Debian Med Project
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Summary
Bugs of task bio-dev
Total bugs: 176
Open bugs: 116
Fixed bugs: 60
Links to other tasks
Biology 229 (1834)
Phylogeny 7 (27)
Cloud 43 (462)
Covid-19 150 (1514)
Medical data 1 (1)
Dental 1 (3)
Epidemiology 11 (185)
Imaging 212 (1037)
Laboratory 1 (9)
Oncology 1 (3)
Pharmacology 1 (9)
Physics 24 (159)
Practice 7 (63)
Psychology 7 (55)
Research 0 (0)
Statistics 3 (7)
Tools 38 (241)
Typesetting 64 (517)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 4 15
important 17 5
normal 18 4
minor 32 6
wishlist 12 3

Summary bugs page of task Biology development

Immediately looking into bugs of the dependencies of this task is advised (826)*

Open bugs in dependent packages

4 serious, 17 important, 18 normal, 32 minor, 12 wishlist
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' ftbfs, upstream
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
1063856 hdf5: new upstream release
1067758 Please provide a nojava build profile
1067789 hdf5: diff for NMU version 1.10.10+repack-3.2 patch, pending
1067950 hdf5: diff for NMU version 1.10.10+repack-3.3 patch, pending
1070861 hdf5: CVE-2024-33877 CVE-2024-33876 CVE-2024-33875 CVE-2024-33874 CVE-2024-33873 CVE-2024-32624 CVE-2024-32623 CVE-2024-32622 CVE-2024-32621 CVE-2024-32620 CVE-2024-32619 CVE-2024-32618 CVE-2024-32617 CVE-2024-32616 CVE-2024-32615 CVE-2024-32614 CVE-2024-32613 CVE-2024-32612 CVE-2024-32611 CVE-2024-32610 CVE-2024-32609 CVE-2024-32607 CVE-2024-32606 CVE-2024-32605 CVE-2024-29166 CVE-2024-29165 CVE-2024-29164 CVE-2024-29163 CVE-2024-29162 CVE-2024-29161 CVE-2024-29160 CVE-2024-29159 CVE-2024-29158 CVE-2024-29157 security, upstream
948463 libai-fann-perl: Integer overflow leading to heap buffer overflow
599961 libbio-scf-perl: FTBFS: Neither BIG nor LITTLE endian defined
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
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
1063191 libcifpp-data: Incorrect URL in update-libcifpp-data script patch
1068860 [INTL:sv] Swedish strings for libcifpp debconf l10n, patch
1015484 libedlib: ftbfs with LTO (link time optimization) enabled 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
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
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
1015525 libssw: ftbfs with LTO (link time optimization) enabled experimental, sid, trixie
1046152 mcl: Fails to build source after successful build ftbfs, sid, trixie
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
1068052 openms: FTBFS on armel,armhf (error: ‘QOpenGLFunctions_2_0’ does not name a type) ftbfs
1061938 pyfai: Segfault when closing a dialg
1064147 ftbfs: test failures affecting Bio.SeqIO.SeqXmIIO fixed-upstream, ftbfs, sid
1067989 python3-cobra: Please replace python3-appdirs dependency with platformdirs sid, trixie
1058479 python-cogent: please (temporarily) drop python3-numba dependencies wontfix
1069359 python-cooler: FTBFS: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpi8kk3ih0/tmp_sf3nv42.multi.cool' ftbfs, sid, trixie
1058482 python-loompy: please (temporarily) drop python3-numba dependencies
1045607 python-pyspoa: 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
1057644 pytorch: build for all supported Python versions wontfix
1070379 pytorch: CVE-2024-31580 CVE-2024-31583 CVE-2024-31584 security, upstream
1069509 r-cran-metamix: FTBFS on armhf: tests fail ftbfs, sid, trixie
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
1064311 rdkit: NMU diff for 64-bit time_t transition patch
1069873 rdkit: FTBFS convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb). ftbfs, sid
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

