Summary
Bugs of task
bio-dev
Total bugs:
152
Open bugs:
124
Fixed bugs:
28
Links to other tasks
Legend
| Severity | Dependent | Suggested |
|---|
| critical |
0 |
0 |
| grave |
0 |
0 |
| serious |
8 |
18 |
| important |
22 |
11 |
| normal |
26 |
12 |
| minor |
11 |
3 |
| wishlist |
11 |
2 |
|
Summary bugs page of task Biology development
Immediately looking into bugs of the dependencies of this task is advised (1111)*
Open bugs in dependent packages
8 serious, 22 important, 26 normal, 11 minor, 11 wishlist
|
|
| 1096356 |
bambamc: ftbfs with GCC-15 |
forky, sid |
|
|
| 865130 |
reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' |
ftbfs, upstream |
|
|
| 1081606 |
cdk: run upstream tests during build |
help |
|
|
| 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 |
| 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 |
|
| 839784 |
libhdf5-dev: pkg-config file references ONLY the C library |
|
| 968559 |
libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing |
moreinfo |
| 1023446 |
libhdf5-openmpi-dev: h5pcc configured as static build |
wontfix |
| 1040862 |
hdf5: S3 VFD pulls in networking dependencies (libcurl), please package it as a VFD plugin |
moreinfo |
| 1052250 |
pkg-config file incorrect for static linking |
|
| 1100440 |
hdf5: CVE-2025-2153 |
security, upstream |
|
|
| 1081273 |
meryl: Meryl should be packaged separately from new upstream location |
|
|
|
| 1097160 |
libace-perl: ftbfs with GCC-15 |
forky, sid |
|
|
| 948463 |
libai-fann-perl: Integer overflow leading to heap buffer overflow |
|
|
|
| 1102795 |
libbio-db-hts-perl: add perl-xs-dev to Build-Depends |
|
|
|
| 599961 |
libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined |
|
|
|
| 1103129 |
libbioparser-dev: FTBFS in testing/i386: make[1]: *** [debian/rules:11: override_dh_auto_configure] Error 2 |
ftbfs, 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 |
|
|
| 1081295 |
libnhgri-blastall-perl: homepage defunct |
|
|
|
| 1102800 |
librg-blast-parser-perl: add perl-xs-dev to Build-Depends |
|
|
|
| 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 |
|
|
| 1102865 |
libsort-key-top-perl: add perl-xs-dev to Build-Depends |
|
|
|
| 1081848 |
libzerg-perl: homepage defunct |
|
| 1102791 |
libzerg-perl: add perl-xs-dev to Build-Depends |
|
|
|
| 1091257 |
mcl: FTBFS on armhf: mcxquery.c:1242:58: error: passing argument 4 of âget_cls_idâ from incompatible pointer type [-Wincompatible-pointer-types] |
ftbfs, sid, trixie |
|
|
| 1099518 |
minimap2: error: type mismatch in conditional expression on loong64 |
patch |
|
|
| 225651 |
ncbi-tools-x11: want Cn3D++ |
|
|
|
| 1095955 |
openmm: please package v8.2.0 |
|
|
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| 1068052 |
openms: FTBFS on armel,armhf (error: âQOpenGLFunctions_2_0â does not name a type) |
ftbfs |
|
|
| 1078268 |
pyfai: please make the package build reproducible |
|
|
|
| 1103074 |
pyranges: FTBFS in testing/i386: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13 |
ftbfs, sid, trixie |
|
|
| 1083596 |
python-airr: (build-)depends on deprecated module python3-pkg-resources |
sid, trixie |
|
|
| 1075928 |
python-anndata: tests fail with scipy 1.13 |
|
| 1094924 |
python-anndata compatibility with zarr3 |
fixed-upstream, ftbfs, sid, trixie |
| 1100261 |
python-anndata: FTBFS: E AttributeError: module 'zarr' has no attribute 'DirectoryStore' |
fixed-upstream, ftbfs, sid, trixie |
|
|
| 1102990 |
please remove examples from dist-packages directory |
|
|
|
| 1092791 |
FTBFS: TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given |
fixed-upstream, ftbfs, upstream |
|
|
| 1058479 |
python-cogent: please (temporarily) drop python3-numba dependencies |
wontfix |
| 1090269 |
python-cogent: FTBFS: E ImportError: Numba could not be imported. |
ftbfs |
|
|
| 1085900 |
python-csb: Python SyntaxWarning |
pending |
|
|
| 1058482 |
python-loompy: please (temporarily) drop python3-numba dependencies |
|
| 1083659 |
python-loompy: (build-)depends on deprecated module python3-pkg-resources |
sid, trixie |
| 1085932 |
python-loompy: Python SyntaxWarning |
|
| 1090279 |
python-loompy: FTBFS: E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' |
ftbfs |
|
|
| 1046218 |
