Debian Med Project
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Summary
Bugs of task bio
Total bugs: 415
Open bugs: 376
Fixed bugs: 39
Links to other tasks
Biology 376 (4285)
Biology development 173 (1873)
Phylogeny 20 (261)
Cloud 78 (1071)
Covid-19 223 (2466)
Medical data 0 (0)
Dental 2 (12)
Epidemiology 20 (234)
Imaging 222 (1139)
Laboratory 1 (9)
Oncology 1 (3)
Pharmacology 1 (9)
Physics 27 (198)
Practice 6 (45)
Psychology 11 (133)
Research 0 (0)
Statistics 4 (16)
Tools 35 (227)
Typesetting 74 (629)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 0
serious 61 20
important 90 29
normal 59 20
minor 54 7
wishlist 29 7

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (4285)*

Open bugs in dependent packages

61 serious, 90 important, 59 normal, 54 minor, 29 wishlist
920282 abyss fails to build on hurd - googletest EXPECT_DEATH
1066334 acedb: FTBFS: acein.c:2045:15: error: implicit declaration of function ‘add_history’ [-Werror=implicit-function-declaration] forky, ftbfs, help, sid, trixie
1067631 src:altree: autopkgtest timeouts on armel, armhf and ppc64el
1096300 altree: ftbfs with GCC-15 forky, ftbfs, sid
1102872 altree: add perl-xs-dev to Build-Depends
1096305 ampliconnoise: ftbfs with GCC-15 forky, ftbfs, sid
1107485 ampliconnoise FTCBFS: misses mpi flags patch
1112710 assembly-stats: FTBFS with CMake 4 forky, ftbfs, sid
1094842 augur: Please update to latest upstream 28.0.0, released 2025-01-30
1110595 autodock-vina ftbfs with boost1.88 forky, sid
1110448 avogadro: FTBFS on arm64 with GCC-15 due to GCS warning
1112715 axe-demultiplexer: FTBFS with CMake 4 forky, ftbfs, sid
1040385 libball1.5-data: broken symlink: /usr/share/BALL-1.5/BALLView/html -> ../../doc/libball1.5-data/BALLView/html
1112717 ball: FTBFS with CMake 4 forky, ftbfs, sid
1114056 ball: FTBFS: /<<PKGBUILDDIR>>/include/BALL/DATATYPE/contourSurface.h:305:80: error: 'const class BALL::TContourSurface<T>' has no member named 'data_' [-Wtemplate-body] forky, ftbfs, sid
1112718 bamtools: FTBFS with CMake 4 forky, ftbfs, sid
1112722 bcalm: FTBFS with CMake 4 forky, ftbfs, sid
1043686 beads: Fails to build source after successful build forky, ftbfs, sid, trixie
1112754 beads: FTBFS with CMake 4 forky, ftbfs, sid
1032034 beagle: broken package on non arm64/amd64 architectures wontfix
1025424 beast-mcmc: please enable autopkgtest help
1107598 beast-mcmc: please honor CFLAGS
1025830 beauti2 fails to start help
1104751 bedtools: FTBFS with GNUMAKEFLAGS=--shuffle=random patch
1105730 bedtools: FTBFS with make --shuffle=random: src/utils/version/version.cpp:2:10: fatal error: version_git.h: No such file or directory forky, ftbfs, sid, trixie
1110628 berkeley-express ftbfs with boost1.88 forky, sid
1112724 berkeley-express: FTBFS with CMake 4 forky, ftbfs, sid
1096367 bifrost: ftbfs with GCC-15 forky, ftbfs, sid
1112726 bifrost: FTBFS with CMake 4 forky, ftbfs, sid
1085363 bioxtasraw: Python SyntaxWarning
1112732 bppphyview: FTBFS with CMake 4 forky, ftbfs, sid
1112733 bppsuite: FTBFS with CMake 4 forky, ftbfs, sid
1104172 btlib - breaks autopkgtests for nthash.
