Summary
Bugs of task
bio
Total bugs:
173
Open bugs:
141
Fixed bugs:
32
Links to other tasks
Legend
| Severity | Dependent | Suggested |
|---|
| critical |
0 |
0 |
| grave |
0 |
1 |
| serious |
17 |
4 |
| important |
21 |
4 |
| normal |
49 |
14 |
| minor |
13 |
0 |
| wishlist |
14 |
4 |
|
Summary bugs page of task Biology
Immediately looking into bugs of the dependencies of this task is advised (1417)*
Open bugs in dependent packages
17 serious, 21 important, 49 normal, 13 minor, 14 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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| 1012893 |
anfo: ftbfs with GCC-12 |
bookworm, ftbfs, sid |
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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 |
| 988848 |
libbamtools-doc: broken symlink: /usr/share/doc/libbamtools-dev/html/jquery.js -> ../../../javascript/jquery/jquery.js |
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| 992143 |
bamtools: autopkgtest failure: times out on armel |
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| 870060 |
bcftools FTBFS on big endian: 107 tests failed |
ftbfs, upstream |
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| 1018317 |
biomaj3-daemon: build-depends on python3-nose or uses it for autopkgtest |
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| 1010653 |
busco: add autopkgtest to check integration with hmmer and prodigal |
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| 1018936 |
busco: unsatisfiable dependency on arm64 |
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| 884475 |
clonalorigin: FTBFS on alpha: tests time out |
upstream, wontfix |
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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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| 921566 |
deepnano: autopkgtest times out since 2019-01-11 |
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| 846858 |
src:ea-utils: New version available |
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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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| 1018351 |
fastaq: build-depends on python3-nose or uses it for autopkgtest |
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| 1008220 |
flexbar 3.5.0-4 FTBFS against libtbb-dev 2021.5.0-7 |
ftbfs, upstream |
| 1011656 |
flexbar ftbfs: cannot find tbb header |
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| 1012127 |
flexbar: FTBFS with onetbb/2021.5.0-8 in experimental |
ftbfs, upstream |
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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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|
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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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| 1014797 |
FTBFS: test failures with new libgd3 |
ftbfs, upstream |
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| 967379 |
gdpc: depends on deprecated GTK 2 |
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| 982103 |
gdpc: autopkgtest failure on s390x |
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| 732691 |
Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button |
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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 |
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| 977067 |
igdiscover: test suite flaky, possibly on high core count machines |
confirmed, moreinfo, unreproducible |
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| 1018377 |
insilicoseq: build-depends on python3-nose or uses it for autopkgtest |
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| 1018382 |
iva: build-depends on python3-nose or uses it for autopkgtest |
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| 1017261 |
jellyfish: FTBFS: dh_missing: error: missing files, aborting |
bookworm, ftbfs, sid |
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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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|
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| 1020110 |
kaptive: FTBFS: make[1]: *** [debian/rules:12: override_dh_auto_clean] Error 25 |
bookworm, ftbfs, sid |
|
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| 1020031 |
khmer: FTBFS: ld: cannot find build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o: No such file or directory |
bookworm, ftbfs, sid |
|
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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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| 967603 |
ltrsift: depends on deprecated GTK 2 |
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| 1013408 |
macsyfinder: FTBFS with Sphinx 5.0, docutils 0.18: dh_auto_test: error: pybuild --test -i python{version} -p 3.10 returned exit code 13 |
ftbfs |
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| 1018407 |
mirtop: build-depends on python3-nose or uses it for autopkgtest |
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| 996981 |
multiqc: Link to jquery missing |
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| 956751 |
mummerplot incompatible with Debian's version of gnuplot |
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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 |
|
| 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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| 964082 |
parsinsert fails it's tests when built with -O3 |
bookworm, bullseye, moreinfo, sid, unreproducible |
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| 993019 |
perm -- Buffer overflows |
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| 1011156 |
picard-tools: FTBFS with OpenJDK 17 due to com.sun.javadoc removal |
bookworm, ftbfs, sid |
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| 986194 |
pique: no autopkgtest available yet |
newcomer |
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| 1009156 |
pplacer: Add autopkgtest |
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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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| 1018501 |
python-gffutils: build-depends on python3-nose or uses it for autopkgtest |
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| 1018560 |
python-pybedtools: build-depends on python3-nose or uses it for autopkgtest |
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| 1018582 |
python-sqt: build-depends on python3-nose or uses it for autopkgtest |
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| 642084 |
qutemol: Cannot start the program |
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| 939033 |
qutemol: Uses GifQuantizeBuffer - stops working with newer giflib |
|
| 1019819 |
qutemol: Please transition to wxwidgets3.2 |
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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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| 1018610 |
recan: build-depends on python3-nose or uses it for autopkgtest |
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| 1008252 |
salmon: FTBFS in unstable and testing |
ftbfs |
| 1008254 |
salmon: FTBFS with glibc 2.34 |
ftbfs |
| 1011662 |
salmon ftbfs against onetbb/experimental: tbb api break |
ftbfs |
| 1011742 |
salmon: FTBFS with onetbb/2021.5.0-8 in experimental |
ftbfs |
|
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| 1015654 |
sambamba: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
|
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| 1018636 |
scoary: build-depends on python3-nose or uses it for autopkgtest |
