Debian Med Project
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Bugs of task bio
Total bugs: 118
Open bugs: 92
Fixed bugs: 26
Links to other tasks
Biology 92 (822)
Phylogeny 8 (66)
Cloud 39 (336)
Medical data 1 (9)
Dental 0 (0)
Epidemiology 0 (0)
Imaging 179 (1053)
Imaging development 106 (1056)
Laboratory 0 (0)
Oncology 1 (15)
Pharmacology 1 (9)
Physics 25 (180)
Practice 2 (9)
Psychology 6 (63)
Research 0 (0)
Statistics 2 (6)
Tools 34 (204)
Typesetting 97 (535)
critical 0 0
grave 0 1
serious 4 0
important 11 1
normal 55 6
minor 2 3
wishlist 6 3

Summary bugs page of task Biology

Immediately looking into bugs of the dependencies of this task is advised (822)*

Open bugs in dependent packages

4 serious, 11 important, 55 normal, 2 minor, 6 wishlist
852839 baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t
784451 [ball] Qt4's WebKit removal upstream
819617 FTBFS: any-i386 - floating point idiosyncracies
780428 beast-mcmc: restrict arch from all to amd64
747337 broken autopkgtest: missing dependency, not testing installed package, test failures upstream
853859 bwa: Segmentation fault with specific data set
856942 circos: broken symlinks: /usr/share/doc/circos/* -> /tools/*/*
853375 disulfinder: ftbfs with GCC-7 buster, sid
846858 src:ea-utils: New version available
682042 emboss-data: ships bulky taxonomy and gene ontology data
853396 fastx-toolkit: ftbfs with GCC-7 buster, sid
851658 ffindex: autopkgtests need 6GB of memory to run
848335 src:filo: Please add autopkgtest newcomer
759006 flexbar: FTBFS on hppa: Flexbar.h:258: undefined reference to `tbb::pipeline::run(unsigned int)'
853403 flexbar: ftbfs with GCC-7 buster, sid
814617 freecontact: adequate reports symbol-size-mismatch /usr/bin/freecontact => _ZN11xercesc_3_16XMLUni18fgXercesLoadSchemaE
853405 freecontact: ftbfs with GCC-7 buster, sid
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
836230 FTBFS in a low memory machine with poor error message
732691 Pressing "alignment or Ctrl+G" only results in a dialog with a cancel button
644397 Provide runtime detection for CPU SIMD capabilities upstream
853440 harvest-tools: ftbfs with GCC-7 buster, sid
749367 htslib FTBFS on testing for mips/mipsel moreinfo, patch, sid, stretch
774109 htslib: FTBFS on hppa
800469 htslib FTBFS on armhf, bus error. patch, sid, stretch
849667 htslib: FTBFS on armhf: [test] Bus error patch, sid, stretch
849025 jalview: FTBFS: error: cannot find symbol EnumCallback
712791 jmol - exporting the image as PDF saves only partial image patch
804579 logol-bin: bogus hardcoded dependency on libncursesw5
848326 src:mapdamage: Please add autopkgtest newcomer
765285 mapsembler2: FTBFS on mips mipsel ppc sparc when 8 byte __sync* builtins are used
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
853604 pbsim: ftbfs with GCC-7 buster, sid
853609 perm: ftbfs with GCC-7 buster, sid
848334 src:picard-tools: Please add autopkgtest newcomer
848332 src:poa: Please add autopkgtest newcomer
716580 [Mayhem] Bug report on populations: populations crashes with exit status 139
848329 src:prank: Please add autopkgtest newcomer
813250 prime-phylo: FTBFS on hppa: undefined boost references
853621 primer3: ftbfs with GCC-7 buster, sid
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
857950 qcumber: [INTL:nl] Dutch translation of debconf messages l10n, 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
767296 rasmol: ftbfs on ppc64el -- conflict with vector keyword patch
790196 rasmol: depends on vte which is deprecated sid, stretch
821023 rasmol: Short descriptions should begin with lowercase l10n, patch
847569 rsem: New version available
853656 sga: ftbfs with GCC-7 buster, sid
848589 snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)
818505 sortmerna FTBFS on !x86 sid
853113 spades: Fails to build with unhelpful error message in a "low" memory machine
853666 spades: ftbfs with GCC-7 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
855340 Spurious build dep on libssl-dev pending

Open bugs in suggested packages

1 grave, 1 important, 6 normal, 3 minor, 3 wishlist
857283 arb-common: broken symlinks: /usr/lib/arb/bin/mafft-*, /etc/arb/inputMasks/format.readme
580670 autodocktools: Please split out non-gui/biochemistry-oriented python bits
585244 autodocktools: Python string exceptions no more allowed in Python 2.6 upstream
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
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
855485 runPmv script does not work
855494 mgltools-pmv: runPmv does not start
855701 runPmv script does not work

Done bugs

749733 GCC warnings that may lead to runtime issues with new GNUstep libraries jessie, sid, stretch
767144 autodocktools: fails to start the GUI
767145 autodocktools: fails to start the GUI
783547 TclError: cannot use geometry manager
857167 autodocktools: broken symlink: /usr/bin/autoligand -> ../share/pyshared/AutoDockTools/ patch
852743 dialign FTCBFS: uses the build architecture compiler patch
856233 edtsurf FTBFS on architectures where char is unsigned patch, sid, stretch
826458 gbrowse: Unescaped left brace in regex is deprecated
833885 gbrowse: ships a deterministic/predictable OpenID consumer secret security
853830 gentle: CXXFLAGS aren't passed properly and package might FTBFS on all archs that don't have PIE enabled
856424 libvcflib-tools: vcflib cannot find its programs in /usr/lib/vcflib/binaries
793193 mgltools-pmv: FTBFS due to pyversions: error parsing Python-Version attribute
857513 mobyle: broken symlink: /usr/share/mobyle/htdocs/portal/js/openid/jquery-1.3.2.js -> ../../../../../javascript/jquery/jquery.min/js patch
853211 phyml: Fails to use mpi
853737 phyml: Beagle library causes trouble on machines without proper graphics hardware
853738 phyml: MPI version uses different number of bootstrap steps breaking applications like seaview
730515 cd-hit-est is cdhit-est in Debian [Why?]
858053 cutadapt does not start due to missing python-xopen dependency
857900 scythe: binNMUs always FTBFS
853835 seaview: Wrong results in connection with multi-processing phyml
858430 seer: Not all scripts are installed in the binary package patch
856479 srst2: insecure handling of system calls patch, security
848464 stacks-web: Should Depends/Recommends the metapackage default-mysql-*
815174 staden: Missing links in /usr/bin
815176 staden: Gap4 contig editor does not show sequences
785035 ugene: FTBFS on amd64
*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: Mon, 27 Mar 2017 18:17:48 -0000