1104777 bustools: do not hardcode CFLAGS and CXXFLAGS patch
1112739 bustools: FTBFS with CMake 4 forky, ftbfs, sid
1112764 cassiopee: FTBFS with CMake 4 forky, ftbfs, sid
1032036 chromhmm: broken package on non arm64/amd64 architectures wontfix
1112778 cif-tools: FTBFS with CMake 4 forky, ftbfs, sid
1112565 clonalorigin: recommends libxml-parserl-perl which is not in unstable
1096450 coils: ftbfs with GCC-15 forky, ftbfs, sid
1072286 coot: add autopkgtest for coot executable patch
1105260 crac: FTBFS with make --shuffle=reverse: dh_auto_test: error: make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 returned exit code 2 forky, ftbfs, sid, trixie
1035182 cutesv: please add autopkgtests (to add coverage for python3-numpy)
982869 datamash FTBFS on !x86 32bit: FAIL: tests/decorate-errors ftbfs, upstream
1044977 datamash: Fails to build source after successful build forky, ftbfs, sid, trixie
903886 dawg: Test suite fails upstream
1112828 dawg: FTBFS with CMake 4 forky, ftbfs, sid
1110577 delly ftbfs with boost1.88 forky, sid
1112842 diamond-aligner: FTBFS with CMake 4 forky, ftbfs, sid
1112847 discosnp: FTBFS with CMake 4 forky, ftbfs, sid
1114089 disulfinder: FTBFS: /usr/include/f2c.h:135:9: error: reference to 'complex' is ambiguous forky, ftbfs, sid
1110576 dnaclust ftbfs with boost1.88 forky, sid
1112859 dssp: FTBFS with CMake 4 forky, ftbfs, sid
1096554 dwgsim: ftbfs with GCC-15 forky, ftbfs, sid
862118 ea-utils: New upstream version available
682042 emboss-data: ships bulky taxonomy and gene ontology data
986043 emboss: uses media types that are not registered
1069098 emboss: all executables segfault on s390x bookworm, bullseye, forky, sid, trixie
1069142 emboss: build time testsuite is failing silently
1106974 emboss: add libcrypt-dev to Build-Depends
1088492 python3-emperor-doc: move from twitter-bootstrap{3,4} to bootstrap-html (v5) upstream
1105316 epcr: FTBFS with make --shuffle=reverse: fahash_lookup.cpp:30:10: fatal error: epcr/fahash.hpp: No such file or directory forky, ftbfs, sid, trixie
1087184 examl: fails to run with tight cores count
1105362 examl: FTBFS with make --shuffle=reverse: dh_install: error: missing files, aborting forky, ftbfs, sid, trixie
1096607 fasta3: ftbfs with GCC-15 forky, ftbfs, sid
1096612 fastlink: ftbfs with GCC-15 forky, ftbfs, sid
1113830 submit@bugs.debian.org
1113845 fastqtl: recommends r-cran-qvalue which is not in unstable
1112919 flexbar: FTBFS with CMake 4 forky, ftbfs, sid
1096651 freecontact: ftbfs with GCC-15 forky, ftbfs, sid
715937 [Mayhem] Bug report on garlic: garlic crashes with exit status 139
749656 garlic: Conflicting declarations of function BlurMainWindow_ to cause undefined behaviour
929564 gatb-core-testdata: broken symlink: /usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit
983926 gatb-core: ftbfs with -march=x86-64-v2
1039206 gbrowse: ships sysv-init script without systemd unit
1102804 gbrowse: add perl-xs-dev to Build-Depends
967379 gdpc: depends on deprecated GTK 2 wontfix
982103 gdpc: autopkgtest failure on s390x
1107684 genometester FTCBFS: C vs C++ confusion patch, upstream
1105366 genomethreader: FTBFS with make --shuffle=reverse: src/libgenomethreader/gthversionfunc.c:3:10: fatal error: gth_config.h: No such file or directory forky, ftbfs, sid, trixie
1105339 genometools: FTBFS with make --shuffle=reverse: ./obj/gt_config.h:1: error: unterminated #ifndef forky, ftbfs, sid, trixie
1114122 genometools: FTBFS: src/extended/md5set.c:32:3: error: conflicting types for 'md5_t'; have 'struct <anonymous>' forky, ftbfs, sid
1092841 genomicsdb: FTBFS with fmtlib 11.1 ftbfs
732691 Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button upstream
1107615 gentle FTCBFS: uses mysql_config and the build architecture pkg-config patch, upstream
1107772 gmap inlining failed in call to ‘always_inline’ ‘_mm_alignr_epi8’: target specific option mismatch confirmed, ftbfs
