Debian Med Project
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Summary
Bugs of task covid-19
Total bugs: 203
Open bugs: 180
Fixed bugs: 23
Links to other tasks
Biology 287 (2532)
Biology development 136 (1184)
Phylogeny 7 (54)
Cloud 46 (504)
Covid-19 180 (1800)
Medical data 2 (10)
Dental 2 (12)
Epidemiology 11 (102)
Imaging 198 (826)
Laboratory 1 (9)
Oncology 1 (3)
Pharmacology 1 (9)
Physics 27 (192)
Practice 8 (51)
Psychology 12 (121)
Research 0 (0)
Statistics 4 (16)
Tools 39 (240)
Typesetting 68 (543)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 15 1
important 30 1
normal 90 2
minor 23 0
wishlist 18 0

Summary bugs page of task Covid-19

Immediately looking into bugs of the dependencies of this task is advised (1800)*

Open bugs in dependent packages

15 serious, 30 important, 90 normal, 23 minor, 18 wishlist
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
1049876 bbhash: FTBFS on 32 bit architectures ftbfs, sid, trixie
1085372 busco: Python SyntaxWarning
1085416 changeo: Python SyntaxWarning
1083349 cwltool: (build-)depends on deprecated module python3-pkg-resources sid, trixie
935879 Update to use CharLS 2.0 upstream
1055872 CP-2275: "NaN", "+Infinity" and "-Infinity"
1055873 dcm2json is missing --convert-un for CP-1066 EVRLE
1056048 Memory leak in dcm2json
1060677 Rounding error in OFStandard::atof confirmed, fixed-upstream, upstream
1085542 discosnp: Python SyntaxWarning
1067271 freebayes: FTBFS: dh_auto_test: error: cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=8 meson test -v --timeout-multiplier 100 returned exit code 5 fixed-upstream, ftbfs
731435 warning: iteration 55823u invokes undefined behavior [-Waggressive-loop-optimizations] upstream
749783 gdcm: Conflicting declarations of jpeg_memory_mgr may lead to invalid function calls
826048 Faulty CMake file impairs compiling against GDCM moreinfo, wontfix
1086435 libgdcm-tools: gdcmscu fails with "ProtocolStream as nullptr is invalid" upstream
644397 Provide runtime detection for CPU SIMD capabilities upstream
983942 gromacs: ftbfs with -march=x86-64-v3
1085638 htseq: Python SyntaxWarning
1047324 kallisto: Fails to build source after successful build ftbfs, sid, trixie
1057131 kallisto: add support for loongarch64 in d/control patch, pending
1006686 libchipcard-dev: undefined variable in libchipcard-client.pc fixed-upstream, patch, upstream
1006687 libchipcard6: card.c leaks memory patch, upstream
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
1047978 lumpy-sv: Fails to build source after successful build ftbfs, sid, trixie
1086362 macromoleculebuilder: FTBFS: /usr/bin/ld: libMMB.so.4.0: undefined reference to `gzerror' ftbfs
1045898 nanook: Fails to build source after successful build ftbfs, sid, trixie
1085733 nanosv: Python SyntaxWarning
956850 ncbi-blast+: Please provide /usr/bin/legacy_blast.pl
984871 ncbi-blast+: Missing headers for shared libraries
1010110 ncbi-blast+: terminate called after throwing an instance of 'ncbi::CIO_Exception' wontfix
1077777 ncbi-blast+: makeblastdb yields broken DBs on s390x (BE generally?) upstream
1080479 ncbi-blast+: failure to create blastdb v5 on riscv64
1001387 Wishlist: Package Stone of Orthanc Webviewer
1081672 FTBFS with Python 3.13 upstream
1084663 pairtools: removal of Python standard libraries in Python 3.13 upstream
1085765 pairtools: Python SyntaxWarning
1048822 plink2: Fails to build source after successful build ftbfs, sid, trixie
1085786 porechop: Python SyntaxWarning
1074546 FTBFS with OCaml 5.2.0 (Uses C functions without caml_ prefix) ftbfs
1085789 presto: Python SyntaxWarning
1082368 FTBFS: TestIntegration.testIntegration: AssertionError: 1 != 0 confirmed, ftbfs
1018448 pynn: build-depends on python3-nose or uses it for autopkgtest fixed-upstream, sid, trixie
1071337 pynn: FTBFS: ERROR: unittests.test_recording.test_get ftbfs
1084632 python-cgecore: removal of Python standard libraries in Python 3.13
1085895 python-cgecore: Python SyntaxWarning
1058479 python-cogent: please (temporarily) drop python3-numba dependencies wontfix
1083626 python-depinfo: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1081673 FTBFS with Python 3.13 fixed-upstream, patch, upstream
1087457 python3-pysam: autopkgtest regression with htslib 1.21 upstream
1079359 SyntaxWarning: invalid escape sequence '\[' newcomer, upstream
1083698 python-pyvcf: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1079788 python-questplus: test_thurstone_scaling fails on arm64 with scipy 1.14
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
1083727 pytorch: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1083729 pytorch: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1086773 Please drop dependency on python3-astunparse
1081150 r-cran-diagnosismed: removed from CRAN repository
1081177 r-cran-epicalc: removed from CRAN repository
1083236 r-cran-seroincidence: homepage defunct, standardize
1083239 r-cran-seroincidence: removed from CRAN repository
1071106 r-cran-sf: autopkgtest regression in testing
1084108 r-cran-spp: removed from CRAN repository
1087041 readucks: Python SyntaxWarning
1087456 samtools: autopkgtest regression with htslib 1.21
1087079 seirsplus: Python SyntaxWarning
1048951 seqan3: Fails to build source after successful build ftbfs, sid, trixie
1086015 build for all supported python3
1087093 spades: Python SyntaxWarning
1075545 sumaclust: ftbfs with GCC-14 ftbfs, sid, trixie, upstream
1005713 tensorflow FTBFS; bazel still tries to download during build.
1084624 tensorflow: removal of Python standard libraries in Python 3.13
170477 xmltex: can't make DVI/PS from DocBook orderedlist/itemizedlist
181444 xmltex: can't make DVI/PS from DocBook orderedlist/itemizedlist
184072 xmltex: can't make DVI/PS from DocBook orderedlist/itemizedlist
184086 xmltex: can't make DVI/PS from DocBook orderedlist/itemizedlist
189616 jadetex: Japanese JadeTeX
234884 Cannot generate PDF when callouts are used
310148 xmlto: pdf output fails with LaTeX errors
345637 xmltex: behaves as if --force-confold had been given
427443 provide a documentation index (like tetex had)
