Summary
Bugs of task
bio
Total bugs:
211
Open bugs:
155
Fixed bugs:
56
Links to other tasks
Legend
Severity | Dependent | Suggested |
critical |
0 |
0 |
grave |
1 |
0 |
serious |
4 |
1 |
important |
25 |
4 |
normal |
81 |
9 |
minor |
10 |
1 |
wishlist |
12 |
7 |
|
Summary bugs page of task Biology
Immediately looking into bugs of the dependencies of this task is advised (1342)*
Open bugs in dependent packages
1 grave, 4 serious, 25 important, 81 normal, 10 minor, 12 wishlist
|
920282 |
abyss fails to build on hurd - googletest EXPECT_DEATH |
|
|
967243 |
acedb: depends on deprecated GTK 2 |
|
|
982365 |
ball: reduce Build-Depends |
|
|
865130 |
reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' |
ftbfs, upstream |
983981 |
bamtools: ftbfs with GCC-11 |
bookworm, sid |
|
819617 |
FTBFS: any-i386 - floating point idiosyncracies |
bullseye, buster, ftbfs, sid, stretch |
860682 |
bcftools: FTBFS on i386: Test failures |
bullseye, buster, ftbfs, sid, stretch |
860704 |
python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1) |
bullseye, buster, ftbfs, sid, stretch |
870060 |
bcftools FTBFS on big endian: 107 tests failed |
ftbfs, upstream |
|
983631 |
blasr FTCBFS: multiple reasons |
patch |
|
962675 |
can cdbfasta be marked Multi-Arch: foreign? |
|
|
970597 |
src:changeo: no autopkgtest available yet |
newcomer |
|
984015 |
cif-tools: ftbfs with GCC-11 |
bookworm, sid |
|
884475 |
clonalorigin: FTBFS on alpha: tests time out |
upstream, wontfix |
984018 |
clonalorigin: ftbfs with GCC-11 |
bookworm, sid |
|
978784 |
clustalw: ftbfs with autoconf 2.70 |
bookworm, sid |
|
978794 |
crac: ftbfs with autoconf 2.70 |
bookworm, sid |
|
982869 |
datamash FTBFS on !x86 32bit: FAIL: tests/decorate-errors |
ftbfs, upstream |
|
903886 |
dawg: Test suite fails |
upstream |
|
921566 |
deepnano: autopkgtest times out since 2019-01-11 |
|
|
984034 |
density-fitness: ftbfs with GCC-11 |
bookworm, sid |
|
984036 |
disulfinder: ftbfs with GCC-11 |
bookworm, sid |
|
984042 |
dssp: ftbfs with GCC-11 |
bookworm, sid |
|
846858 |
src:ea-utils: New version available |
|
862118 |
ea-utils: New upstream version available |
|
984043 |
ea-utils: ftbfs with GCC-11 |
bookworm, sid |
|
682042 |
emboss-data: ships bulky taxonomy and gene ontology data |
|
982036 |
emboss: FTBFS with OpenJDK 17 due to com.sun.net.ssl removal |
bookworm, ftbfs, help, sid |
|
902132 |
falcon: FTBFS since python-networkx version 2.1-1; fails in test suite |
ftbfs, pending |
936503 |
falcon: Python2 removal in sid/bullseye |
bullseye, fixed-upstream, pending, sid, upstream |
|
984055 |
fastqtl: ftbfs with GCC-11 |
bookworm, sid |
|
984139 |
freebayes: ftbfs with GCC-11 |
bookworm, sid |
|
750139 |
gamgi: Conflicting return types of function gamgi_engine_iarray_push |
upstream |
967366 |
gamgi: depends on deprecated GTK 2 |
|
|
907905 |
garli: FTBFS randomly (failing tests) |
fixed-upstream, ftbfs, upstream |
|
715937 |
[Mayhem] Bug report on garlic: garlic crashes with exit status 139 |
|
749656 |
garlic: Conflicting declarations of function BlurMainWindow_ to cause undefined behaviour |
|
|
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 |
|
984145 |
gatb-core: ftbfs with GCC-11 |
bookworm, sid |
|
967379 |
gdpc: depends on deprecated GTK 2 |
|
981876 |
gdpc: flaky autopkgtest on i386 |
bullseye, sid |
982103 |
gdpc: autopkgtest failure on s390x |
|
|
982692 |
gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2 |
bullseye, ftbfs, moreinfo, sid, unreproducible |
|
732691 |
Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button |
|
|
967392 |
ghemical: depends on deprecated GTK 2 |
|
967865 |
ghemical: depends on deprecated libglade2 |
|
|
981688 |
graphlan: Wrong homepage |
|
|
644397 |
