Debian Med Project
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Bugs of task covid-19
Total bugs: 165
Open bugs: 134
Fixed bugs: 31
Links to other tasks
Biology 153 (1738)
Phylogeny 4 (45)
Cloud 35 (396)
Covid-19 134 (1294)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 1 (30)
Imaging 221 (1191)
Laboratory 1 (9)
Oncology 0 (0)
Pharmacology 1 (9)
Physics 23 (177)
Practice 2 (18)
Psychology 4 (63)
Research 0 (0)
Statistics 0 (0)
Tools 33 (243)
Typesetting 69 (544)
critical 0 0
grave 0 0
serious 7 1
important 33 3
normal 59 1
minor 10 0
wishlist 20 0

Summary bugs page of task Covid-19

Immediately looking into bugs of the dependencies of this task is advised (1294)*

Open bugs in dependent packages

7 serious, 33 important, 59 normal, 10 minor, 20 wishlist
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
964532 abyss: replace transitional bsdmainutils dependency
819617 FTBFS: any-i386 - floating point idiosyncracies bullseye, buster, ftbfs, sid, stretch
860682 bcftools: FTBFS on i386: Test failures bullseye, buster, ftbfs, sid, stretch
860704 python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1) bullseye, buster, ftbfs, sid, stretch
870060 bcftools FTBFS on big endian: 107 tests failed ftbfs
955403 bedtools ftbfs, failing tests on armel, armhf, i386, mipsel bullseye, ftbfs, pending, sid
970597 src:changeo: no autopkgtest available yet newcomer
956675 cyvcf2: test failures on ppc64el and s390x bullseye, ftbfs, sid
637687 libdcmtk2-dev: Dcmtk headers cause compile failure upstream, wontfix
675448 dcmtk: dcmdjpeg does not set (0028, 2114) LossyImageCompressionMethod when decompressing lossy compressed DICOM file confirmed, fixed-upstream, upstream
697073 dcmtk: dcmdjpeg fails to decode a lossless JPEG confirmed, upstream
714943 Fwd: getscu stops working with dcmtk 3.6.0 upstream, wontfix
715029 Fwd: dcmnet/libsrc/ confirmed, upstream, wontfix
718557 dcmtk: Missing transition in dcmqrscp upstream, wontfix
724886 IHE Radiology Technical Framework, Volume 2 (RAD TF-2) upstream, wontfix
730610 C-STORE SCU not working with JPIP Transfer Syntax confirmed, upstream
731433 iteration 9396u invokes undefined behavior [-Waggressive-loop-optimizations] upstream, wontfix
748403 Conflicting declarations of jpeg_memory_mgr may lead to invalid function calls upstream
810926 dcmtk-www: missing file name extension of /etc/apache2/conf-available/dcmtk wontfix
859202 warning: 'int readdir_r(DIR*, dirent*, dirent**)' is deprecated fixed-upstream
900196 dcmtk: wrongly assumes that CMAKE_SYSTEM_VERSION to be non-empty patch, upstream
913227 warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 128 fixed-upstream
913585 warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'Sint32' {aka 'int'} [-Wformat=] fixed-upstream
935879 Update to use CharLS 2.0 upstream
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
962553 gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr bullseye, sid
644397 Provide runtime detection for CPU SIMD capabilities upstream
921784 gromacs: unhelpful error message from mpicxx.openmpi unreproducible
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call ftbfs, help, upstream
960634 nanopolish: FTBFS on ppc64el (as well as ppc64 and powerpc), enumerator conflict ftbfs
891197 Please switch to pcre2
956850 ncbi-blast+: Please provide /usr/bin/
975587 odil: FTBFS against boost_1.74 ftbfs
975858 pplacer: FTBFS: Error: Unbound module Gsl_error bullseye, ftbfs, sid
950474 python-cogent FTBFS on armel and i386: test failures fixed-upstream, ftbfs, upstream
972504 python-cogent ftbfs with python3.9 as supported python3 version bullseye, ftbfs, sid
965361 python-cooler: please make the build reproducible patch, pending
860158 python-pbcore: prints warnings with recent h5py on ppc64el
919052 python-pbcore: some docs for pbcore are not found
949974 Finish hangs after flush
974210 pytorch's autopkg tests fail
956220 FTBFS: FileNotFoundError ftbfs
974716 q2-cutadapt: unsatisfiable build-dependency
974840 qa-feature-table: unsatisfiable build-dependencies
974733 q2-quality-filter: unsatisfiable build-dependencies
970404 shovill: Please provide autopkgtest
853113 spades: Fails to build with unhelpful error message in a "low" memory machine
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
536393 HTML mode is specifing image sizes in points, in violation of HTML standard (and sanity)
537284 Ligature fi becoming ø in avant garde
550381 tex4ht: Creates invalid html document
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
581960 tex4ht: wrong charset in htlatex output
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
637127 biblatex: Version 1.6-1 breaks "refsection=part" functionality
659772 landscape sciposter + hyperref + latex + dvips = center-mirrored image
670040 pdfannotextractor & pax do not work at all patch
675869 make PDF smaller with version1.4
683163 xmlto fail to convert example docbook to PDF (LaTeX Error, missing \item?)
697728 pdfjam: No --no-landscape with --nup possible
742276 pdfannotextractor & pax do not work at all patch
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
792676 libpdfbox-java: fails to find org.pdfbox.cos.ICOSVisitor class patch
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
943723 texlive-extra-utils: JRE is not a dependency even though some programs (e.g. arara) need it
947064 texlive-fonts-extra: fourier-orns.sty broken, docs using the Fourier font no longer compile
953072 texlive-fonts-extra: NotoColorEmoji.ttf is included in 3 Debian packages
953073 texlive-fonts-extra: TwemojiMozilla.ttf is included in 4 Debian packages
958562 texlive-extra-utils: missing man page for pdfcrop
973732 texlive-bibtex-extra: bbl2bib fails to load BibTeX/ pending
974724 no useful documentation of pdfjam commands
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
783845 workrave: Pulls in a lot of libraries from xfce4
783872 [workrave] xfce4 panel plugin uses the wrong path in desktop file
789044 workrave: lock was blocked by another application
802511 Please split off gnome-shell extension into separate package with proper dependencies
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
955965 workrave: Depends on deprecated dbus-glib bullseye, sid
967815 workrave: depends on deprecated GTK 2

