requesting 2.0 cores) |
ftbfs |
|
1048281 |
unifrac-tools: Fails to build source after successful build |
ftbfs, sid, trixie |
|