Open bugs in suggested packages

15 serious, 5 important, 4 normal, 6 minor, 3 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 wontfix
1032358 btllib: Depends on libsdsl-dev, breaking installability when not needed patch, pending
1058455 btllib: add build support for loongarch64 patch
1043870 concurrentqueue: Fails to build source after successful build ftbfs, sid, trixie
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
1069552 freecontact: FTBFS on armel: make[1]: *** [Makefile:469: all-recursive] Error 1 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 sid, trixie
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
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)
1065945 q2-emperor: Please drop dependencies on python3-distutils
1065946 q2-sample-classifier: Please drop dependencies on python3-distutils
1065333 q2-types: test data heavily outweighs actual code
1066085 q2cli: please make the build reproducible patch, pending
1068006 qiime: Please replace python3-appdirs dependency with platformdirs sid, trixie
1071340 r-bioc-affxparser: FTBFS: R_affx_cdf_parser.cpp:1099:17: error: format not a string literal and no format arguments ftbfs
1071341 r-bioc-genefilter: FTBFS: nd.c:75:21: error: format not a string literal and no format arguments ftbfs
1070841 r-bioc-iranges: autopkgtest regression with r-base 4.4.0
1071344 r-bioc-oligo: FTBFS: basecontent.c:54:15: error: format not a string literal and no format arguments ftbfs
1071346 r-bioc-rsamtools: FTBFS: samtools_patch.c:37:13: error: format not a string literal and no format arguments ftbfs
1071347 r-bioc-rtracklayer: FTBFS: handlers.c:10:11: error: format not a string literal and no format arguments ftbfs
1070843 r-bioc-s4vectors: autopkgtest regression with r-base 4.4.0
1071349 r-bioc-s4vectors: FTBFS: Rle_class.c:1136:17: error: format not a string literal and no format arguments ftbfs
1071350 r-bioc-shortread: FTBFS: readBfaToc.cc:30:14: error: format not a string literal and no format arguments ftbfs
1071352 r-bioc-variantannotation: FTBFS: vcffile.c:46:5: error: format not a string literal and no format arguments ftbfs
1071353 r-bioc-xvector: FTBFS: RDS_random_access.c:136:17: error: format not a string literal and no format arguments ftbfs