Provide runtime detection for CPU SIMD capabilities |
upstream |
921784 |
gromacs: unhelpful error message from mpicxx.openmpi |
unreproducible |
983942 |
gromacs: ftbfs with -march=x86-64-v3 |
|
984161 |
gromacs: ftbfs with GCC-11 |
bookworm, sid |
|
958244 |
Use system libinih-dev |
|
|
978835 |
htslib: ftbfs with autoconf 2.70 |
bookworm, sid |
|
977067 |
igdiscover: test suite flaky, possibly on high core count machines |
confirmed, moreinfo, unreproducible |
|
978837 |
indelible: ftbfs with autoconf 2.70 |
bookworm, sid |
|
978841 |
infernal: ftbfs with autoconf 2.70 |
bookworm, sid |
|
983579 |
jalview: [INTL:de] initial German debconf translation |
l10n, patch |
983580 |
jalview: Questions/Corrections for Debconf template |
|
|
978843 |
jellyfish: ftbfs with autoconf 2.70 |
bookworm, sid |
983273 |
jellyfish: Homepage: needs updating |
|
|
875328 |
jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined |
upstream, wontfix |
978842 |
jellyfish1: ftbfs with autoconf 2.70 |
bookworm, sid |
|
712791 |
jmol - exporting the image as PDF saves only partial image |
patch |
872418 |
jmol: Weblinks in Help do not work |
|
981989 |
jmol: FTBFS with OpenJDK 17 due to JSObject.getWindow() removal |
bookworm, ftbfs, sid |
|
984073 |
kallisto: ftbfs with GCC-11 |
bookworm, sid |
|
851830 |
arm64 has flaky tests |
|
984079 |
khmer: ftbfs with GCC-11 |
bookworm, sid |
|
983930 |
kmc: ftbfs with -march=x86-64-v2 |
|
|
984080 |
lamarc: ftbfs with GCC-11 |
bookworm, sid |
|
984081 |
lastz: ftbfs with GCC-11 |
bookworm, sid |
|
984104 |
libfastahack: ftbfs with GCC-11 |
bookworm, sid |
|
984188 |
libncl: ftbfs with GCC-11 |
bookworm, sid |
|
984207 |
libsmithwaterman: ftbfs with GCC-11 |
bookworm, sid |
|
984212 |
libvcflib: ftbfs with GCC-11 |
bookworm, sid |
|
967603 |
ltrsift: depends on deprecated GTK 2 |
|
|
984226 |
mapsembler2: ftbfs with GCC-11 |
bookworm, sid |
|
982005 |
mauve-aligner: FTBFS with OpenJDK 17 due to rmic removal |
bookworm, ftbfs, sid |
|
984243 |
mothur: ftbfs with GCC-11 |
bookworm, sid |
|
956751 |
mummerplot incompatible with Debian's version of gnuplot |
|
|
984250 |
murasaki: ftbfs with GCC-11 |
bookworm, sid |
|
891197 |
Please switch to pcre2 |
|
956850 |
ncbi-blast+: Please provide /usr/bin/legacy_blast.pl |
|
|
225651 |
ncbi-tools-x11: want Cn3D++ |
|
|
935340 |
obitools: Port to Python3 needed |
upstream |
|
964082 |
parsinsert fails it's tests when built with -O3 |
bullseye, moreinfo, sid, unreproducible |
|
983630 |
pbdagcon FTCBFS: python3 dependency not installable |
patch |
|
978880 |
phyx: ftbfs with autoconf 2.70 |
bookworm, sid |
|
984293 |
plink: ftbfs with GCC-11 |
bookworm, sid |
|
970599 |
src:prime-phylo: no autopkgtest available yet |
newcomer |
|
897605 |
profphd failure in stretch |
|
942064 |
profphd: autopkgtest failure |
bullseye, help, sid |
|
984301 |
proftmb: ftbfs with GCC-11 |
bookworm, sid |
|
602610 |
Package freemol.mengine for full modeling capabilities |
|
709306 |
pymol: Crashes when running within xrdp/vnc (no 3D support) |
|
765794 |
Race condition when running scripts in "stdin" mode |
|
783653 |
pymol: Segmentation fault immediately after loading pdb |
|
929700 |
pymol: Deprecation warning during startup |
|
|
642084 |
qutemol: Cannot start the program |
|
939033 |
qutemol: Uses GifQuantizeBuffer - stops working with newer giflib |
|
984316 |
qutemol: ftbfs with GCC-11 |
bookworm, sid |
|
961234 |
r-cran-treescape: FTBFS on ppc64el:Segmentation fault |
bullseye, ftbfs, sid |
|
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) |
bullseye, ftbfs, sid |
|
892222 |
seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta |
upstream |
917851 |
seqan2 2.4.0+dfsg-9: FTBFS, alignment problem |
