Gentoo Project

Biology Project

Bug Reports

• sci-biology/ucsc-genome-browser-260-r1 does not respect LDFLAGS

  339557 - Assigned to Gentoo Science Biology related packages
• sci-biology/unafold - add graphic capabilities of mfold_utils

  389765 - Assigned to Gentoo Science Biology related packages
• sci-biology/ucsc-genome-browser: add -fPIC to CFLAGS and USE=+static-libs

  402835 - Assigned to Gentoo Science Biology related packages
• sci-biology/ucsc-genome-browser-260: tries to link libpng.a and fails (due to missing -lm)

  438636 - Assigned to Gentoo Science Biology related packages
• sci-biology/foldingathome - add install options through USE flags for FAHviewer and FAHcontrol

  498886 - Assigned to Gentoo Science Biology related packages
• sci-biology/bioperl-9999-r1 - Can't rename 'blib/script/bp_meta_gff.pl' to 'blib/script/bp_meta_gff.pl': No such file or directory at /usr/lib64/perl5/vendor_perl/5.18.2/Bio/Root/Build.pm line 219.

  513672 - Assigned to Gentoo Science Biology related packages
• sci-biology/bioperl should install executable tools from examples

  514916 - Assigned to Gentoo Science Biology related packages
• sci-biology/emboss: try to install mimetype information

  549644 - Assigned to Gentoo Science Biology related packages
• sci-biology/bioperl: introduce USE=staden flag so that newer versions of io_lib can be installed

  566466 - Assigned to Gentoo Science Biology related packages
• sci-biology/plink-1.90_pre140514 - plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory

  589068 - Assigned to Gentoo Science Biology related packages
• sci-biology/bioperl-db-9999-r1 - should DEPEND on dev-perl/DBD-Oracle

  590032 - Assigned to Gentoo Science Biology related packages
• sci-biology/velvet-1.2.10 : src/splay.c:25:17: fatal error: omp.h: No such file or directory

  591296 - Assigned to Gentoo Science Biology related packages
• sci-biology/plink-1.90_pre140514 : plink_cluster.c:(.text+<snip>): undefined reference to `dsyevr_'

  595984 - Assigned to Gentoo Science Biology related packages
• sci-biology/gmap-2015.12.31.5 : ../.../mpidebug.c:29:31: error: ‘MPI_MODE_RDONLY’ undeclared (first use in this function)

  617658 - Assigned to Gentoo Science Biology related packages
• sci-biology/wise-2.4.0_alpha will not build with USE doc

  625808 - Assigned to Gentoo Science Biology related packages
• sci-libs/htslib - provide USE flags for curl and gcs s3 plugins

  645674 - Assigned to Gentoo Science Biology related packages
• sci-biology/wise Please set VARTEXFONTS=${T}/fonts to prevent sandbox violations

  652030 - Assigned to Gentoo Science Biology related packages
• sci-biology/foldingathome-7.5.1: FAHClient: segmentation fault at startup with media-libs/mesa libOpenCL.so

  670012 - Assigned to Gentoo Science Biology related packages
• sci-libs/dcmtk-3.6.3 still put files in /usr/etc instead of /etc

  672198 - Assigned to Gentoo Science Biology related packages
• sci-biology/mothur-1.27.0-r1 : classifyseqscommand.cpp:571:17: error: MPI_MODE_CREATE was not declared in this scope

  681640 - Assigned to Gentoo Science Biology related packages
• sci-biology/ucsc-genome-browser-260-r1: cpio: command not found

  688748 - Assigned to Gentoo Science Biology related packages
• sci-biology/plink-1.90_pre140514 : plink_calc.c:(.text+<snip>): undefined reference to cblas_dger

  689202 - Assigned to Gentoo Science Biology related packages
• dev-python/intervaltree-3.0.2 should depend on >=dev-python/sortedcontainers-2.0

  705382 - Assigned to Gentoo Science Biology related packages
• sci-biology/seaview-4.6 : ebuild uses colon (:) as a sed delimiter