644397 Provide runtime detection for CPU SIMD capabilities upstream
983942 gromacs: ftbfs with -march=x86-64-v3
1112991 hhsuite: FTBFS with CMake 4 forky, ftbfs, sid
1053499 hilive: flaky autopkgtest on several archs: segfault upstream
1113687 Should hilive be removed from unstable?
958244 Use system libinih-dev
986193 hinge: no autopkgtest available yet newcomer
1035178 hinge: please add autopkgtests (to add coverage for python3-numpy)
1036500 hinge: please add autopkgtests (to add coverage for python3-matplotlib)
1112992 hinge: FTBFS with CMake 4 forky, ftbfs, sid
1048028 hisat2: Fails to build source after successful build forky, ftbfs, sid, trixie
1076524 hisat2: autopkgtest uses absurd amount of memory on s390x
1103312 hmmer: FTBFS with the nocheck build profile forky, ftbfs, sid, trixie
1096850 iqtree: ftbfs with GCC-15 forky, ftbfs, sid
1113054 iqtree: FTBFS with CMake 4 forky, ftbfs, sid
1021557 jellyfish: Performance regression in 2.3.0 (orders of magnitude for some inputs) upstream
1102846 jellyfish: add perl-xs-dev to Build-Depends
1105388 jellyfish: FTBFS with make --shuffle=reverse: jellyfish/fastq2sam.cc:12:10: fatal error: jellyfish/fastq2sam_cmdline.hpp: No such file or directory forky, ftbfs, sid, trixie
875328 jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined upstream, wontfix
1095078 jmodeltest: reduce the permissions on /var/log/jmodeltest
1099239 jmodeltest: FTBFS: rc/main/java/es/uvigo/darwin/jmodeltest/io/HtmlReporter.java:38: error: cannot find symbol forky, ftbfs, sid, trixie
872418 jmol: Weblinks in Help do not work
1047324 kallisto: Fails to build source after successful build forky, ftbfs, sid, trixie
1057131 kallisto: add support for loongarch64 in d/control patch, pending
1113067 kallisto: FTBFS with CMake 4 forky, ftbfs, sid
1103315 kineticstools: FTBFS with the nocheck build profile forky, ftbfs, sid, trixie
1081273 meryl: Meryl should be packaged separately from new upstream location
1105422 kmer: FTBFS with make --shuffle=reverse: make[2]: *** No rule to make target '/build/reproducible-path/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a', needed by 'atac-driver/chimera/happy-clones-span-clumps'. Stop. forky, ftbfs, sid, trixie
1009159 kmerresistance: Add autopkgtest newcomer
1113092 lambda-align: FTBFS with CMake 4 forky, ftbfs, sid
1113093 lambda-align2: FTBFS with CMake 4 forky, ftbfs, sid
1048396 last-align: Fails to build source after successful build forky, ftbfs, sid, trixie
1097151 lastz: ftbfs with GCC-15 forky, ftbfs, sid
1110624 libpwiz ftbfs with boost 1.88 forky, sid
967603 ltrsift: depends on deprecated GTK 2 upstream, wontfix
1048669 ltrsift: Fails to build source after successful build forky, ftbfs, sid, trixie
1105470 ltrsift: FTBFS with make --shuffle=reverse: Fatal error: can't create obj/src/ltrsift_encode.o: No such file or directory forky, ftbfs, sid, trixie
1047978 lumpy-sv: Fails to build source after successful build forky, ftbfs, sid, trixie
1113261 macromoleculebuilder: FTBFS with CMake 4 forky, ftbfs, sid
1114196 macromoleculebuilder: FTBFS: dh_auto_configure: err [too-long-redacted] on -O0" .. returned exit code 1 forky, ftbfs, sid
1113263 maffilter: FTBFS with CMake 4 forky, ftbfs, sid
1113267 mapsembler2: FTBFS with CMake 4 forky, ftbfs, sid
1045227 massxpert: Fails to build source after successful build forky, ftbfs, sid, trixie
1084296 massxpert: FTBFS: rror: static assertion failed: No Q_OBJECT in the class passed to QObject::findChildren forky, ftbfs, sid, trixie
1113273 megadepth: FTBFS with CMake 4 forky, ftbfs, sid
1088028 megahit: consider unembedding parallel-hashmap
1113276 megahit: FTBFS with CMake 4 forky, ftbfs, sid
1048833 melting: Fails to build source after successful build forky, ftbfs, sid, trixie
1113279 metabat: FTBFS with CMake 4 forky, ftbfs, sid
1113280 metaeuk: FTBFS with CMake 4 forky, ftbfs, sid
1035188 microbegps: please add autopkgtests (to add coverage for python3-numpy)
1113288 mindthegap: FTBFS with CMake 4 forky, ftbfs, sid
1113290 minia: FTBFS with CMake 4 forky, ftbfs, sid
