Debian Med Project
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Summary
Bugs of task covid-19
Total bugs: 146
Open bugs: 135
Fixed bugs: 11
Links to other tasks
Biology 140 (1387)
Phylogeny 3 (12)
Cloud 29 (354)
Covid-19 135 (1331)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 5 (74)
Imaging 212 (1057)
Laboratory 1 (9)
Oncology 0 (0)
Pharmacology 1 (9)
Physics 26 (201)
Practice 6 (45)
Psychology 2 (24)
Research 0 (0)
Statistics 0 (0)
Tools 32 (209)
Typesetting 60 (464)
Legend
SeverityDependentSuggested
critical 0 0
grave 1 0
serious 9 1
important 26 2
normal 64 2
minor 13 0
wishlist 17 0

Summary bugs page of task Covid-19

Immediately looking into bugs of the dependencies of this task is advised (1331)*

Open bugs in dependent packages

1 grave, 9 serious, 26 important, 64 normal, 13 minor, 17 wishlist
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
870060 bcftools FTBFS on big endian: 107 tests failed ftbfs, upstream
1010653 busco: add autopkgtest to check integration with hmmer and prodigal
1018936 busco: unsatisfiable dependency on arm64
935879 Update to use CharLS 2.0 upstream
988644 Defined Term: ISO 2022 IR 87 is not supported upstream, confirmed
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
995966 epigrass: epirunner and epidash fail to run due to missing dash modules
998265 epigrass: autopkgtest regression: The 'panel' distribution was not found
731435 warning: iteration 55823u invokes undefined behavior [-Waggressive-loop-optimizations] upstream, patch
749783 gdcm: Conflicting declarations of jpeg_memory_mgr may lead to invalid function calls
826048 Faulty CMake file impairs compiling against GDCM wontfix, moreinfo
1013156 gdcm: vtk[6,7] removal
644397 Provide runtime detection for CPU SIMD capabilities upstream
983942 gromacs: ftbfs with -march=x86-64-v3
762353 libaqbanking-data: Missing sentence to translate l10n
1006686 libchipcard-dev: undefined variable in libchipcard-client.pc patch, upstream, fixed-upstream
1006687 libchipcard6: card.c leaks memory patch, upstream
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call ftbfs, upstream, help, fixed-upstream
996981 multiqc: Link to jquery missing
891197 Please switch to pcre2
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
1017871 shiny-server: server-function don't run
1001387 Wishlist: Package Stone of Orthanc Webviewer
1011156 picard-tools: FTBFS with OpenJDK 17 due to com.sun.javadoc removal bookworm, ftbfs, sid
1009156 pplacer: Add autopkgtest
1018448 pynn: build-depends on python3-nose or uses it for autopkgtest
1018464 python-biom-format: build-depends on python3-nose or uses it for autopkgtest
1009118 python3-biopython: incompatible with muscle >= 5 wontfix, upstream, confirmed, fixed-upstream
979625 autopkgtest: ModuleNotFoundError (ipytree) and AssertionError
1018501 python-gffutils: build-depends on python3-nose or uses it for autopkgtest
860158 python-pbcore: prints warnings with recent h5py on ppc64el
1018551 python-pbcore: build-depends on python3-nose or uses it for autopkgtest
1018559 python-pyani: build-depends on python3-nose or uses it for autopkgtest
1018560 python-pybedtools: build-depends on python3-nose or uses it for autopkgtest
998854 undefined symbol: _PyUnicode_DecodeUnicodeEscape upstream, sid, fixed-upstream, wontfix, bookworm
983517 pytorch: Build documentation
997931 libtorch-dev: Caffe2Targets.cmake is broken
1018610 recan: build-depends on python3-nose or uses it for autopkgtest
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
1020035 seqan3: FTBFS: char_traits.h:431:56: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets 4 and 3 may overlap up to 9223372036854775813 bytes at offset -3 [-Werror=restrict] bookworm, ftbfs, sid
1019317 snakemake: HTML dashboard (--gui) is broken due to use of local jquery/bootstrap patch
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" sid, bookworm, bullseye, ftbfs
1015668 spades: ftbfs with LTO (link time optimization) enabled bookworm, sid
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 upstream, patch, pending, fixed-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?
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, sid, bullseye, ftbfs
987184 vg -- excessive variants built, and not tested
1013061 vg: ftbfs with GCC-12 bookworm, sid, ftbfs
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

1 serious, 2 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
1018577 python-seqcluster: 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 experimental, sid, bookworm, ftbfs, upstream
1005713 tensorflow FTBFS; bazel still tries to download during build.

Done bugs

1016331 gdcm: FTBFS: make[2]: *** [Makefile:12: refman.pdf] Error 1 sid, bookworm, ftbfs
1017027 gdcm: ftbfs, sed command in debian/rules fails ftbfs, sid
1018433 paleomix: build-depends on python3-nose or uses it for autopkgtest
1017070 python-etelemetry: server offline, DEP8 tests fail
994423 pytorch: Baseline violation on armhf bullseye, sid, bookworm, ftbfs
1004782 pytorch: FTBFS with ffmpeg 5.0 sid, ftbfs, bookworm
1009200 pytorch: (autopkgtest) needs update for python3.10: 'float' object cannot be interpreted as an integer sid, bookworm
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
1018608 q2-quality-filter: build-depends on python3-nose or uses it for autopkgtest
955965 workrave: Depends on deprecated dbus-glib bullseye, sid, bookworm
*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: Sat, 24 Sep 2022 19:59:00 -0000