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| 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 |
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| 967743 |
seqtools: depends on deprecated GTK 2 |
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|
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| 848589 |
snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated) |
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| 853113 |
spades: Fails to build with unhelpful error message in a "low" memory machine |
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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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| 956848 |
t-coffee: should use "example" blastpgp.pl |
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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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|
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| 1013182 |
twopaco FTBFS with oneTBB 2021.5.0 |
ftbfs |
|
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| 980509 |
umap-learn: Binary package name should be python3-umap-learn |
pending |
| 1018656 |
umap-learn: build-depends on python3-nose or uses it for autopkgtest |
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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 |
|
| 1013061 |
vg: ftbfs with GCC-12 |
bookworm, ftbfs, sid |
| 1015699 |
vg: ftbfs with LTO (link time optimization) enabled |
bookworm, sid |
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| 446750 |
reading vmol files: coord factor ignored and misdefined |
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| 446753 |
pdb import is broken |
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| 716250 |
[Mayhem] Bug report on viewmol: readpdb crashes with exit status 139 |
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| 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 |
bookworm, bullseye, sid |
| 967229 |
viewmol: Unversioned Python removal in sid/bullseye |
bookworm, bullseye, sid |
Open bugs in suggested packages
1 grave, 4 serious, 4 important, 14 normal, 4 wishlist
|
|
| 916406 |
libarb-dev: Missing symbols in static libraries |
|
| 918015 |
[INTL:sv] Swedish strings for arb debconf |
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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| 995966 |
epigrass: epirunner and epidash fail to run due to missing dash modules |
|
| 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 |
|
| 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 |
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| 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 |
|
|
| 997059 |
intake FTBFS on IPV6-only buildds |
confirmed, ftbfs, ipv6 |
|
|
| 1018477 |
python-deeptools: build-depends on python3-nose or uses it for autopkgtest |
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|
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| 1018577 |
python-seqcluster: build-depends on python3-nose or uses it for autopkgtest |
|
|
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| 994459 |
libjs-jquery removed symlinked files |
moreinfo |
|
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| 995224 |
relion-cuda: FTBFS with cub 1.14 |
bookworm, ftbfs, sid |
|
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| 986200 |
sift: Please provide autopkgtest |
newcomer |
| 987606 |
sift: does not autobuild on buildds |
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|
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| 1010358 |
ugene: Fix for non-constant SIGSTKSZ |
ftbfs, patch, pending |
| 1018252 |
Is ugene still non-free? |
|
Done bugs
|
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| 1015861 |
bamtools: FTBFS with upcoming doxygen 1.9.4 |
ftbfs |
|
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| 1010834 |
biosyntax-vim: Unusable with vim-addon-manager because of outdated manifest |
|
| 1010836 |
biosyntax-gedit: No longer works with recent versions of gedit |
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|
|
| 1012906 |
cif-tools: ftbfs with GCC-12 |
bookworm, sid |
|
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| 1012913 |
dssp: ftbfs with GCC-12 |
bookworm, sid |
|
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| 1020305 |
src:emmax: fails to migrate to testing for too long: autopkgtest failure |
bookworm, sid |
|
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| 1019809 |
gentle: Please transition to wxwidgets3.2 |
help |
|
|
| 972537 |
please add --enable-ros3-vfd to the build options to allow RO access to HDF5 on S3 |
|
|
|
| 1018683 |
igv: FTBFS (calls internet during tests) |
confirmed |
| 1018751 |
igv: FTBFS (calls internet during tests new round) |
confirmed |
|
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| 1012953 |
jellyfish: ftbfs with GCC-12 |
bookworm, confirmed, sid, upstream |
| 1017989 |
src:jellyfish: fails to migrate to testing for too long: unresolved RC bug |
bookworm, sid |
|
|
| 1008402 |
khmer: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13 |
bookworm, ftbfs, sid |
|
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| 1019834 |
lamarc: Please transition to wxwidgets3.2 |
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|
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| 1020106 |
macsyfinder: FTBFS: AssertionError: "Models Parsing\nunable to parse model def[104 chars]del." != "unable to parse model definition 'foo/mod[88 chars]del." |
bookworm, ftbfs, sid |
|
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| 1016645 |
metaphlan2: package name and description can become confusing |
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| 1018433 |
paleomix: build-depends on python3-nose or uses it for autopkgtest |
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| 1016941 |
phyml: flaky autopkgtest on armel: test duration around autopkgtest timeout |
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| 1015250 |
q2-feature-table: Conflict with biom-format 2.1.12 |
upstream |
| 1017515 |
q2-feature-table: needs update for python-biom-format/2.1.12-1 |
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|
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| 1018608 |
q2-quality-filter: build-depends on python3-nose or uses it for autopkgtest |
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| 1017514 |
q2-types: needs update for python-biom-format/2.1.12-1 |
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|
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| 1015136 |
q2cli: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10 returned exit code 13 |
bookworm, ftbfs, sid |
| 1018606 |
q2cli: build-depends on python3-nose or uses it for autopkgtest |
|
|
|
| 1014100 |
qiime: autopkgtest needs update for new version of python-decorator |
bookworm, sid |
| 1018609 |
qiime: build-depends on python3-nose or uses it for autopkgtest |
|
|
|
| 1017167 |
theseus: FTBFS: DLTutils.c:427:11: error: pointer âoutfileâ used after âfcloseâ [-Werror=use-after-free] |
bookworm, ftbfs, sid |
|
|
| 1019811 |
treeviewx: Please transition to wxwidgets3.2 |
help |
|
|
| 1002400 |
umap-learn: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 --system=custom "--test-args=PYTHONPATH={build_dir} {interpreter} -m pytest" returned exit code 13 |
bookworm, ftbfs, sid |
|
|
| 1017778 |
vcfanno: Please replace golang-toml-dev with golang-github-burntsushi-toml-dev |
|
|
|
| 1013064 |
vmatch: ftbfs with GCC-12 |
bookworm, sid |
|
|
| 1016743 |
zalign: autopkgtest failure on 32 bit architectures: Segmentation fault |
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|