1099518 minimap2: error: type mismatch in conditional expression on loong64 patch
1105480 mlv-smile: FTBFS with make --shuffle=reverse: ld: cannot find grep+/obj/global_fonctions.o: No such file or directory forky, ftbfs, sid, trixie
1113291 mmseqs2: FTBFS with CMake 4 forky, ftbfs, sid
1112654 mosdepth: FTBFS: /usr/share/nimble/regex/regex.nim(859, 18) Error: Exception can raise an unlisted exception: Exception forky, ftbfs, sid
1105502 mptp: FTBFS with make --shuffle=reverse: lex_rtree.l:22:10: fatal error: parse_rtree.h: No such file or directory forky, ftbfs, sid, trixie
1088472 multiqc: move from twitter-bootstrap{3,4} to bootstrap-html (v5) upstream
1110615 murasaki ftbfs with boost 1.88 forky, sid
1105460 muscle: FTBFS with make --shuffle=reverse: Fatal error: can't create Linux/usage.o: No such file or directory forky, ftbfs, sid, trixie
1097430 nanopolish: ftbfs with GCC-15 forky, ftbfs, sid
1103286 Autopkgtest not working in s390x architecture
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
1077777 ncbi-blast+: makeblastdb yields broken DBs on s390x (BE generally?) upstream
1080479 ncbi-blast+: failure to create blastdb v5 on riscv64
1048966 ncbi-igblast: Fails to build source after successful build forky, ftbfs, sid, trixie
1097435 ncbi-igblast: ftbfs with GCC-15 forky, ftbfs, sid
1113797 ncbi-igblast FTCBFS: does not pass --host to configure patch
1097436 ncbi-seg: ftbfs with GCC-15 forky, ftbfs, sid
225651 ncbi-tools-x11: want Cn3D++
1113324 ngmlr: FTBFS with CMake 4 forky, ftbfs, sid
1049529 norsnet: Fails to build binary packages again after successful build forky, ftbfs, sid, trixie
1025370 ntcard: ftbfs with nthash 2.3.0 ftbfs, upstream
1047870 obitools: Fails to build source after successful build forky, ftbfs, sid, trixie
1068052 openms: FTBFS on armel,armhf (error: ‘QOpenGLFunctions_2_0’ does not name a type) ftbfs
1112634 openms FTBFS: error from pdflatex ftbfs
1113360 openms: FTBFS with CMake 4 forky, ftbfs, sid
1069488 parsinsert: FTBFS on armhf: make[1]: *** [debian/rules:30: override_dh_auto_test] Error 1 confirmed, forky, ftbfs, sid, trixie
1091721 pbsuite: autopkgtest regression in testing confirmed
1103318 pftools: FTBFS with the nocheck build profile forky, ftbfs, sid, trixie
1097575 phast: ftbfs with GCC-15 forky, ftbfs, sid
1106652 phyml FTCBFS: cross compilation support reverted patch, upstream
1113404 physamp: FTBFS with CMake 4 forky, ftbfs, sid
1114262 pigx-rnaseq: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 forky, ftbfs, sid
1113407 pizzly: FTBFS with CMake 4 forky, ftbfs, sid
1047303 plast: Fails to build source after successful build forky, ftbfs, sid, trixie
1097619 plast: ftbfs with GCC-15 forky, ftbfs, sid
1113412 plast: FTBFS with CMake 4 forky, ftbfs, sid
1107047 plink: add libcrypt-dev to Build-Depends
1113418 populations: FTBFS with CMake 4 forky, ftbfs, sid
1074546 FTBFS with OCaml 5.2.0 (Uses C functions without caml_ prefix) ftbfs
1093109 pplacer: FTBFS with OCaml 5.3.0 (error in C stubs) ftbfs
1078584 prime-phylo fails to build with mpi-defaults 1.17 on armhf wontfix
1097647 prime-phylo: ftbfs with GCC-15 forky, ftbfs, sid
1113421 prime-phylo: FTBFS with CMake 4 forky, ftbfs, sid
1097649 primer3: ftbfs with GCC-15 forky, ftbfs, sid
1091575 probabel: FTBFS on i386: dh_auto_test: error: make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 returned exit code 2 forky, ftbfs, sid, trixie
1105698 proteinortho: FTBFS with make --shuffle=reverse: rm: cannot remove 'remove.*': No such file or directory forky, ftbfs, sid, trixie
1048520 psortb: Fails to build source after successful build forky, ftbfs, sid, trixie
1102847 psortb: add perl-xs-dev to Build-Depends
709306 pymol: Crashes when running within xrdp/vnc (no 3D support)
765794 Race condition when running scripts in "stdin" mode
783653 pymol: Segmentation fault immediately after loading pdb
1058479 python-cogent: please (temporarily) drop python3-numba dependencies wontfix
1090269 python-cogent: FTBFS: E ImportError: Numba could not be imported. ftbfs