444084 tex4ht: you-on gets extra space moreinfo
450941 texlive-fonts-extra: cannot use mathtime/belleek
468225 pdfjam: pdfnup does not use /etc/papersize moreinfo
536380 HTML mode is spewing some XML wontfix
536393 HTML mode is specifing image sizes in points, in violation of HTML standard (and sanity)
537284 Ligature fi becoming ø in avant garde
554637 tex4ht: Leaves intermediate files wontfix
554998 Glitches when using hyperref and math mode
554999 tex4ht: mk4ht should fail when it encounters errors
572226 tex4ht: Incorrect output for align, eqnarray, inline longrightarrow
596703 texlive-publishers has dependencies on files texlive-bibtex-extra but doesn't even recommend it
604054 if hyperref is loaded before glossaries then text size is adapted wrongly
615596 tex4ht: mk4ht dblatex file.tex fails with xtpipes error fixed-upstream, patch, pending, upstream
635834 texlive-latex-extra: dependency problem: fancytooltips requires acrotex which is not packaged wontfix
659772 landscape sciposter + hyperref + latex + dvips = center-mirrored image
675869 make PDF smaller with version1.4
683163 xmlto fail to convert example docbook to PDF (LaTeX Error, missing \item?)
744309 FTBFS Please rebuilt from source flash file
764122 MnSymbol and new[tp]x shouldn't be in the texlive-fonts-extra ghetto
767872 tex4ht: htlatex fails without non-zero exit status
772378 texlive-latex-extra-doc: bashism in /bin/sh script
774942 texlive-latex-extra: package description has too many blank lines and is too long
862966 texlive-fonts-extra: Missing yinitas.tfm which makes yfonts.sty unusable
866114 texlive-fonts-extra: Icon errors when installed alongside fonts-font-awesome moreinfo
877769 Q: files (.tex, .cls, Makefile, etc...) compressed to .gz (but seem should not)
877770 Q: Why -doc package depends on tex?
916796 IEEEfull.bib: cannot be read in encoding 'utf8' by biber
917996 texlive-pstricks: gs gives undefined in --execute-- when using color.tex with pstricks on plain tex.
929558 texlive-fonts-extra: STIX2 fonts cannot called by their font names by xelatex & fontspec.sty
930850 texlive-latex-extra: Update listings macro separator
941823 tabu: cell background colours broken
953073 texlive-fonts-extra: TwemojiMozilla.ttf is included in 4 Debian packages
958562 texlive-extra-utils: missing man page for pdfcrop
974724 no useful documentation of pdfjam commands
997024 [greek]babel + cleveref + pagenumbering + label = ☇
1008808 texlive-games: [chess.sty] Incorrect usage of babel breaks package wontfix
1011759 texlive-extra-utils: Script pdfjoin has vanished wontfix
1019236 Why does mere inclusion of pstricks change A4 to letter?
1021166 texlive-fonts-extra: sourceserifpro doesn't work with xeLaTeX
1023586 texlive-extra-utils: pythontex won't find python (when on python3)
1026789 Broken vf files in package?
1029325 texlive-latex-extra: adequate reports broken-symlink
1040158 texlive-latex-extra: tex4ebook with mathml prints \lim, limsup etc. in italics
1043258 texlive-latex-extra-doc: moderncv.tex fails to build
1067614 texlive-latex-extra: pdfcomment docs reference the cloud instead of local files; also font option broken wontfix
1070721 texlive-fonts-extra: Weird dependencies
1070802 texlive-latex-extra: (regression) acro no longer compiles upstream
1072743 texlive-extra-utils: pdfxup: --pages option fails if page range omits start or end of range
1086757 texlive-latex-extra: Minted stopped to work: Error: 'sh: 1: latexminted: not found' pending
1083799 tnseq-transit: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1073358 toil: FTBFS: ModuleNotFoundError: No module named 'boto' ftbfs, sid, trixie
1084681 toil: removal of Python standard libraries in Python 3.13 fixed-upstream
1087116 toil: Python SyntaxWarning
1049071 tombo: Fails to build source after successful build ftbfs, sid, trixie
1083801 tombo: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1087117 tombo: Python SyntaxWarning
1048043 trinculo: Fails to build source after successful build ftbfs, sid, trixie
980509 umap-learn: Binary package name should be python3-umap-learn pending
1058489 umap-learn: please (temporarily) drop python3-numba dependencies
1071816 umap-learn: FTBFS: E TypeError: exceptions must be derived from Warning, not <class 'NoneType'> ftbfs
1087155 umis: Python SyntaxWarning
1087156 uncalled: Python SyntaxWarning
1048635 unicycler: Fails to build source after successful build ftbfs, sid, trixie
1087157 unicycler: Python SyntaxWarning
976511 vg: FTBFS on arm64: configure: error: Could not find a version of the library! bookworm, bullseye, ftbfs, sid, trixie
987184 vg -- excessive variants built, and not tested
1013061 vg: ftbfs with GCC-12 bookworm, ftbfs, sid, trixie
1015699 vg: ftbfs with LTO (link time optimization) enabled sid, trixie
1043312 vg: Replace transitional bsdmainutils pending
1084554 vg: removal of Python standard libraries in Python 3.13
348845 please provide a male character as well upstream
359991 Please add 'daemon' mode
371826 new exercises upstream
388570 option for less disk intensity upstream
533294 Improve .desktop file: Office category fits better than Accesibility and german comment
545585 workrave: Cant resume after unlocking screen
598402 workrave: Should count suspend time as pauses
632232 workrave: Changing sound options has no effect
695344 Installs gobject-introspection / library files into system wide paths
783872 [workrave] xfce4 panel plugin uses the wrong path in desktop file
789044 workrave: lock was blocked by another application
804170 workrave: Workrave resets system volume levels
829450 workrave: Cannot interract with Workrave icon in KDE system tray
843563 Workrave applet unusable
853933 workrave: segfault when trying to start under wayland upstream
911054 workrave: desktop instability in multimonitor (3) setup
921765 workrave: occasionally runs into false activity detection
943477 workrave: multiple overlaying popups in multimonitor setup
980873 workrave: Break warning window grabs keyboard focus on Wayland
988064 workrave: applet does not display timer after screen lock
1087194 yanosim: Python SyntaxWarning