ftbfs |
|
970598 |
src:seqsero: no autopkgtest available yet |
newcomer |
|
967743 |
seqtools: depends on deprecated GTK 2 |
|
|
983700 |
sga: reduce Build-Depends |
patch |
|
970404 |
shovill: Please provide autopkgtest |
|
|
984334 |
skewer: ftbfs with GCC-11 |
bookworm, sid |
|
848589 |
snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated) |
|
|
853113 |
spades: Fails to build with unhelpful error message in a "low" memory machine |
|
976523 |
spades: FTBFS: jemalloc_internal.h:292:6: error: #error "No LG_QUANTUM definition for architecture; specify via CPPFLAGS" |
bullseye, ftbfs, sid |
|
984348 |
spoa: ftbfs with GCC-11 |
bookworm, sid |
|
956848 |
t-coffee: should use "example" blastpgp.pl |
|
|
984367 |
tigr-glimmer: ftbfs with GCC-11 |
bookworm, sid |
|
984369 |
tortoize: ftbfs with GCC-11 |
bookworm, sid |
|
846481 |
src:treeviewx: Please remove statically linked code copy of libncl |
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|
981874 |
trinityrnaseq: flaky autopkgtest |
bullseye, sid |
|
984370 |
tvc: ftbfs with GCC-11 |
bookworm, sid |
|
980509 |
umap-learn: Binary package name should be python3-umap-learn |
pending |
|
976511 |
vg: FTBFS on arm64: configure: error: Could not find a version of the library! |
bullseye, ftbfs, sid |
|
446750 |
reading vmol files: coord factor ignored and misdefined |
|
446753 |
pdb import is broken |
|
716250 |
[Mayhem] Bug report on viewmol: readpdb crashes with exit status 139 |
|
716256 |
[Mayhem] Bug report on viewmol: readgamess crashes with exit status 139 |
|
875522 |
viewmol: Please stop installing deprecated mimelnk files |
|
938774 |
viewmol: Python2 removal in sid/bullseye |
bullseye, sid |
967229 |
viewmol: Unversioned Python removal in sid/bullseye |
bullseye, sid |
|
978918 |
vsearch: ftbfs with autoconf 2.70 |
bookworm, sid |
|
978928 |
zalign: ftbfs with autoconf 2.70 |
bookworm, sid |
Open bugs in suggested packages
1 serious, 4 important, 9 normal, 1 minor, 7 wishlist
|
916406 |
libarb-dev: Missing symbols in static libraries |
|
918015 |
[INTL:sv] Swedish strings for arb debconf |
l10n, patch |
926017 |
arb: Typo in package description: "website links unreachable, description outdated" |
|
|
928076 |
bcbio: Workflows not ready for non-developers to depend on. |
|
|
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 |
972537 |
please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3 |
|
973261 |
libhdf5-openmpi-dev: installing requires /proc being mounted |
|
|
970312 |
src:intake: Please provide autopkgtest |
newcomer |
982699 |
intake: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13 |
bullseye, ftbfs, sid |
|
970309 |
src:python-loompy: Please provide autopkgtest |
newcomer |
|
982139 |
q2-quality-control: test skipped on ppc64el |
|
Done bugs
|
982608 |
axe-demultiplexer: FTCBFS: unsatisfiable python3-sphinx dependency |
patch |
|
982965 |
bedops: reduce Build-Depends |
patch |
|
982168 |
biomaj3-daemon: autopkgtest failure: No module named 'biomaj3_daemon' |
|
|
983142 |
circlator: reproducible builds: Generated tarball includes file mode |
patch |
|
982989 |
codonw FTCBFS: Multiple reasons |
patch |
|
956675 |
cyvcf2: test failures on ppc64el and s390x |
bullseye, ftbfs, sid |
|
982290 |
disulfinder FTCBFS: hard codes the build architecture compiler g++ |
patch, upstream |
|
982352 |
drop-seq-tools: Excessive dependendies |
|
982617 |
drop-seq: autopkgtest regression |
confirmed |
|
980765 |
eigensoft: absolute path to fixgreen in /usr/bin/ploteig |
|
|
981684 |
src:estscan: fails to migrate to testing for too long: FTBFS on mipsel |
bullseye, ftbfs, sid |
|
909713 |
fastlink: Please provide autopkgtest |
newcomer |
|
980484 |
gmap FTCBFS: AC_RUN_IFELSE |
