Summary
Bugs of task
bio
Total bugs:
158
Open bugs:
144
Fixed bugs:
14
Links to other tasks
Legend
| Severity | Dependent | Suggested |
|---|
| critical |
1 |
0 |
| grave |
0 |
2 |
| serious |
9 |
6 |
| important |
20 |
8 |
| normal |
45 |
15 |
| minor |
14 |
1 |
| wishlist |
18 |
5 |
|
Summary bugs page of task Biology
Immediately looking into bugs of the dependencies of this task is advised (1213)*
Open bugs in dependent packages
1 critical, 9 serious, 20 important, 45 normal, 14 minor, 18 wishlist
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| 920282 |
abyss fails to build on hurd - googletest EXPECT_DEATH |
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| 967243 |
acedb: depends on deprecated GTK 2 |
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| 1032625 |
please drop transitional package acedb-other-belvu from src:acedb |
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| 1032626 |
please drop transitional package acedb-other-dotter from src:acedb |
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| 1012893 |
anfo: ftbfs with GCC-12 |
bookworm, ftbfs, help, sid |
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| 1035113 |
arden: please add autopkgtests (to add coverage for python3-numpy) |
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| 1036488 |
arden: please add autopkgtests (to add coverage for python3-matplotlib) |
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| 1035116 |
assemblytics: please add autopkgtests (to add coverage for python3-numpy) |
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| 865130 |
reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' |
ftbfs, upstream |
|
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| 870060 |
bcftools FTBFS on big endian: 107 tests failed |
ftbfs, upstream |
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| 1032034 |
beagle: broken package on non arm64/amd64 architectures |
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| 1025424 |
beast-mcmc: please enable autopkgtest |
help |
|
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| 1025830 |
beauti2 fails to start |
help |
|
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| 1035121 |
bitseq: please add autopkgtests (to add coverage for python3-numpy) |
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|
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| 1022772 |
btllib: fails to build on 32-bit archs |
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| 1032358 |
btllib: Depends on libsdsl-dev, breaking installability when not needed |
patch |
|
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| 1010653 |
busco: add autopkgtest to check integration with hmmer and prodigal |
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| 1032036 |
chromhmm: broken package on non arm64/amd64 architectures |
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| 884475 |
clonalorigin: FTBFS on alpha: tests time out |
upstream, wontfix |
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| 1035182 |
cutesv: please add autopkgtests (to add coverage for python3-numpy) |
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|
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| 982869 |
datamash FTBFS on !x86 32bit: FAIL: tests/decorate-errors |
ftbfs, upstream |
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| 903886 |
dawg: Test suite fails |
upstream |
|
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| 862118 |
ea-utils: New upstream version available |
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| 682042 |
emboss-data: ships bulky taxonomy and gene ontology data |
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| 986043 |
emboss: uses media types that are not registered |
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| 750139 |
gamgi: Conflicting return types of function gamgi_engine_iarray_push |
upstream |
| 967366 |
gamgi: depends on deprecated GTK 2 |
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| 715937 |
[Mayhem] Bug report on garlic: garlic crashes with exit status 139 |
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| 749656 |
garlic: Conflicting declarations of function BlurMainWindow_ to cause undefined behaviour |
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| 929564 |
gatb-core-testdata: broken symlink: /usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit |
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| 983926 |
gatb-core: ftbfs with -march=x86-64-v2 |
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| 1015412 |
gatb-core: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 967379 |
gdpc: depends on deprecated GTK 2 |
wontfix |
| 982103 |
gdpc: autopkgtest failure on s390x |
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|
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| 732691 |
Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button |
upstream |
|
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| 1033703 |
gffread: autopkgtest regression: test dependency not in testing |
bookworm-ignore |
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| 967392 |
ghemical: depends on deprecated GTK 2 |
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| 967865 |
ghemical: depends on deprecated libglade2 |
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| 996006 |
ghemical: Segmentation fault when starting |
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| 644397 |
Provide runtime detection for CPU SIMD capabilities |
upstream |
| 983942 |
gromacs: ftbfs with -march=x86-64-v3 |
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|
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| 958244 |
Use system libinih-dev |
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| 986193 |
hinge: no autopkgtest available yet |
newcomer |
| 1035178 |
hinge: please add autopkgtests (to add coverage for python3-numpy) |
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| 1036500 |
hinge: please add autopkgtests (to add coverage for python3-matplotlib) |
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| 1032975 |
igdiscover -- Broken, unusable package due to incomplete code in the binary package |
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| 1021557 |
jellyfish: Performance regression in 2.3.0 (orders of magnitude for some inputs) |
upstream |
|
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| 875328 |
jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined |
upstream, wontfix |