Open bugs in suggested packages

1 serious, 1 important, 2 normal
928076 bcbio: Workflows not ready for non-developers to depend on.
1018312 bcbio: build-depends on python3-nose or uses it for autopkgtest sid, trixie
1075928 python-anndata: tests fail with scipy 1.13
1035277 python-seqcluster: please add autopkgtests (to add coverage for python3-numpy)

Done bugs

1074483 dcmtk: CVE-2024-27628 fixed-upstream, patch, security, upstream
1044536 fasta3: Fails to build source after successful build ftbfs, sid, trixie
1070387 gdcm: CVE-2024-25569 CVE-2024-22373 CVE-2024-22391 security, upstream
1033703 gffread: autopkgtest regression: test dependency not in testing bookworm-ignore
1086272 gromacs: FTBFS with OpenMPI 5 on systems with less than 4 CPUs ftbfs
1082688 node-shiny-server: FTBFS: TypeError: Cannot read properties of undefined (reading 'define') ftbfs
1083552 poretools: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1086156 ftbfs: test failure: DSSP failed to produce an output ftbfs
1086899 python-pauvre: Python SyntaxWarning
1083675 python-pbcore: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1083691 python-pyfaidx: (build-)depends on deprecated module python3-pkg-resources sid, trixie
1086965 python-treetime: Python SyntaxWarning
994423 pytorch: Baseline violation on armhf bookworm, bullseye, experimental, ftbfs, sid, trixie
1056388 FTBFS with fmtlib 10 fixed-upstream, ftbfs
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
1070379 pytorch: CVE-2024-31580 CVE-2024-31583 CVE-2024-31584 security, upstream
1085004 pytorch: FTBFS: error: no matching function for call to ‘llvm::TargetMachine::registerPassBuilderCallbacks(llvm::PassBuilder&, bool)’ ftbfs
1087373 seqan3: FTBFS: Some parallel tests fail on single-cpu systems ftbfs
976523 spades: FTBFS: jemalloc_internal.h:292:6: error: #error "No LG_QUANTUM definition for architecture; specify via CPPFLAGS" bookworm, bullseye, ftbfs, sid, trixie
1035857 texlive-fonts-extra: broken font symlinks for junicode bookworm-ignore
1085685 texlive-extra-utils: chklref does not find perl
1081347 vg: intent to file removal bug sid, trixie
955965 workrave: Depends on deprecated dbus-glib bookworm, bullseye, sid
*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: Thu, 14 Nov 2024 18:19:11 -0000