Done bugs

1061931 biosquid: NMU diff for 64-bit time_t transition patch
1067499 libconsensuscore-dev: ships /usr/include/meson.build
1069261 cwlformat: fails with newer ruamel.yaml patch, sid, trixie
1062588 ffindex: NMU diff for 64-bit time_t transition patch, sid, trixie
1062403 freecontact: NMU diff for 64-bit time_t transition patch, sid, trixie
1062071 genometools: NMU diff for 64-bit time_t transition patch
1033703 gffread: autopkgtest regression: test dependency not in testing bookworm-ignore
1064095 hdf5: NMU diff for 64-bit time_t transition patch, sid, trixie
1062344 htslib: NMU diff for 64-bit time_t transition patch
1062229 libbigwig: NMU diff for 64-bit time_t transition patch, sid, trixie
1065759 libbio-samtools-perl: FTBFS: lib/Bio/DB/Sam.xs:324:4: error: implicit declaration of function ‘bam_sort_core’; did you mean ‘bam_format1_core’? [-Werror=implicit-function-declaration] confirmed, ftbfs, help, patch
1047210 libbio-scf-perl: Fails to build source after successful build ftbfs, sid, trixie
1062230 libbpp-core: NMU diff for 64-bit time_t transition patch
1062234 libbpp-phyl: NMU diff for 64-bit time_t transition patch
1062232 libbpp-phyl-omics: NMU diff for 64-bit time_t transition patch
1062236 libbpp-popgen: NMU diff for 64-bit time_t transition patch
1015476 libbpp-qt: ftbfs with LTO (link time optimization) enabled patch, sid, trixie
1062237 libbpp-qt: NMU diff for 64-bit time_t transition patch
1062240 libbpp-seq: NMU diff for 64-bit time_t transition patch
1062239 libbpp-seq-omics: NMU diff for 64-bit time_t transition patch
1062316 libgkarrays: NMU diff for 64-bit time_t transition patch, sid, trixie
1068573 libmaus2: fix error caused by sysconf function
1062416 libmems: NMU diff for 64-bit time_t transition patch, sid, trixie
1062580 libpwiz: NMU diff for 64-bit time_t transition patch, sid, trixie
1062602 librcsb-core-wrapper: NMU diff for 64-bit time_t transition patch, sid, trixie
1062612 librostlab: NMU diff for 64-bit time_t transition patch
1048643 librostlab-blast: Fails to build source after successful build ftbfs, sid, trixie
1067961 python3-sbml5 depends on swig
1069876 libsbml: autopkgtest regression
1063136 libslow5lib: NMU diff for 64-bit time_t transition patch, sid, trixie
1063137 libtabixpp: NMU diff for 64-bit time_t transition patch, sid, trixie
1066716 libtfbs-perl: FTBFS: ./lib/pwm_searchPFF.c:55:7: error: implicit declaration of function ‘announce’ [-Werror=implicit-function-declaration] ftbfs, sid, trixie
1062695 libvbz-hdf-plugin: NMU diff for 64-bit time_t transition patch, sid, trixie
1045603 libwfa2: Fails to build source after successful build ftbfs, sid, trixie
1062731 libwfa2: NMU diff for 64-bit time_t transition patch, sid, trixie
1068925 macromoleculebuilder: FTBFS on armhf (error: inconsistent deduction for auto return type: 'long int' and then 'long long int') ftbfs
1064245 ncbi-tools6: NMU diff for 64-bit time_t transition patch, sid, trixie
1060444 python3-networkx: SyntaxWarning during package installation if python3.12 is installed
1064503 Please pacakge new upstream release 3.2.1
1061814 openmm fails its autopkg tests with Python 3.12 ftbfs, patch, sid, trixie
1063095 openmm: NMU diff for 64-bit time_t transition patch
1065911 openmm: Please drop dependencies on python3-distutils
1068996 python3-bx: maf_word_frequency.py fails to run
1069985 python-cobra: Manual build-depends on NBS package libsbml5 ftbfs, sid, trixie
1068960 python-pybedtools: FTBFS: testsuite error: 14 failed, 491 passed, 2 deselected, 3 xfailed ftbfs
1054591 python3-pyflow: ${VERSION} not expanded in package metadata, causing PEP-440 validation failures
994423 pytorch: Baseline violation on armhf bookworm, bullseye, experimental, ftbfs, sid, trixie
1060097 pytorch: FBFS: /<<PKGBUILDDIR>>/aten/src/ATen/native/quantized/cpu/qlinear_prepack.cpp:249:103: error: cannot convert ‘dnnl::memory::data_type’ to ‘const ideep::dims&’ {aka ‘const std::vector<long int>&’} ftbfs
1065941 pytorch: Please drop dependencies on python3-distutils ftbfs
1070988 src:q2-feature-table: fails to migrate to testing for too long: autopkgtest regression sid, trixie
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
1069296 sbmltoolbox: Depends on pre-t64 libsbml5
1069370 shasta: FTBFS: dpkg-shlibdeps: error: cannot find library shasta.cpython-311-aarch64-linux-gnu.so needed by debian/shasta/usr/bin/shasta ftbfs, help, 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
1065961 sra-sdk: Please drop dependencies on python3-distutils ftbfs
1063189 staden-io-lib: NMU diff for 64-bit time_t transition patch, sid, trixie
1070055 toil: FTBFS: ModuleNotFoundError: No module named 'pytz' ftbfs
*To estimate the overall status of the packages in the dependencies of a metapackage a weighted severity is calculated. Done bugs are ignored and bugs in dependent and recommended packages are weighted by factor three compared to suggested packages. Release critical bugs have a much larger weight than important, while the contribution of normal bugs is even smaller and minor bugs have a very small weight. Wishlist bugs are ignored in this calculation. The resulting sum is compared to some boundaries to find a verbal form. The actual numbers need some adjustment to make real sense - this evaluation method is in testing phase.
The severities of bugs are weighted as follows:
critical10
grave10
serious10
important5
normal3
minor1
wishlist0
Last update: Tue, 21 May 2024 04:14:25 -0000