Debian Med Project
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Summary
Bugs of task bio
Total bugs: 175
Open bugs: 144
Fixed bugs: 31
Links to other tasks
Biology 144 (1426)
Phylogeny 9 (75)
Cloud 43 (507)
Medical data 1 (9)
Dental 0 (0)
Epidemiology 1 (9)
Imaging 190 (1158)
Laboratory 0 (0)
Oncology 2 (30)
Pharmacology 3 (27)
Physics 30 (288)
Practice 2 (9)
Psychology 8 (93)
Research 0 (0)
Statistics 2 (6)
Tools 35 (209)
Typesetting 64 (322)
Legend
SeverityDependentSuggested
critical 0 0
grave 0 2
serious 14 1
important 37 2
normal 41 9
minor 4 3
wishlist 27 4

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (1426)*

Open bugs in dependent packages

14 serious, 37 important, 41 normal, 4 minor, 27 wishlist
869126 augustus: explicit dependency on libhts1, blocks transition
852839 baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t
784451 [ball] Qt4's WebKit removal upstream
867660 ball: FTBFS with sip 4.19.x: sip: File::CannotWrite has not been defined
819617 FTBFS: any-i386 - floating point idiosyncracies buster, sid, stretch
860682 bcftools: FTBFS on i386: Test failures buster, sid, stretch
860704 python-pysam: FTBFS on i386: build-dependency not installable: bcftools (>= 1.3.1) buster, sid, stretch
868958 bcftools FTBFS on 32bit: test failures
747337 broken autopkgtest: missing dependency, not testing installed package, test failures upstream
866074 bio-tradis: autopkgtest regression
860655 blasr: FTBFS on i386: unsatisfiable build-dependencies: libpbseq-dev (>= 0~20160912), libpbbam-dev buster, sid, stretch
864439 bowtie: FTBFS on mips64el - /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI
864448 bowtie FTBFS on mips64el: /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI
715691 [Mayhem] Bug report on bppsuite: bppalnscore crashes with exit status 139
715692 [Mayhem] Bug report on bppsuite: bppancestor crashes with exit status 139
715693 [Mayhem] Bug report on bppsuite: bppconsense crashes with exit status 139
715694 [Mayhem] Bug report on bppsuite: bppdist crashes with exit status 139
715695 [Mayhem] Bug report on bppsuite: bppml crashes with exit status 139
860639 circlator: FTBFS on i386: unsatisfiable build-dependencies: python3-pysam (>= 0.8.1), spades, bwa (>= 0.7.12) buster, sid, stretch
859300 crac: please make the build reproducible patch
860690 crac: FTBFS on i386: build-dependency not installable: libjellyfish-2.0-dev buster, sid, stretch
865132 diamond-aligner FTBFS on ppc64el: undefined reference to Fixed_score_buffer
853375 disulfinder: ftbfs with GCC-7 buster, sid
846858 src:ea-utils: New version available
862118 ea-utils: New upstream version available
682042 emboss-data: ships bulky taxonomy and gene ontology data
864376 falcon: properly fix test failure: Task Node(1-preads_ovl/m_00001) failed with exit-code=256
864378 falcon accidentally still built on x32
853396 fastx-toolkit: ftbfs with GCC-7 buster, sid
848335 Filo should be removed from Debian after Stretch release since it is unmaintained and can be replaced newcomer
860653 fitgcp: FTBFS on i386: build-dependency not installable: python-pysam buster, sid, stretch
759006 flexbar: FTBFS on hppa: Flexbar.h:258: undefined reference to `tbb::pipeline::run(unsigned int)'
853403 flexbar: ftbfs with GCC-7 buster, sid
866646 freebayes FTBFS with libhts-dev 1.4.1-2
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
853405 freecontact: ftbfs with GCC-7 buster, sid
860661 fsm-lite: FTBFS on i386: build-dependency not installable: libsdsl-dev buster, sid, stretch
750139 gamgi: Conflicting return types of function gamgi_engine_iarray_push
669296 garlic: debcheckout fails pending
715937 [Mayhem] Bug report on garlic: garlic crashes with exit status 139
749656 garlic: Conflicting declarations of function BlurMainWindow_ to cause undefined behaviour
857213 gbrowse: broken symlink: /usr/share/gbrowse/htdocs/i -> debian/gbrowse/var/cache/gbrowse/images
732691 Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button
826069 ghemical: does not display color or allow building help
644397 Provide runtime detection for CPU SIMD capabilities upstream
853440 harvest-tools: ftbfs with GCC-7 buster, sid
866137 htslib autopkgtest is broken in 1.4.1-2
860640 iva: FTBFS on i386: build-dependency not installable: python3-pysam buster, sid, stretch
849025 jalview: FTBFS: error: cannot find symbol EnumCallback
863015 jellyfish: please make the output reproducible patch
865608 jellyfish shouldn't disable PIE patch
712791 jmol - exporting the image as PDF saves only partial image patch
851830 arm64 has flaky tests
862380 khmer: FTBFS with Python 3.6 buster, patch, sid
860636 kineticstools: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.8) buster, sid, stretch
866438 last-align: depends on obsolete python-imaging (replace with python3-pil or python-pil) buster, sid