python-streamz: Fails to build source after successful build |
ftbfs, sid, trixie |
| 1083714 |
python-streamz: (build-)depends on deprecated module python3-pkg-resources |
sid, trixie |
|
|
| 983517 |
pytorch: Build documentation |
|
| 1057644 |
pytorch: build for all supported Python versions |
wontfix |
| 1102203 |
pytorch: CVE-2025-3136 |
security, upstream |
| 1102219 |
pytorch: CVE-2025-2148 |
security, upstream |
| 1102220 |
pytorch: CVE-2025-2149 |
security, upstream |
| 1102229 |
pytorch: CVE-2025-2953 |
security, upstream |
| 1102230 |
pytorch: CVE-2025-2998 |
security, upstream |
| 1102231 |
pytorch: CVE-2025-2999 |
security, upstream |
| 1102232 |
pytorch: CVE-2025-3000 |
security, upstream |
| 1102233 |
pytorch: CVE-2025-3001 |
security, upstream |
| 1102236 |
pytorch: CVE-2025-3121 |
security, upstream |
|
|
| 927955 |
python-rdkit: missing module pyAvalonTools |
|
|
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| 1097784 |
relion: ftbfs with GCC-15 |
forky, sid |
|
|
| 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 |
| 1103097 |
seqan3: FTBFS in testing/i386: alphabet_base.hpp:56:24: error: static assertion failed: alphabet size must be >= 1 |
ftbfs, sid, trixie |
|
|
| 1088534 |
snakemake: move from twitter-bootstrap{3,4} to bootstrap-html (v5) |
upstream |
| 1095394 |
snakemake: tests randomly failing or hanging |
ftbfs, sid, trixie |
|
|
| 1097922 |
spoa: ftbfs with GCC-15 |
forky, sid |
|
|
| 1097930 |
sra-sdk: ftbfs with GCC-15 |
forky, sid |
Open bugs in suggested packages
18 serious, 11 important, 12 normal, 3 minor, 2 wishlist
|
|
| 1049876 |
bbhash: FTBFS on 32 bit architectures |
ftbfs, sid, trixie |
| 1096359 |
bbhash: ftbfs with GCC-15 |
forky, sid |
|
|
| 928076 |
bcbio: Workflows not ready for non-developers to depend on. |
|
|
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| 1096367 |
bifrost: ftbfs with GCC-15 |
forky, sid |
|
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| 1103105 |
cthreadpool: FTBFS in testing/i386: E: Build killed with signal TERM after 150 minutes of inactivity |
ftbfs, sid, trixie |
|
|
| 1096651 |
freecontact: ftbfs with GCC-15 |
forky, sid |
|
|
| 1096676 |
gatk-bwamem: ftbfs with GCC-15 |
forky, sid |
|
|
| 1092841 |
genomicsdb: FTBFS with fmtlib 11.1 |
ftbfs |
| 1103009 |
genomicsdb: FTBFS in testing/arm64: tests failed |
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 |
patch, pending, sid, trixie |
| 1088416 |
intake: move from twitter-bootstrap{3,4} to bootstrap-html (v5) |
upstream |
| 1094915 |
intake commatibility with zarr3 |
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|
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| 1102805 |
libfreecontact-perl: add perl-xs-dev to Build-Depends |
|
|
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| 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) |
confirmed, ftbfs, upstream |
| 1091144 |
libmaus2: ftbfs on arm64 prevents building biobambam2 |
ftbfs, sid, trixie |
| 1091568 |
libmaus2: FTBFS on i386: ld: ./.libs/libmaus2.so: undefined reference to `libmaus2::posix::PosixFunctions::fstatSizeAndMode(int, long long&, unsigned char*)' |
ftbfs, sid, trixie |
|
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| 1097278 |
libtfbs-perl: ftbfs with GCC-15 |
forky, sid |
| 1102835 |
libtfbs-perl: add perl-xs-dev to Build-Depends |
|
|
|
| 1083502 |
networkx: (build-)depends on deprecated module python3-pkg-resources |
sid, trixie |
| 1093516 |
python3-networkx: please drop the extraneous runtime dependency on python3-pkg-resources |
|
|
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| 1097555 |
pbcopper: ftbfs with GCC-15 |
forky, sid |
|
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| 1046648 |
python-ncls: Fails to build source after successful build |
ftbfs, sid, trixie |
|
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| 1035277 |
python-seqcluster: please add autopkgtests (to add coverage for python3-numpy) |
|
|
|
| 1076318 |
q2-alignment hard-codes python 3.11 without depending on it |
sid, trixie |
|
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| 1076315 |
q2-demux hard-codes python 3.11 without depending on it |
sid, trixie |
|
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| 1071882 |