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| 872418 |
jmol: Weblinks in Help do not work |
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| 1009159 |
kmerresistance: Add autopkgtest |
newcomer |
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| 1015486 |
libfastahack: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 1015505 |
libncl: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 1015525 |
libssw: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 1032557 |
libvcflib breaks ABI without SONAME bump |
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| 967603 |
ltrsift: depends on deprecated GTK 2 |
upstream, wontfix |
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| 1035175 |
metaphlan: please add autopkgtests (to add coverage for python3-numpy) |
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| 1035188 |
microbegps: please add autopkgtests (to add coverage for python3-numpy) |
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| 1036480 |
microbegps: please add autopkgtests (to add coverage for python3-matplotlib) |
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| 996981 |
multiqc: Link to jquery missing |
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| 891197 |
Please switch to pcre2 |
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| 956850 |
ncbi-blast+: Please provide /usr/bin/legacy_blast.pl |
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| 984871 |
ncbi-blast+: Missing headers for shared libraries |
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| 1010110 |
ncbi-blast+: terminate called after throwing an instance of 'ncbi::CIO_Exception' |
wontfix |
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| 225651 |
ncbi-tools-x11: want Cn3D++ |
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| 1025370 |
ntcard: ftbfs with nthash 2.3.0 |
ftbfs, upstream |
| 1032672 |
ntcard: disabling "32-bit" disabled too many archs |
patch |
|
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| 964082 |
parsinsert fails it's tests when built with -O3 |
bookworm, bullseye, moreinfo, sid, unreproducible |
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| 986194 |
pique: no autopkgtest available yet |
newcomer |
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| 1009156 |
pplacer: Add autopkgtest |
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| 1024889 |
pplacer: build-depedends on dropped package. |
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| 602610 |
Package freemol.mengine for full modeling capabilities |
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| 709306 |
pymol: Crashes when running within xrdp/vnc (no 3D support) |
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| 765794 |
Race condition when running scripts in "stdin" mode |
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| 783653 |
pymol: Segmentation fault immediately after loading pdb |
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| 1036374 |
[INTL:es] Spanish translation of qcumber debconf template |
l10n, patch |
| 1036506 |
qcumber: please add autopkgtests (to add coverage for python3-matplotlib) |
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| 1030954 |
quorum: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 642084 |
qutemol: Cannot start the program |
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| 939033 |
qutemol: Uses GifQuantizeBuffer - stops working with newer giflib |
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| 1024661 |
r-bioc-bitseq: orphaned upstream and blocking BioC 3.16 transition |
ftbfs |
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| 1033853 |
r-bioc-megadepth: autopkgtest regression: different output |
bookworm-ignore |
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| 961234 |
r-cran-treescape: FTBFS on ppc64el:Segmentation fault |
bookworm, bullseye, ftbfs, sid |
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| 909766 |
Use Debian packaged spdlog instead of code copy of old version |
help, upstream |
| 976588 |
rapmap: FTBFS on arm64 (when trying to build arch:all) |
bookworm, bullseye, ftbfs, sid |
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| 1027384 |
rnahybrid: please enable riscv64 build |
ftbfs, pending |
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| 1015654 |
sambamba: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
|
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| 917851 |
seqan2 2.4.0+dfsg-9: FTBFS, alignment problem |
ftbfs |
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| 967743 |
seqtools: depends on deprecated GTK 2 |
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| 848589 |
snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated) |
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| 1031465 |
snippy: FTBFS: make[2]: *** [Makefile:32: S1/snps.tab] Error 2 |
bookworm, ftbfs, sid |
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| 1029202 |
snippy: Error when using snpeff 5.1 |
upstream |
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| 976523 |
spades: FTBFS: jemalloc_internal.h:292:6: error: #error "No LG_QUANTUM definition for architecture; specify via CPPFLAGS" |
bookworm, bullseye, ftbfs, sid |
| 1015668 |
spades: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 1015667 |
spoa: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 1033089 |
subread: reproducible-builds: Embedded build path in various binaries |
patch |
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| 956848 |
t-coffee: should use "example" blastpgp.pl |
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| 1031192 |
toil: FTBFS (The job JobClass is requesting 2.0 cores) |
ftbfs |
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| 846481 |
src:treeviewx: Please remove statically linked code copy of libncl |
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| 981874 |
trinityrnaseq: flaky autopkgtest |
bookworm, bullseye, sid |
| 1004773 |
trinityrnaseq: test loops until disk full (with r-cran-readr from unstable on arm64) |
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| 1006336 |
trinityrnaseq: autopkgtest regression in testing: segmentation fault |
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| 980509 |
umap-learn: Binary package name should be python3-umap-learn |
pending |
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| 976511 |
vg: FTBFS on arm64: configure: error: Could not find a version of the library! |
bookworm, bullseye, ftbfs, sid |
| 987184 |
