Debian Med Project
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Summary
Bugs of task covid-19
Total bugs: 149
Open bugs: 134
Fixed bugs: 15
Links to other tasks
Tasks overview
Biology 165 (1383)
Phylogeny 3 (21)
Cloud 37 (315)
Covid-19 134 (1151)
Medical data 1 (3)
Dental 0 (0)
Epidemiology 3 (18)
Imaging 231 (1075)
Laboratory 1 (9)
Oncology 3 (48)
Pharmacology 1 (9)
Physics 25 (180)
Practice 3 (27)
Psychology 7 (65)
Research 0 (0)
Statistics 0 (0)
Tools 33 (218)
Typesetting 67 (538)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 1 0
important 33 1
normal 65 0
minor 12 0
wishlist 22 0

Summary bugs page of task Covid-19

Immediately looking into bugs of the dependencies of this task is advised (1151)*

Open bugs in dependent packages

1 serious, 33 important, 65 normal, 12 minor, 22 wishlist
abyss (1) Homepage: https://github.com/bcgsc/abyss Vcs Debian Med Packaging Team
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
bcftools (4) Homepage: http://samtools.github.io/bcftools/ Vcs Debian Med Packaging Team
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, upstream
bustools (1) Homepage: https://bustools.github.io/ Vcs Debian Med Packaging Team
986203 bustools: Please provide autopkgtest newcomer
dcmtk (15) Homepage: http://dicom.offis.de/dcmtk Vcs Debian Med Packaging Team
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/dulfsm.cc 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
935879 Update to use CharLS 2.0 upstream
981326 dcmtk 3.6.6 has been released
gdcm (3) Homepage: http://gdcm.sourceforge.net/ Vcs Debian Med Packaging Team
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
gromacs (4) Homepage: http://www.gromacs.org/ Vcs Debichem Team
644397 Provide runtime detection for CPU SIMD capabilities upstream
921784 gromacs: unhelpful error message from mpicxx.openmpi unreproducible
983942 gromacs: ftbfs with -march=x86-64-v3
984161 gromacs: ftbfs with GCC-11 bookworm, sid
imagej (1) Homepage: https://imagej.nih.gov/ij Vcs Debian Med Packaging Team
986041 imagej script bug in a system with no swap patch
ivar (1) Homepage: https://github.com/andersen-lab/ivar Vcs Debian Med Packaging Team
984067 ivar: ftbfs with GCC-11 bookworm, sid
lastz (1) Homepage: https://github.com/lastz/lastz Vcs Debian Med Packaging Team
984081 lastz: ftbfs with GCC-11 bookworm, sid
libmaus2 (1) Homepage: https://gitlab.com/german.tischler/libmaus2 Vcs Debian Med Packaging Team
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call ftbfs, help, upstream
nanopolish (1) Homepage: https://github.com/jts/nanopolish Vcs Debian Med Packaging Team
983767 nanopolish ftbfs with the nocheck profile
ncbi-blast+ (3) Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Vcs Debian Med Packaging Team
891197 Please switch to pcre2
956850 ncbi-blast+: Please provide /usr/bin/legacy_blast.pl
984871 ncbi-blast+: Missing headers for shared libraries
orthanc-dicomweb (1) Homepage: https://www.orthanc-server.com/static.php?page=dicomweb Vcs Debian Med Packaging Team
981753 COPY cannot find "/usr/share/nodejs/axios/dist/axios.min.js" patch
pigx-rnaseq (1) Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq Vcs Debian Med Packaging Team
985144 pigx-rnaseq -- Fails to build reproducibly: different binaries on usrmerge system patch
python-biopython (1) Homepage: http://biopython.org Vcs Debian Med Packaging Team
986410 autopkg tests don't run with the same dependencies as during the build
python-cooler (2) Homepage: https://github.com/mirnylab/cooler Vcs Debian Med Packaging Team
965361 python-cooler: please make the build reproducible patch, pending
979625 autopkgtest: ModuleNotFoundError (ipytree) and AssertionError
python-pbcore (2) Homepage: https://github.com/PacificBiosciences/pbcore Vcs Debian Med Packaging Team
860158 python-pbcore: prints warnings with recent h5py on ppc64el
919052 python-pbcore: some docs for pbcore are not found
python-tornado (1) Homepage: https://www.tornadoweb.org/ Vcs Debian Python Team
949974 Finish hangs after flush
pytorch (2) Homepage: https://pytorch.org/ Vcs Debian Deep Learning Team
983517 pytorch: Build documentation
984304 pytorch: ftbfs with GCC-11 bookworm, sid
r-cran-sf (1) Homepage: https://cran.r-project.org/package=sf Vcs Debian R Packages Maintainers
983749 The autopkgtest test depends are not available on s390x
shovill (1) Homepage: https://github.com/tseemann/shovill Vcs Debian Med Packaging Team
970404 shovill: Please provide autopkgtest
spades (2) Homepage: http://cab.spbu.ru/software/spades/ Vcs Debian Med Packaging Team
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" bullseye, ftbfs, sid
texlive-extra (56) Homepage: http://www.tug.org/texlive/ Vcs Debian TeX Task Force
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
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: pdfannotextractor.pl 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
974724 no useful documentation of pdfjam commands wontfix
976080 pdfxup doesn't work anymore
tnseq-transit (1) Homepage: http://saclab.tamu.edu/essentiality/transit/ Vcs Debian Med Packaging Team
984958 tnseq-transit: spews SyntaxWarning during installation
umap-learn (1) Homepage: https://github.com/lmcinnes/umap Vcs Debian Med Packaging Team
980509 umap-learn: Binary package name should be python3-umap-learn pending
vg (1) Homepage: https://github.com/vgteam/vg#vg Vcs Debian Med Packaging Team
976511 vg: FTBFS on arm64: configure: error: Could not find a version of the library! bullseye, ftbfs, sid
vsearch (1) Homepage: https://github.com/torognes/vsearch/ Vcs Debian Med Packaging Team
978918 vsearch: ftbfs with autoconf 2.70 bookworm, sid
workrave (23) Homepage: http://www.workrave.org/ Vcs Francois Marier
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
980873 workrave: Break warning window grabs keyboard focus on Wayland