1085900 python-csb: Python SyntaxWarning pending
1103326 qcat: FTBFS with the nocheck build profile forky, ftbfs, sid, trixie
1036374 [INTL:es] Spanish translation of qcumber debconf template l10n, patch
1036506 qcumber: please add autopkgtests (to add coverage for python3-matplotlib)
1049117 qcumber: Fails to build source after successful build forky, ftbfs, sid, trixie
1068856 [INTL:sv] Swedish strings for qcumber debconf l10n, patch
1088515 qcumber: move from twitter-bootstrap{3,4} to bootstrap-html (v5) upstream
1103459 qcumber: [INTL:pt_BR] Brazilian Portuguese debconf templates translation l10n, patch
1076314 qiime hard-codes python 3.11 without depending on it forky, pending, sid, trixie
1084668 qiime: removal of Python standard libraries in Python 3.13 fixed-upstream, pending
642084 qutemol: Cannot start the program
939033 qutemol: Uses GifQuantizeBuffer - stops working with newer giflib
1085689 r-bioc-mofa: Python SyntaxWarning
1103201 r-cran-genabel: FTBFS: fexact.c:181:37: error: implicit declaration of function 'Calloc' forky, ftbfs, sid, trixie
1081161 r-cran-sdmtools: removed from CRAN repository
1084108 r-cran-spp: removed from CRAN repository
1081175 r-cran-tcr: removed from CRAN repository
1097767 racon: ftbfs with GCC-15 forky, ftbfs, sid
1047092 rambo-k: Fails to build source after successful build forky, ftbfs, pending, sid, trixie
909766 Use Debian packaged spdlog instead of code copy of old version help, upstream
976588 rapmap: FTBFS on arm64 (when trying to build arch:all) bookworm, bullseye, forky, ftbfs, sid, trixie
1097770 rapmap: ftbfs with GCC-15 forky, ftbfs, sid
1097771 rasmol: ftbfs with GCC-15 forky, ftbfs, sid
1097773 raster3d: ftbfs with GCC-15 forky, ftbfs, sid
1105671 raster3d: FTBFS with make --shuffle=reverse: Fatal Error: Cannot open module file ‘lists.mod’ for reading at (1): No such file or directory forky, ftbfs, sid, trixie
1105678 raxml: FTBFS with make --shuffle=reverse: ld: cannot find multiple.o: No such file or directory forky, ftbfs, sid, trixie
1099282 rdp-classifier: FTBFS: src/edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.java:28: error: cannot find symbol confirmed, forky, ftbfs, help, sid, trixie
1108589 rdp-classifier: FTBFS with default Java 25 ftbfs
1097779 readseq: ftbfs with GCC-15 forky, ftbfs, sid
1097784 relion: ftbfs with GCC-15 forky, ftbfs, sid
1113466 relion: FTBFS with CMake 4 forky, ftbfs, sid
1097803 roguenarok: ftbfs with GCC-15 forky, ftbfs, sid
1105603 saint: FTBFS with make --shuffle=reverse: mv: target '/build/reproducible-path/saint-2.5.0+dfsg/build': No such file or directory forky, ftbfs, sid, trixie
1088027 salmon: consider unembedding parallel-hashmap
1097838 salmon: ftbfs with GCC-15 forky, ftbfs, sid
1103327 salmon: FTBFS with the nocheck build profile forky, ftbfs, sid, trixie
1015654 sambamba: ftbfs with LTO (link time optimization) enabled forky, sid, trixie
1095434 sambamba: rare segmentation fault makes nanosv autopkgtest flaky
1113483 savvy: FTBFS with CMake 4 forky, ftbfs, sid
1113489 scrappie: FTBFS with CMake 4 forky, ftbfs, sid
1111716 seqan-raptor: FTBFS pdflatex refman ftbfs
1114369 seqan-raptor: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 forky, ftbfs, sid
917851 seqan2 2.4.0+dfsg-9: FTBFS, alignment problem ftbfs
1047218 seqan2: Fails to build source after successful build forky, ftbfs, sid, trixie
1049489 seqprep: Fails to build binary packages again after successful build forky, ftbfs, sid, trixie
967743 seqtools: depends on deprecated GTK 2
1047310 seqtools: Fails to build source after successful build forky, ftbfs, sid, trixie
1110602 shasta ftbfs with boost 1.88 forky, sid
1113499 sibelia: FTBFS with CMake 4 forky, ftbfs, sid
1097885 sim4: ftbfs with GCC-15 forky, ftbfs, sid
1113504 simka: FTBFS with CMake 4 forky, ftbfs, sid
1112688 skesa FTCBFS: uses variable CC for the C++ compiler patch, upstream
848589 snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)
1097906 soapaligner: ftbfs with GCC-15 forky, ftbfs, sid