vg -- excessive variants built, and not tested |
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| 1013061 |
vg: ftbfs with GCC-12 |
bookworm, ftbfs, sid |
| 1015699 |
vg: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 1035276 |
xpore: please add autopkgtests (to add coverage for python3-numpy) |
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Open bugs in suggested packages
2 grave, 6 serious, 8 important, 15 normal, 1 minor, 5 wishlist
|
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| 916406 |
libarb-dev: Missing symbols in static libraries |
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| 918015 |
[INTL:sv] Swedish strings for arb debconf |
l10n, patch |
| 1026401 |
arb: [INTL:pt_BR] Brazilian Portuguese debconf templates translation |
l10n, patch |
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| 928076 |
bcbio: Workflows not ready for non-developers to depend on. |
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| 1018312 |
bcbio: build-depends on python3-nose or uses it for autopkgtest |
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| 976506 |
conda-package-handling: FTBFS in bullseye (failing tests) |
bullseye, ftbfs, patch, sid |
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| 1030327 |
science-numericalcomputation: please stop recommending python3-theano as it is being removed |
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| 1032638 |
please drop transitional package science-electronics from src:debian-science |
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| 995966 |
epigrass: epirunner and epidash fail to run due to missing dash modules |
pending |
| 998265 |
epigrass: autopkgtest regression: The 'panel' distribution was not found |
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| 638753 |
libhdf5-serial-1.8.7: threadsafe memory leaks |
moreinfo |
| 715959 |
[Mayhem] Bug report on hdf5-tools: gif2h5 crashes with exit status 139 |
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| 716008 |
[Mayhem] Bug report on hdf5-tools: h5copy crashes with exit status 139 |
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| 716010 |
[Mayhem] Bug report on hdf5-tools: h5diff crashes with exit status 139 |
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| 716011 |
[Mayhem] Bug report on hdf5-tools: h5dump crashes with exit status 139 |
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| 716012 |
[Mayhem] Bug report on hdf5-tools: h5import crashes with exit status 139 |
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| 740613 |
libhdf5-7: Please include support for compression with libaec |
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| 748587 |
Duplicate and conflicting definitions of variable FILENAME |
upstream |
| 839784 |
libhdf5-dev: pkg-config file references ONLY the C library |
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| 915807 |
hdf5: CVE-2017-17507 |
security, upstream |
| 958174 |
hdf5: please add the hdf5plugins |
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| 968559 |
libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing |
moreinfo |
| 1023446 |
libhdf5-openmpi-dev: h5pcc configured as static build |
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| 1023820 |
hdf5: Dependencies not tight enough |
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| 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 |
|
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| 1027386 |
pysam -- no definition for bam_dup1 |
confirmed |
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| 1035277 |
python-seqcluster: please add autopkgtests (to add coverage for python3-numpy) |
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| 1034852 |
r-bioc-annotationhub: autopkgtest regression: download failed |
bookworm-ignore |
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| 1025045 |
r-bioc-structuralvariantannotation: Test failures in autopkgtest |
bookworm-ignore, upstream |
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| 1036681 |
relion-cuda: FTBFS with CUDA 12: nvcc fatal : Value 'sm_35' is not defined for option 'gpu-architecture' |
ftbfs, sid |
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| 986200 |
sift: Please provide autopkgtest |
newcomer |
| 987606 |
sift: does not autobuild on buildds |
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| 1010358 |
ugene: Fix for non-constant SIGSTKSZ |
ftbfs, patch, pending |
| 1018252 |
Is ugene still non-free? |
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| 1032688 |
ugene: unused build-dependency on removed libprocps-dev |
patch |
Done bugs
|
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| 1010834 |
biosyntax-vim: Unusable with vim-addon-manager because of outdated manifest |
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| 1010836 |
biosyntax-gedit: No longer works with recent versions of gedit |
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| 1029689 |
emperor: tests fail with scipy 1.10 |
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| 1032566 |
fastqc: new upstream version 0.12.1 |
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| 1036260 |
freecontact: FTBFS in testing: make[1]: *** [debian/rules:29: override_dh_install] Error 1 |
bookworm, confirmed, ftbfs, patch, sid |
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| 972537 |
please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3 |
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| 1025739 |
hmmer2: missing source for configure |
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| 1035484 |
jmol: broken symlink: /usr/share/jmol/JSpecView.jar -> ../java/JSpecView.jar |
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| 1004053 |
kallisto: reproducible-builds: timestamps and build path embedded in test suite metadata |
patch |
|
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| 1036743 |
kleborate: debsums reports modified files after apt-get upgrade && apt-get dist-upgrade |
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| 1016941 |
phyml: flaky autopkgtest on armel: test duration around autopkgtest timeout |
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| 1034552 |
pullseq hangs on arm64 |
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| 1029699 |
q2-metadata: tests fail with scipy 1.10 |
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| 1029700 |
q2-quality-control: tests fail with scipy 1.10 |
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