Open bugs in suggested packages

1 serious, 3 important, 1 normal
928076 bcbio: Workflows not ready for non-developers to depend on.
971408 simde: FTBFS when dpkg-buildflags passes -ffile-prefix-map patch
971429 simde: autopkgtest failure on armhf bullseye, fixed-upstream, sid
973947 python3-rna, librna-perl: Cannot fulfill the dependencies
973956 vienna-rna: build-depends on python3-all-dev, but only builds for the default python3 version ftbfs

Done bugs

973804 bcbio: FTBFS undeclared build-dependency on git ftbfs
973977 centrifuge FTCBFS: uses uname for bits detection patch
971412 libdcmtk-dev: undeclared conflict with libcharls-dev
971433 libcharls-dev: Problem with latest unstable install bullseye, confirmed, experimental, fixed-upstream, ftbfs, patch, sid, upstream
973723 libcharls-dev ships which is also in libdcmtk-dev bullseye, confirmed, experimental, fixed-upstream, ftbfs, patch, sid, upstream
939670 gdcm-doc: depends on cruft package. bullseye, sid
974660 ginkgocadx: FTBFS in sid ftbfs, patch
971470 gnumed-client: autopkgtest must be marked superficial
974529 gnumed-client: new upstream available upstream
973639 libgromacs6: missing Breaks+Replaces: libgromacs5 upstream
971111 gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...) bullseye, ftbfs, help, patch, sid, upstream
972933 lumpy-sv: binary-all FTBFS ftbfs
972934 lumpy-sv: Cannot fulfill the build dependencies ftbfs
972935 lumpy-sv must build depend on python3-pysam ftbfs
973622 lumpy-sv,lumpy-sv-examples: both ship /usr/share/lumpy-sv/scripts/lumpyexpress.config
973624 nanofilt: ships /usr/lib/python3/dist-packages/scripts/
973612 orthanc: libcivetweb version mismatch
974850 proteinortho must not use -march=native -mtune=native
813821 pynn: FTBFS: TypeError: 'float' object cannot be interpreted as an index ftbfs, help
950929 python-biom-format: FTBFS with pandas 1.0: test failures fixed-upstream, ftbfs, upstream
973964 python-biom-format: please make the build reproducible patch
974050 python3-biom-format: ships /usr/lib/python3/dist-packages/.coverage
974178 python3-biom-format: debci tests fail: Object of type bytes is not JSON serializable
973018 python-etelemetry's autopkg tests are failing with python3.9 bullseye, sid
973801 python-pairix: please make the build reproducible patch
973178 python-streamz: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.9 3.8" returned exit code 13 bullseye, ftbfs, sid
972137 r-bioc-tcgabiolinks: autopkgtest regression bullseye, help, sid, upstream
966433 seqan autopkg test failures triggered by gcc-defaults bullseye, sid
973001 seqan3: autopackage tests need updating for new googletest ftbfs
972250 vienna-rna needs a sourceful upload for python3.9 bullseye, ftbfs, sid
971793 vt: conflicting build-dependencies. patch
*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: Sun, 29 Nov 2020 08:39:06 -0000