Open bugs in suggested packages

1 important
bcbio (1) Homepage: https://github.com/bcbio/bcbio-nextgen Vcs Debian Med Packaging Team
928076 bcbio: Workflows not ready for non-developers to depend on.

Done bugs

assembly-stats (2) Homepage: https://github.com/sanger-pathogens/assembly-stats Vcs Debian Med Packaging Team
984889 assembly-stats natively FTBFS: error: gtest/gtest.h: No such file or directory patch
984890 assembly-stats FTCBFS: uses DEB_BUILD_GNU_TYPE patch
changeo (1) Homepage: https://changeo.readthedocs.io Vcs Debian Med Packaging Team
970597 src:changeo: no autopkgtest available yet newcomer
gdcm (1) Homepage: http://gdcm.sourceforge.net/ Vcs Debian Med Packaging Team
939670 gdcm-doc: depends on cruft package. bullseye, sid
gromacs (1) Homepage: http://www.gromacs.org/ Vcs Debichem Team
985157 gromacs-data: broken bash-completion scripts for gmx
gubbins (1) Homepage: https://sanger-pathogens.github.io/gubbins/ Vcs Debian Med Packaging Team
986238 gubbins: broken symlink: /usr/bin/gubbins_drawer -> ../share/gubbins/gubbins_drawer.py
imagej (1) Homepage: https://imagej.nih.gov/ij Vcs Debian Med Packaging Team
986038 imagej currently has an undeclared and substitutable dependency
pynn (1) Homepage: https://neuralensemble.org/trac/PyNN Vcs Debian Med Packaging Team
813821 pynn: FTBFS: TypeError: 'float' object cannot be interpreted as an index ftbfs, help
scrappie (1) Homepage: https://github.com/nanoporetech/scrappie Vcs Debian Med Packaging Team
986307 scrappie: flaky armhf autopkgtest: Invalid control character at: line 1 column 91 (char 90) bullseye, sid
snakemake (1) Homepage: https://snakemake.readthedocs.io/ Vcs Debian Med Packaging Team
986768 snakemake: autopkgtest regression: Missing input files for rule remote_ancient
texlive-extra (4) Homepage: http://www.tug.org/texlive/ Vcs Debian TeX Task Force
581960 tex4ht: wrong charset in htlatex output
985437 texlive-fonts-extra: broken font symlinks
985582 texlive-latex-extra: Dangling link
986233 texlive-fonts-extra: no further upgrades until #923423 is resolved
workrave (1) Homepage: http://www.workrave.org/ Vcs Francois Marier
986968 GNOME extension crashes on startup and disables all other extensions fixed-upstream, patch, upstream
*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: Sun, 18 Apr 2021 04:22:10 -0000