860665 libvcflib: FTBFS on i386: build-dependency not installable: libssw-dev buster, sid, stretch
804579 logol-bin: bogus hardcoded dependency on libncursesw5
765285 mapsembler2: FTBFS on mips mipsel ppc sparc when 8 byte __sync* builtins are used
860672 mhap: FTBFS on i386: build-dependency not installable: libssw-java buster, sid, stretch
853568 nanopolish: ftbfs with GCC-7 buster, sid
225651 ncbi-tools-x11: want Cn3D++
784502 [openms] Qt4's WebKit removal
816562 libopenms2.0: fails to upgrade from 'jessie' - trying to overwrite /usr/share/man/man3/libopenms.3.gz
822412 openms: non-free WSDL-Schema (ND); incomplete copyright (missing DSL, BSL-1.0 licenses)
853595 openms: ftbfs with GCC-7 buster, sid
865240 Please update dependencies from latex-xcolor to tl-latex-recommended buster, sid
860676 pbalign: FTBFS on i386: build-dependency not installable: python-pbcore (>= 0.8.5) buster, sid, stretch
860631 pbbarcode: FTBFS on i386: unsatisfiable build-dependencies: python-pbcore, pbh5tools buster, sid, stretch
860711 pbdagcon: FTBFS on i386: unsatisfiable build-dependencies: libpbseq-dev, libpbbam-dev buster, sid, stretch
860669 pbgenomicconsensus: FTBFS on i386: build-dependency not installable: python-pbcore (>= 1.2.9) buster, sid, stretch
860616 pbh5tools: FTBFS on i386: build-dependency not installable: python-pbcore buster, sid, stretch
853604 pbsim: ftbfs with GCC-7 buster, sid
853609 perm: ftbfs with GCC-7 buster, sid
868919 physamp: FTBFS: AlignmentOptimizer.cpp:39:32: fatal error: Bpp/Seq/Alphabet.all: No such file or directory buster, sid
861367 pirs: Please do not depend on transitional dummy pkg ttf-liberation
865655 pirs shouldn't disable PIE patch
848332 src:poa: Please add autopkgtest newcomer
864558 poa FTCBFS: uses the build architecture compiler, runs tests despite DEB_BUILD_OPTIONS=nocheck patch
716580 [Mayhem] Bug report on populations: populations crashes with exit status 139
813250 prime-phylo: FTBFS on hppa: undefined boost references
853621 primer3: ftbfs with GCC-7 buster, sid
865191 probabel FTBFS on big endian: FAIL: 5
848333 src:proda: Please add autopkgtest newcomer
602610 Package freemol.mengine for full modeling capabilities
651609 pymol: Setting-Error: type read mismatch (int) 667
703782 pymol: Unable to launch the Menu
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
866547 python-biomaj3 encoding issue during build fixed-upstream, patch
866548 src:python-biomaj3: Excessive build-depends complicate python3 transition patch
820308 qiime: many unsatisfiable dependencies
857454 qtltools: please make the build reproducible patch, pending
845753 r-cran-treescape FTBFS on armhf, i386: Error: segfault from C stack overflow
860688 rapmap: FTBFS on i386: build-dependency not installable: libjellyfish-2.0-dev buster, sid, stretch
767296 rasmol: ftbfs on ppc64el -- conflict with vector keyword patch
790196 rasmol: depends on vte which is deprecated buster, sid, stretch
821023 rasmol: Short descriptions should begin with lowercase l10n, patch
865130 reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' upstream
868742 rna-star should remove s390x from the architecture list
861281 rnahybrid: FTBFS on armel help
847569 rsem: New version available
860681 salmon: FTBFS on i386: unsatisfiable build-dependencies: libjellyfish-2.0-dev (> 2.2.3-2), libbwa-dev buster, sid, stretch
853656 sga: ftbfs with GCC-7 buster, sid
860643 sga: FTBFS on i386: build-dependency not installable: python-pysam buster, sid, stretch
848589 snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)
860652 snap-aligner: FTBFS on i386: SNAPLib/SortedDataWriter.cpp:338:70: error: no matching function for call to 'max(long unsigned int, _int64)' buster, sid, stretch
818505 sortmerna FTBFS on !x86 buster, sid
853113 spades: Fails to build with unhelpful error message in a "low" memory machine
853666 spades: ftbfs with GCC-7 buster, sid
860677 spades: FTBFS on i386: unsatisfiable build-dependencies: libssw-dev, bwa buster, sid, stretch
868864 stacks doesn't migrate to testing, dependency doesn't exist on some architectures buster, sid
710225 staden-io-lib: library name should follow ABI version (not project version)
716373 [Mayhem] Bug report on t-coffee: t_coffee crashes with exit status 139 help
853677 t-coffee: ftbfs with GCC-7 buster, sid
853681 theseus: ftbfs with GCC-7 buster, sid
780816 tophat: contains and uses convience copy of samtools 0.1.18
806214 tree-puzzle: Package fails test suite
846481 src:treeviewx: Please remove statically linked code copy of libncl
853687 trinityrnaseq: ftbfs with GCC-7 buster, sid
860645 trinityrnaseq: FTBFS on i386: unsatisfiable build-dependencies: jellyfish (>= 2.1.4), parafly buster, sid, stretch
865262 trinityrnaseq: please build-depend on automake, not obsolete automake1.11