1097907 soapdenovo: ftbfs with GCC-15 forky, ftbfs, sid
1097909 soapdenovo2: ftbfs with GCC-15 forky, ftbfs, sid
1105578 soapdenovo2: FTBFS with make --shuffle=reverse: ld: cannot find sparsePregraph/*.o: No such file or directory forky, ftbfs, sid, trixie
1072346 sortmerna: please update autopkgtest newcomer
1097910 sortmerna: ftbfs with GCC-15 forky, ftbfs, sid
1113530 sortmerna: FTBFS with CMake 4 forky, ftbfs, sid
1114393 sourmash: FTBFS: error: failed to select a version for the requirement `typed-builder = "^0.20"` forky, ftbfs, sid
1086015 build for all supported python3
1088026 spades: consider unembedding parallel-hashmap
1097913 spades: ftbfs with GCC-15 forky, ftbfs, sid
1113531 spades: FTBFS with CMake 4 forky, ftbfs, sid
1112687 spaln FTCBFS: uses -l flags in Makefile dependencies patch, upstream
1097922 spoa: ftbfs with GCC-15 forky, ftbfs, sid
1097934 staden: ftbfs with GCC-15 forky, ftbfs, sid
1048111 surankco: Fails to build source after successful build forky, ftbfs, sid, trixie
1097956 sweed: ftbfs with GCC-15 forky, ftbfs, sid
956848 t-coffee: should use "example" blastpgp.pl
1113569 terraphast: FTBFS with CMake 4 forky, ftbfs, sid
1105687 theseus: FTBFS with make --shuffle=reverse: ld: cannot find -ltheseus: No such file or directory forky, ftbfs, sid, trixie
1097993 thesias: ftbfs with GCC-15 forky, ftbfs, sid
1108056 toil: FTBFS: Some tests fail on single-cpu systems forky, ftbfs, help, sid, trixie
1098011 tracetuner: ftbfs with GCC-15 forky, ftbfs, sid
1113584 transrate-tools: FTBFS with CMake 4 forky, ftbfs, sid
1106704 tree-puzzle FTCBFS: uses mpicc patch, upstream
1108273 tree-puzzle: please make the build reproducible patch
846481 src:treeviewx: Please remove statically linked code copy of libncl
981874 trinityrnaseq: flaky autopkgtest bookworm, bullseye, forky, sid, trixie
1113587 trinityrnaseq: FTBFS with CMake 4 forky, ftbfs, sid
1113589 tvc: FTBFS with CMake 4 forky, ftbfs, sid
1047488 twopaco: Fails to build source after successful build forky, ftbfs, sid, trixie
1105670 uc-echo: FTBFS with make --shuffle=reverse: ././NeighborSet.hpp:200:(.text.startup+0x801): undefined reference to `NeighborSetLoader::CacheSize' forky, ftbfs, sid, trixie
980509 umap-learn: Binary package name should be python3-umap-learn pending
1058489 umap-learn: please (temporarily) drop python3-numba dependencies
1071816 umap-learn: FTBFS: E TypeError: exceptions must be derived from Warning, not <class 'NoneType'> ftbfs
1112612 Should umap-learn be removed from unstable? wontfix
1089115 umis: tracebacks normally fatal during autopkgtest runs upstream
1114433 vcfanno: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 forky, ftbfs, sid
1105569 velvet: FTBFS with make --shuffle=reverse: Fatal error: can't create obj/autoOpen.o: No such file or directory forky, ftbfs, sid, trixie
976511 vg: FTBFS on arm64: configure: error: Could not find a version of the library! bookworm, bullseye, forky, ftbfs, sid, trixie
987184 vg -- excessive variants built, and not tested
1015699 vg: ftbfs with LTO (link time optimization) enabled forky, sid, trixie
1089275 vg: FTBFS with make 4.4.1 forky, ftbfs, sid, trixie
1113618 vg: FTBFS with CMake 4 forky, ftbfs, sid
1105602 vmatch: FTBFS with make --shuffle=reverse: Fatal error: can't create ../lib/libfiles/kurtz-basic/verbosealpha.dbg.o: No such file or directory forky, ftbfs, sid, trixie
1105561 yaha: FTBFS with make --shuffle=reverse: src/Math.c:343:1: fatal error: opening dependency file obj/Math.d: No such file or directory forky, ftbfs, sid, trixie

Open bugs in suggested packages

20 serious, 29 important, 20 normal, 7 minor, 7 wishlist
1089541 override_dh_auto_build Error
1100471 [INTL:es] Spanish translation of arb debconf template l10n, patch
1102185 arb: Update/add debconf template translation [INTL:ca] l10n, patch
1102816 arb: add perl-xs-dev to Build-Depends
1114476 arb: FTBFS: CAP2.c:317:14: error: too many arguments to function 'ckopen'; expected 0, have 2 forky, ftbfs, sid
928076 bcbio: Workflows not ready for non-developers to depend on.
