Debian Med Project
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Bugs of task covid-19
Total bugs: 153
Open bugs: 125
Fixed bugs: 28
Links to other tasks
Biology 118 (1036)
Phylogeny 5 (33)
Cloud 22 (249)
Covid-19 125 (1171)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 5 (80)
Imaging 206 (945)
Laboratory 1 (9)
Oncology 1 (5)
Pharmacology 1 (9)
Physics 25 (186)
Practice 4 (27)
Psychology 3 (25)
Research 0 (0)
Statistics 1 (1)
Tools 36 (227)
Typesetting 64 (501)
critical 0 0
grave 1 0
serious 6 3
important 25 2
normal 56 1
minor 13 0
wishlist 18 0

Summary bugs page of task Covid-19

Immediately looking into bugs of the dependencies of this task is advised (1171)*

Open bugs in dependent packages

1 grave, 6 serious, 25 important, 56 normal, 13 minor, 18 wishlist
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
1027731 aeskulap: Depends on deprecated libglademm2.4
870060 bcftools FTBFS on big endian: 107 tests failed ftbfs, upstream
1010653 busco: add autopkgtest to check integration with hmmer and prodigal
1030713 cwltool: Installs the text of 'Moby-Dick' under /usr/lib/python3/dist-packages patch
1030714 cwltool: please make the build reproducible patch
935879 Update to use CharLS 2.0 upstream
988644 Defined Term: ISO 2022 IR 87 is not supported confirmed, upstream
1030360 diamond-aligner FTBFS on !amd64 ftbfs
995966 epigrass: epirunner and epidash fail to run due to missing dash modules pending
998265 epigrass: autopkgtest regression: The 'panel' distribution was not found
731435 warning: iteration 55823u invokes undefined behavior [-Waggressive-loop-optimizations] patch, 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
644397 Provide runtime detection for CPU SIMD capabilities upstream
983942 gromacs: ftbfs with -march=x86-64-v3
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
996981 multiqc: Link to jquery missing
891197 Please switch to pcre2
956850 ncbi-blast+: Please provide /usr/bin/
984871 ncbi-blast+: Missing headers for shared libraries
1010110 ncbi-blast+: terminate called after throwing an instance of 'ncbi::CIO_Exception' wontfix
1017871 shiny-server: server-function don't run
1001387 Wishlist: Package Stone of Orthanc Webviewer
1009156 pplacer: Add autopkgtest
1024889 pplacer: build-depedends on dropped package.
1018448 pynn: build-depends on python3-nose or uses it for autopkgtest
1027386 pysam -- no definition for bam_dup1 confirmed
983517 pytorch: Build documentation
1024903 pytorch: CVE-2022-45907: torch.jit.annotations.parse_type_line prone to command injection security, upstream
1028713 salmon call causing pigx-rnaseq to infinitely loop bookworm, confirmed, ftbfs, sid
1029202 snippy: Error when using snpeff 5.1 upstream
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
1005713 tensorflow FTBFS; bazel still tries to download during build.
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
801505 texlive-latex-extra: complaint about weong file in dpkg trigger
807211 texlive-latex-extra: bug in cool.sty; dependency on texlive-fonts-extra
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?
899413 texlive-latex-extra: beamerthemeAachen.sty is missing package tangocolors
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 wontfix
992269 texlive-bibtex-extra: Missing beebe bst stiles like abstract.bst
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
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
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
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
967815 workrave: depends on deprecated GTK 2
980873 workrave: Break warning window grabs keyboard focus on Wayland
988064 workrave: applet does not display timer after screen lock

Open bugs in suggested packages

3 serious, 2 important, 1 normal
928076 bcbio: Workflows not ready for non-developers to depend on.
1018312 bcbio: build-depends on python3-nose or uses it for autopkgtest
1002223 simde: fails test with clang: error: cd clang_test && LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 meson test returned exit code 6 bookworm, experimental, ftbfs, sid, upstream
1021247 simde: FTBFS on i386 ftbfs
1030577 simde: autopkgtest regressions on i386 and ppc64el
1025746 vienna-rna: FTBFS: Package 'RNAlib2', required by 'virtual:world', not found bookworm, ftbfs, sid

Done bugs

1028449 changeo fails with python3.11: "invalid mode rU" patch
989108 dcmtk-doc: broken symlink: /usr/share/doc/dcmtk-doc/html/jquery.js -> ../../../javascript/jquery/jquery.js
990134 dcmtk: legacy conffiles leftover
990135 dcmtk: leftovers after package purge
1027828 macromoleculebuilder: FTBFS in bullseye (a2x: ERROR: "xsltproc" [...] returned non-zero exit status 5) ftbfs
1028856 paleomix: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13 bookworm, ftbfs, sid
1028812 pynn: FTBFS: AttributeError: module 'numpy' has no attribute 'int' bookworm, ftbfs, sid
1030512 python3-anndata needs a source upload to fix the missing python3-h5py dependency
979625 autopkgtest: ModuleNotFoundError (ipytree) and AssertionError
1027251 python-cooler: autopkgtest fail with numpy/1.24.1
1028108 python-cooler: binary-any FTBFS ftbfs
1029694 python-cooler: tests fail with scipy 1.10
1018551 python-pbcore: build-depends on python3-nose or uses it for autopkgtest
1027211 python-pbcore: autopkgtest fail with numpy/1.24.1
1027335 pairtools -- current repo in salsa FTBFS confirmed
1018577 python-seqcluster: build-depends on python3-nose or uses it for autopkgtest
994423 pytorch: Baseline violation on armhf bookworm, bullseye, ftbfs, sid
997931 libtorch-dev: Caffe2Targets.cmake is broken
1027851 pytorch FTBFS with Python 3.11 as default version bookworm, ftbfs, help, sid
1028749 tpot: FTBFS: unsatisfiable build-dependency: python3 (< 3.11) but 3.11.1-1 is to be installed bookworm, ftbfs, help, sid
1029580 sepp fails with python3.11: "invalid mode rU" patch
1023687 simde build depends on gcc-10 that should not be in bookworm
1019317 snakemake: HTML dashboard (--gui) is broken due to use of local jquery/bootstrap patch
1026576 spaln: FTBFS: error: cannot convert ‘gzFile’ {aka ‘gzFile_s*’} to ‘FILE*’ bookworm, ftbfs, sid, upstream
1026554 toil: FTBFS: ModuleNotFoundError: No module named 'cwltool.expression' bookworm, ftbfs, sid
1030558 toil build-depends on missing python3-xdist ftbfs
955965 workrave: Depends on deprecated dbus-glib bookworm, bullseye, sid
1025249 wtdbg2: flaky autopkgtest: Segmentation fault
*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:
Last update: Wed, 08 Feb 2023 16:31:56 -0000