Open bugs in suggested packages

2 grave, 1 serious, 2 important, 9 normal, 3 minor, 4 wishlist
857283 arb-common: broken symlinks: /usr/lib/arb/bin/mafft-*, /etc/arb/inputMasks/format.readme
862913 [INTL:id] initial Indonesian debconf translation l10n, patch
866151 arb: transfig package renamed to fig2dev patch
580670 autodocktools: Please split out non-gui/biochemistry-oriented python bits
585244 autodocktools: Python string exceptions no more allowed in Python 2.6 upstream
780428 beast-mcmc: restrict arch from all to amd64
732858 Add MariaDB as alternative dependency
803116 biomaj: references to non-existent license "CeCILL-A"
848497 src:biomaj: New upstream version available
732862 Add MariaDB as an alternative dependency
866980 biomaj-watcher: fails to upgrade from 'jessie': Exception in thread "main" java.lang.UnsupportedClassVersionError: WatcherConfigurator : Unsupported major.minor version 52.0
715587 [Mayhem] Bug report on cain-solvers: HomogeneousHistogramsAverage crashes with exit status 139 help
715588 [Mayhem] Bug report on cain-solvers: HomogeneousHistogramsAverageAps crashes with exit status 139 help
772407 science-config: bashism in /bin/sh script
796771 science-geography: Depends on no longer built qgis-plugin-grass
861038 emboss-explorer: broken symlink: /usr/share/doc/emboss-explorer/html -> ../../EMBOSS/doc/html/emboss/apps
855485 runPmv script does not work
855494 mgltools-pmv: runPmv does not start
855701 runPmv script does not work
866442 mobyle: depends on obsolete python-imaging (replace with python3-pil or python-pil) buster, sid
868885 ugene wont find translate

Done bugs

749733 adun.app: GCC warnings that may lead to runtime issues with new GNUstep libraries buster, jessie, sid, stretch
859111 ariba FTBFS with bowtie2 2.3.1-1 buster, fixed-upstream, sid, upstream
865006 bcftools FTBFS with htslib 1.4.1-2: [E::hts_idx_push] Region 536870912..536870913 cannot be stored in a tbi index. Try using a csi index with min_shift = 14, n_lvls >= 6 buster, sid
865060 bcftools FTBFS: Usage: test-regidx [OPTIONS] patch
866066 biomaj-watcher: throws ClassNotFoundException: org.slf4j.LoggerFactory in tomcat logs
853859 bwa: Segmentation fault with specific data set
866330 cd-hit: please make the build reproducible patch
851658 ffindex: autopkgtests need 6GB of memory to run patch
826458 gbrowse: Unescaped left brace in regex is deprecated
833885 gbrowse: ships a deterministic/predictable OpenID consumer secret security
865099 hmmer2 FTBFS on i386: prep command at line 7 failed with status 34304
749367 htslib FTBFS on testing for mips/mipsel buster, moreinfo, patch, sid, stretch
774109 htslib: FTBFS on hppa
800469 htslib FTBFS on armhf, bus error. buster, patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error buster, patch, sid, stretch
865010 htslib: use -fPIC to fix FTBFS on s390x patch
865012 htslib FTBFS on i386: test_vcf_{api,sweep} failed patch, upstream
865654 phyml shouldn't disable PIE patch
866139 phyml uses -march=native
848329 src:prank: Please add autopkgtest newcomer
865251 Please update dependencies from latex-xcolor to tl-latex-recommended buster, sid
865244 Please update dependencies from latex-xcolor to tl-latex-recommended buster, sid
730515 cd-hit-est is cdhit-est in Debian [Why?]
862039 r-bioc-gviz: accesses the internet during build
865658 raxml shouldn't disable PIE patch
865008 samtools FTBFS with htslib 1.4.1-2: error: conflicting types for 'errmod_t' buster, sid
862484 seqan2: please make the build reproducible patch
848464 stacks-web: Should Depends/Recommends the metapackage default-mysql-*
865668 stacks shouldn't disable PIE patch
867535 trimmomatic fails on spaces in filenames patch
855340 Spurious build dep on libssl-dev
*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: Mon, 24 Jul 2017 18:42:41 -0000