q2-feature-classifier: FTBFS: unsatisfiable build-dependencies |
ftbfs |
|
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| 1076317 |
q2-phylogeny hard-codes python 3.11 without depending on it |
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|
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| 1076914 |
q2-quality-control: FTBFS: rm: cannot remove '/<<PKGBUILDDIR>>/debian/*/usr/lib/python3*/dist-packages/run_decontam.R': No such file or directory |
ftbfs |
|
|
| 1065333 |
q2-types: test data heavily outweighs actual code |
|
| 1076316 |
q2-types hard-codes python 3.11 without depending on it |
sid, trixie |
|
|
| 1076080 |
q2cli: FTBFS in sid (python3.12) |
ftbfs |
|
|
| 1088514 |
q2templates: move from twitter-bootstrap{3,4} to bootstrap-html (v5) |
upstream |
|
|
| 1076314 |
qiime hard-codes python 3.11 without depending on it |
pending, sid, trixie |
| 1084668 |
qiime: removal of Python standard libraries in Python 3.13 |
fixed-upstream, pending |
|
|
| 1103217 |
r-bioc-affxparser: FTBFS: R_affx_cel_parser.cpp:37:33: error: expected primary-expression before 'char' |
ftbfs, sid, trixie |
|
|
| 1097762 |
r-bioc-cner: ftbfs with GCC-15 |
forky, sid |
| 1103198 |
r-bioc-cner: FTBFS: ucsc/common.c:360:9: error: too many arguments to function 'free' |
ftbfs, sid, trixie |
|
|
| 1085689 |
r-bioc-mofa: Python SyntaxWarning |
|
|
|
| 1103199 |
r-bioc-oligo: FTBFS: ParserGzXYS.c:62:11: error: implicit declaration of function 'Calloc'; did you mean 'calloc'? [-Wimplicit-function-declaration] |
ftbfs, sid, trixie |
|
|
| 1083247 |
r-bioc-org.hs.eg.db: homepage defunct, standardize |
|
|
|
| 1097765 |
r-bioc-rtracklayer: ftbfs with GCC-15 |
forky, sid |
| 1103200 |
r-bioc-rtracklayer: FTBFS: ucsc/common.c:249:9: error: too many arguments to function 'free' |
ftbfs, sid, trixie |
|
|
| 1100292 |
r-cran-fastcluster: FTBFS: FAIL: test_vector (tests.fastcluster_test.test_vector) |
ftbfs, help, sid, trixie, upstream |
Done bugs
|
|
| 1022772 |
btllib: fails to build on 32-bit archs |
wontfix |
| 1032358 |
btllib: Depends on libsdsl-dev, breaking installability when not needed |
patch |
| 1058455 |
btllib: add build support for loongarch64 |
patch |
|
|
| 1067499 |
libconsensuscore-dev: ships /usr/include/meson.build |
|
|
|
| 1033703 |
gffread: autopkgtest regression: test dependency not in testing |
bookworm-ignore |
|
|
| 915807 |
hdf5: CVE-2017-17507 |
security, upstream |
|
|
| 1055447 |
htsjdk: FTBFS: 35741 tests completed, 9 failed, 10 skipped |
bookworm, ftbfs, sid, trixie |
|
|
| 1075199 |
libpwiz: ftbfs with GCC-14 |
ftbfs, patch, sid, trixie |
|
|
| 1015525 |
libssw: ftbfs with LTO (link time optimization) enabled |
experimental, sid, trixie |
|
|
| 1054591 |
python3-pyflow: ${VERSION} not expanded in package metadata, causing PEP-440 validation failures |
|
| 1081243 |
python3-pyflow: helloWorld and other examples not runnable, possibly since python2 dropped |
upstream, wontfix |
|
|
| 994423 |
pytorch: Baseline violation on armhf |
bookworm, bullseye, experimental, ftbfs, sid, trixie |
| 1083727 |
pytorch: (build-)depends on deprecated module python3-pkg-resources |
sid, trixie |
| 1083729 |
pytorch: (build-)depends on deprecated module python3-pkg-resources |
sid, trixie |
| 1102472 |
python3-torch: -march=native leaks into rdeps |
|
|
|
| 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 |
|
|
| 1099926 |
src:r-cran-vegan: fails to migrate to testing for too long |
sid, trixie |
|
|
| 1086226 |
rdkit: autopkgtests fail |
|
|
|
| 1084404 |
sra-sdk: move from fuse to fuse3 |
|
| 1087096 |
sra-sdk: Python SyntaxWarning |
patch |
| 1099933 |
autopkgtest requires internet and ca-certificates |
patch |
|
|
| 1073358 |
toil: FTBFS: ModuleNotFoundError: No module named 'boto' |
ftbfs, sid, trixie |
| 1084681 |
toil: removal of Python standard libraries in Python 3.13 |
fixed-upstream, patch |
| 1087116 |
toil: Python SyntaxWarning |
patch |
| 1100817 |
toil: FTBFS: AssertionError: None == None |
ftbfs, sid, trixie |
| 1101085 |
toil: FTBFS: toil.batchSystems.DeadlockException: Deadlock encountered: The workflow is service deadlocked - all 1 running jobs have been the same active services for at least 60 seconds |
ftbfs, sid, trixie |
|
