Debian Med Project
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Bugs of task covid-19
Total bugs: 155
Open bugs: 129
Fixed bugs: 26
Links to other tasks
Biology 150 (1981)
Phylogeny 11 (129)
Cloud 46 (585)
Covid-19 129 (1337)
Medical data 0 (0)
Dental 0 (0)
Epidemiology 1 (30)
Imaging 229 (1174)
Laboratory 1 (30)
Oncology 0 (0)
Pharmacology 1 (9)
Physics 27 (201)
Practice 2 (18)
Psychology 5 (45)
Research 0 (0)
Statistics 1 (3)
Tools 31 (225)
Typesetting 73 (543)
critical 0 0
grave 0 0
serious 9 0
important 33 1
normal 60 0
minor 9 0
wishlist 17 0

Summary bugs page of task Covid-19

Immediately looking into bugs of the dependencies of this task is advised (1337)*

Open bugs in dependent packages

9 serious, 33 important, 60 normal, 9 minor, 17 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, sid
956675 cyvcf2: test failures on ppc64el and s390x bullseye, ftbfs, sid
964677 cyvcf2: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 returned exit code 13 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
961013 diamond-aligner: Diamond faill with the error: Assertion `index >= 0 && index < size()' failed. fixed-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
957268 genometools: ftbfs with GCC-10 bullseye, fixed-upstream, patch, sid, upstream
644397 Provide runtime detection for CPU SIMD capabilities upstream
921784 gromacs: unhelpful error message from mpicxx.openmpi unreproducible
962550 libgclib1: ABI break without soname change bullseye, sid
934619 libmaus2 FTBFS (mostly 32bit): error: no matching function for call ftbfs, help, upstream
961101 mmseqs2 FTBFS on i386 ftbfs, patch, pending
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/
933750 paleomix: Port to Python3 needed upstream
937232 paleomix: Python2 removal in sid/bullseye bullseye, sid, upstream
924128 prokka: creates world writable directory tree /var/lib/prokka/*
964650 pydicom: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.8 returned exit code 13 bullseye, ftbfs, sid
950929 python-biom-format: FTBFS with pandas 1.0: test failures upstream
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
956220 FTBFS: FileNotFoundError ftbfs
964086 r-cran-sf: autopkgtest failures with PROJ 7.1.0
963326 seqmagick: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 returned exit code 13 bullseye, ftbfs, help, sid, upstream
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
964101 tiddit: generates extremely large file during autopkgtesting help
964039 vg: FTBFS on mips64el ftbfs
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

Open bugs in suggested packages

1 important
928076 bcbio: Workflows not ready for non-developers to depend on.

Done bugs

964348 bbhash: Missing test dependencies
960316 src:bcbio: fails to migrate to testing for too long: depends on package not migrating bullseye, sid
962834 bcftools: Have dependency on Perl demoted to "recommended"
933937 biobambam2: /usr/bin/fastaexplode is already provided by exonerate upstream
963257 cat-bat must build depend on diamond-aligner ftbfs
963318 cwltool: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.8 returned exit code 13 bullseye, ftbfs, sid
964344 src:fastqc: fails to migrate to testing for too long: B-D on package that fails to migrate bullseye, sid
939670 gdcm-doc: depends on cruft package. bullseye, sid
963738 gnumed-client: new upstream available upstream
962999 mmtf-python: missing test dependencies
962887 multiqc: should depend on fonts-font-awesome and/or fonts-glyphicons-halflings (not fonts-glewlwyd)
963277 orthanc-dicomweb: FTBFS: ./Build/CMakeFiles/CMakeTmp/./Build/CMakeFiles/CMakeTmp/src.c:11: undefined reference to `pthread_create' bullseye, ftbfs, sid
961700 picard-tools build depends on the removed libguava-java-doc bullseye, ftbfs, sid
961865 picard-tools needs a source-only upload.
813821 pynn: FTBFS: TypeError: 'float' object cannot be interpreted as an index ftbfs, help
959587 python-biopython: FTBFS: AssertionError: False is not true bullseye, ftbfs, sid, upstream
960756 python-biopython FTBFS on 32bit: test_NCBI_BLAST_tools.BlastDB failures ftbfs, upstream
962944 python3-biopython needs Breaks: cnvkit (<< 0.9.7-1~)
962841 python3-nanomath: ships /usr/LICENSE
962698 python-pauvre: FTBFS if the "DISPLAY" environment variable is exported patch
962702 python-pauvre: please make the build reproducible patch
963093 samtools: recommended dependencies are unnecessary
943956 snakemake: please make the build reproducible fixed-upstream, patch
955056 snakemake: FTBFS with Sphinx 2.4: AttributeError: 'member_descriptor' object has no attribute 'expandtabs' ftbfs, upstream
963246 vg FTBFS with Protobuf 3.12.3 ftbfs, upstream
963313 vg: FTBFS: configure: error: Could not find a version of the library! bullseye, ftbfs, 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:
Last update: Fri, 10 Jul 2020 07:59:05 -0000