patch, upstream |
|
749367 |
htslib FTBFS on testing for mips/mipsel |
bullseye, buster, moreinfo, patch, sid, stretch |
800469 |
htslib FTBFS on armhf, bus error. |
bullseye, buster, ftbfs, patch, sid, stretch |
849667 |
htslib: FTBFS on armhf: [test] Bus error |
bullseye, buster, ftbfs, patch, sid, stretch |
|
961382 |
hyphy: baseline violation on amd64/i386 |
|
977992 |
hyphy: FTBFS on hurd-i386: wrong reference to the build directory |
patch |
|
849025 |
jalview: FTBFS: error: cannot find symbol EnumCallback |
ftbfs |
|
973431 |
jellyfish ftbfs when built with -O3 |
bullseye, ftbfs, sid |
976340 |
jellyfish FTBFS with -I in builddir |
ftbfs |
|
958471 |
src:kineticstools: Non-free data included in source |
|
|
954270 |
kmc: autopgktest times out on multimulticore hosts |
confirmed |
|
982045 |
libssw: FTBFS with OpenJDK 17 due to unsupported javac source/target level 6 |
bookworm, ftbfs, sid |
|
933928 |
macsyfinder: Port to Python3 needed |
fixed-upstream |
936977 |
macsyfinder: Python2 removal in sid/bullseye |
bullseye, fixed-upstream, sid |
|
970875 |
mash: inconsistent results on 32 vs 64 bits architectures |
|
|
981293 |
metastudent-data breaks metastudent autopkgtest: 255 |
bullseye, help, sid, upstream |
981294 |
src:metastudent-data: fails to migrate to testing for too long: autopkgtest regression |
bullseye, sid |
|
890788 |
mipe: Please provide autopkgtest |
newcomer |
|
982718 |
msxpertsuite: FTBFS: [ERROR] LazyFont - Failed to read font file /usr/share/texlive/texmf-dist/fonts/opentype/public/stix2-otf/STIX2Math.otf <java.io.FileNotFoundException: /usr/share/texlive/texmf-dist/fonts/opentype/public/stix2-otf/STIX2Math.otf (No such file or directory)>java.io.FileNotFoundException: /usr/share/texlive/texmf-dist/fonts/opentype/public/stix2-otf/STIX2Math.otf (No such file or directory) |
bullseye, ftbfs, patch, sid |
|
960634 |
nanopolish: FTBFS on ppc64el (as well as ppc64 and powerpc), enumerator conflict |
ftbfs |
983767 |
nanopolish ftbfs with the nocheck profile |
|
|
981926 |
neobio: FTBFS with OpenJDK 17 due to unsupported javac source/target level 6 |
bookworm, ftbfs, sid |
|
975588 |
openms: FTBFS against boost_1.74 |
ftbfs |
982567 |
openms build-depends on removed package. |
upstream |
|
982181 |
pbsuite: autopkgtest regression |
|
|
974003 |
src:plink2: fails to migrate to testing for too long: FTBFS on ppc64el |
bullseye, sid |
|
962190 |
primer3: please disable Big Endian tests on autopkgtests too |
patch |
|
905206 |
profnet: autopkgtest regression |
upstream |
|
982098 |
python-anndata: autopkgtest failure on 32bit |
|
|
974839 |
q2-feature-classifier: unsatisfiable build-dependency |
|
|
983027 |
r-bioc-mutationalpatterns: autopkgtest regression in testing: no package called âBSgenome.Hsapiens.UCSC.hg19â |
|
|
982115 |
r-bioc-scater: autopkgtest failure on i386 |
|
|
982421 |
r-cran-seurat: autopkgtest failure on i386/armhf |
patch |
|
982912 |
repeatmasker-recon FTCBFS: hardcodes "make" in d/rules |
patch |
|
983723 |
rna-star FTBFS on ppc64el due to -march=native |
ftbfs |
|
984328 |
seer: ftbfs with GCC-11 |
bookworm, sid |
|
972603 |
seqan: Needs update for new googletest |
|
980685 |
seqan: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j4 test ARGS\+=-j4 returned exit code 2 |
bullseye, ftbfs, sid |
|
972752 |
seqan2: FTBFS with DEB_BUILD_OPTIONS=reproducible=+fixfilepath |
patch |
|
982212 |
simka: autopkgtest needs same architecture list as simka |
|
|
890790 |
tree-puzzle: Please provide autopkgtest |
newcomer |
|
979760 |
vdjtools: autopkgtest failure: "java: not found" |
|
982116 |
vdjtools: autopkgtest fails due to slightly differing result on !x86 |
|
|
982930 |
wham-align: FTCBFS: multiple reasons |
patch |
|