1114069 blimps: FTBFS: blksort.c:228:19: error: too many arguments to function 'read_config'; expected 0, have 3 forky, ftbfs, sid
1085412 catfishq: Python SyntaxWarning
1110578 cufflinks ftbfs with boost1.88 forky, sid
1114084 cufflinks: FTBFS: locfit/adap.c:32:3: error: too many arguments to function 'wdiag'; expected 0, have 6 forky, ftbfs, sid
1030327 science-numericalcomputation: please stop recommending python3-theano as it is being removed
1032638 please drop transitional package science-electronics from src:debian-science
1055339 debian-science: please replace recommendation of src:dolfin by src:fenics-dolfinx
1081508 getdata: homepage defunct
638753 libhdf5-serial-1.8.7: threadsafe memory leaks moreinfo
716008 [Mayhem] Bug report on hdf5-tools: h5copy crashes with exit status 139
716010 [Mayhem] Bug report on hdf5-tools: h5diff crashes with exit status 139
716011 [Mayhem] Bug report on hdf5-tools: h5dump crashes with exit status 139
716012 [Mayhem] Bug report on hdf5-tools: h5import crashes with exit status 139
839784 libhdf5-dev: pkg-config file references ONLY the C library
968559 libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing moreinfo
1023446 libhdf5-openmpi-dev: h5pcc configured as static build wontfix
1040862 hdf5: S3 VFD pulls in networking dependencies (libcurl), please package it as a VFD plugin moreinfo
1052250 pkg-config file incorrect for static linking
1100440 hdf5: CVE-2025-2153 security, upstream
1103531 hdf5: CVE-2025-2926 security, upstream
1103532 hdf5: CVE-2025-2925 security, upstream
1103533 hdf5: CVE-2025-2924 security, upstream
1103534 hdf5: CVE-2025-2923 security, upstream
1103536 hdf5: CVE-2025-2915 security, upstream
1103537 hdf5: CVE-2025-2914 security, upstream
1103538 hdf5: CVE-2025-2913 security, upstream
1103539 hdf5: CVE-2025-2912 security, upstream
1103540 hdf5: CVE-2025-2310 security, upstream
1103541 hdf5: CVE-2025-2309 security, upstream
1103542 hdf5: CVE-2025-2308 security, upstream
1105370 hdf5: FTBFS with make --shuffle=reverse: ln: failed to create symbolic link 'hdf5/serial/libhdf5.settings': File exists forky, ftbfs, sid, trixie
1108155 hdf5: CVE-2025-6269 security, upstream
1108156 hdf5: CVE-2025-6270 fixed-upstream, security, upstream
1108409 hdf5: CVE-2025-6750 security, upstream
1108480 hdf5: CVE-2025-6818 security, upstream
1108481 hdf5: CVE-2025-6817 security, upstream
1108482 hdf5: CVE-2025-6816 security, upstream
1108884 hdf5: CVE-2025-7069 fixed-upstream, security, upstream
1108885 hdf5: CVE-2025-7068 security, upstream
1108886 hdf5: CVE-2025-7067 security, upstream
1112653 hts-nim-tools: FTBFS: /usr/share/nimble/regex/regex.nim(859, 18) Error: Exception can raise an unlisted exception: Exception forky, ftbfs, sid
1063953 intake: autopkgtest regression with pytest 8
1088416 intake: move from twitter-bootstrap{3,4} to bootstrap-html (v5) upstream
1094915 intake commatibility with zarr3
1112615 Should intake be removed from unstable?
1067957 FTBFS: error: call of overloaded ‘__gmp_expr(__time64_t&)’ is ambiguous forky, ftbfs, sid, trixie
1108456 pybel: Drop python3-click (build) dependency forky, patch, sid, upstream
1082368 FTBFS: TestIntegration.testIntegration: AssertionError: 1 != 0 confirmed, ftbfs
1047039 pyrle: Fails to build source after successful build forky, ftbfs, sid, trixie
1114293 python-anndata: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13 forky, ftbfs, sid
1058482 python-loompy: please (temporarily) drop python3-numba dependencies
1046648 python-ncls: Fails to build source after successful build forky, ftbfs, sid, trixie
1035277 python-seqcluster: please add autopkgtests (to add coverage for python3-numpy)
1076318 q2-alignment hard-codes python 3.11 without depending on it forky, sid, trixie
1104285 q2-cutadapt: Fix unstable/amd64 debci failure
1076315 q2-demux hard-codes python 3.11 without depending on it forky, sid, trixie
1071882 q2-feature-classifier: FTBFS: unsatisfiable build-dependencies ftbfs
1114504 Should q2-feature-classifier be removed from unstable?
1076317 q2-phylogeny hard-codes python 3.11 without depending on it
1076914 q2-quality-control: FTBFS with the nocheck build profile ftbfs
1065333 q2-types: test data heavily outweighs actual code
1076316 q2-types hard-codes python 3.11 without depending on it forky, sid, trixie
1104050 q2-types: Fix unstable/amd64 debci failure patch
1076080 q2cli: FTBFS in sid (python3.12) ftbfs
1088514 q2templates: move from twitter-bootstrap{3,4} to bootstrap-html (v5) upstream
1083247 r-bioc-org.hs.eg.db: homepage defunct, standardize
1036681 relion-cuda: FTBFS with CUDA 12: nvcc fatal : Value 'sm_35' is not defined for option 'gpu-architecture' forky, ftbfs, sid, trixie
1040128 relion-cuda: FTBFS with cub 2.0.1: error: function "cub::Debug" has already been defined forky, ftbfs, sid, trixie
1049268 resfinder-db: Fails to build source after successful build forky, ftbfs, sid, trixie
1114370 seq-gen: FTBFS: seq-gen.c:143:6: error: conflicting types for 'ReadParams'; have 'void(int, char **)' forky, ftbfs, sid
986200 sift: Please provide autopkgtest newcomer
987606 sift: does not autobuild on buildds
1103329 sift: FTBFS with the nocheck build profile forky, ftbfs, sid, trixie
1114377 sift: FTBFS: Matrix_Info.c:822:1: error: number of arguments doesn't match prototype forky, ftbfs, sid
1114419 trnascan-se: FTBFS: src/gnuregex.c:1175:20: error: too many arguments to function 'at_begline_loc_p'; expected 0, have 3 forky, ftbfs, sid
1102852 vienna-rna: add perl-xs-dev to Build-Depends
1114434 vienna-rna: FTBFS: subopt.c:618:28: error: passing argument 2 of 'lst_kill' from incompatible pointer type [-Wincompatible-pointer-types] forky, ftbfs, sid

Done bugs

1096281 aegean: ftbfs with GCC-15 forky, ftbfs, sid
1109688 aegean: please enable build for loong64 patch
1060741 ball: Please port from sip4 to sip6 confirmed, help, patch, sid, trixie, upstream
1096362 beads: ftbfs with GCC-15 forky, sid
1035121 bitseq: please add autopkgtests (to add coverage for python3-numpy)
1111394 src:bitseq: fails to migrate to testing for too long forky, sid
1110806 cif-tools: FTBFS: make[1]: *** [debian/rules:9: override_dh_auto_configure] Error 2 forky, ftbfs, sid
1096504 datamash: ftbfs with GCC-15 forky, sid
1110795 dssp: FTBFS: make: *** [debian/rules:15: binary] Error 2 forky, ftbfs, sid
1096578 emboss: ftbfs with GCC-15 forky, ftbfs, sid
1067271 freebayes: FTBFS: dh_auto_test: error: cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=8 meson test -v --timeout-multiplier 100 returned exit code 5 ftbfs
750139 gamgi: Conflicting return types of function gamgi_engine_iarray_push upstream
967366 gamgi: depends on deprecated GTK 2
1044244 gamgi: Fails to build source after successful build ftbfs, sid, trixie
1103009 genomicsdb: FTBFS in testing/arm64: tests failed ftbfs, sid, trixie, upstream
1106611 ghmm ftbfs with libxml 2.14.x from experimental forky, ftbfs, patch, sid
915807 hdf5: CVE-2017-17507 security, upstream
1114023 hdf5 ftbfs in unstable forky, ftbfs, sid
1111788 htslib: autopkgtest regression
1064752 intake: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13 forky, ftbfs, sid, trixie
1067969 python3-intake: Please replace python3-appdirs dependency with platformdirs fixed-upstream, forky, patch, sid, trixie
1104128 jalview: Update/add debconf template translation [INTL:ca] l10n, patch
1082721 khmer: FTBFS: failing tests ftbfs
1085660 khmer: Python SyntaxWarning
1015525 libssw: ftbfs with LTO (link time optimization) enabled experimental, sid, trixie
1097352 mafft: ftbfs with GCC-15 forky, ftbfs, sid
1097365 massxpert2: ftbfs with GCC-15 forky, sid
1097402 minexpert2: ftbfs with GCC-15 forky, sid
964082 parsinsert fails it's tests when built with -O2 bookworm, bullseye, sid, trixie
1085786 porechop: Python SyntaxWarning
1111708 probcons: Uses deprecated BSD file reference patch
1111758 r-bioc-beachmat: autopkgtest regression: isNamespaceLoaded("beachmat.hdf5") is not TRUE
1111412 ska: autopkgtest fails due to googletest 1.17 no longer supporting C++ prior to C++17
976523 spades: FTBFS: jemalloc_internal.h:292:6: error: #error "No LG_QUANTUM definition for architecture; specify via CPPFLAGS" bookworm, bullseye, ftbfs, sid, trixie
1087093 spades: Python SyntaxWarning
1106622 sra-sdk ftbfs with libxml 2.14.x from experimental forky, ftbfs, patch, sid
1098008 tnseq-transit: ftbfs with GCC-15 forky, sid
1098031 ugene: ftbfs with GCC-15 forky, sid
1098098 wise: ftbfs with GCC-15 forky, 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:
critical10
grave10
serious10
important5
normal3
minor1
wishlist0
Last update: Wed, 17 Sep 2025 02:27:47 -0000