  710968 - Assigned to Gentoo Science Biology related packages
• sci-biology/emboss-6.6.0-r2 : embossversion.c: error: _USE_FORTIFY_LEVEL undeclared (first use in this function)

  712504 - Assigned to Gentoo musl team
• sci-biology/blat-34-r3 : fof.c: error: arithmetic on pointer to an incomplete type

  712652 - Assigned to Gentoo musl team
• sci-biology/foldingathome-7.5.1: broken systemd service ExecStart

  712744 - Assigned to Gentoo Science Biology related packages
• sci-biology/foldingathome-7.5.1: /etc/init.d/foldingathome broken

  714160 - Assigned to Gentoo Science Biology related packages
• sci-biology/foldingathome: notify about nvidia-drivers[nvm] for optional runtime CUDA support

  715646 - Assigned to Gentoo Science Biology related packages
• sci-biology/abyss-2.3.4 : Uncompress.cpp: error: redefinition of FILE* fopen(const char*, const char*)

  715718 - Assigned to Gentoo musl team
• sci-biology/ucsc-genome-browser-260-r1 : fof.c: error: arithmetic on pointer to an incomplete type

  716078 - Assigned to Gentoo musl team
• =sci-biology/foldingathome-7.6.9 wants missing libhsa-ext-finalize64.so.1 (fix included)

  719676 - Assigned to Gentoo Science Biology related packages
• sci-biology/foldingathome-7.6.9: general protection fault in libc-2.31.so

  720684 - Assigned to Gentoo Science Biology related packages
• sci-biology/velvet-1.2.10 installs files with broken symlink

  725308 - Assigned to Gentoo Science Biology related packages
• sci-biology/plink-1.90_pre140514 does not respect LDFLAGS

  725310 - Assigned to Gentoo Science Biology related packages
• sci-biology/t-coffee-11.00-r2 does not respect LDFLAGS

  725312 - Assigned to Gentoo Science Biology related packages
• sci-biology/mafft-7.490 fails tests: ../core/mafft: line 911: /dev/stderr: Permission denied

  725322 - Assigned to Gentoo Science Biology related packages
• sci-biology/ucsc-genome-browser calls ar directly

  725328 - Assigned to Gentoo Science Biology related packages
• sci-biology/infernal-1.0.2-r1 fails tests

  729230 - Assigned to Gentoo Science Biology related packages
• sci-biology/t-coffee-11.00-r3 fails to compile: dp_lib/evaluate_dirichlet.c:543:8: error: 'lgamma_r' is missing exception

  731862 - Assigned to Gentoo Science Biology related packages
• sci-biology/foldingathome-7.6.13 with x11-drivers/nvidia-drivers-450.57 crashes system(?)

  734330 - Assigned to Gentoo Science Biology related packages
• sci-biology/libgtextutils-0.6.1-r1 fails tests

  741178 - Assigned to Martin Mokrejš
• sci-biology/wise-2.4.0_alpha-r1 does not respect LDFLAGS

  741202 - Assigned to Gentoo Science Biology related packages
• sci-biology/bcftools-1.10.2 - support for extra features is disabled without a USE flag

  741540 - Assigned to Gentoo Science Biology related packages
• sci-biology/gmap-2020.10.27 : file collision with sys-apps/cpuid-20201006

  752150 - Assigned to Gentoo Science Biology related packages
• sci-biology/trf-4.04-r1 : file collision with sci-biology/trf-bin-4.09

  755788 - Assigned to Gentoo Science Biology related packages
• dev-libs/igraph: bundled libraries

  761924 - Assigned to Gentoo Science Biology related packages
• sci-biology/ucsc-genome-browser-260-r1 - * ERROR: sci-biology/ucsc-genome-browser-260-r1::gentoo failed (install phase):

  776877 - Assigned to Gentoo Science Biology related packages
• sci-biology/fasttree-2.1.11 - FastTree-2.1.11.c:(.text+<snip>): undefined reference to mm_sum

  794868 - Assigned to Gentoo Science Biology related packages
• sci-libs/dcmtk: is OFFIS license free?

  796491 - Assigned to Licenses team
• sci-biology/bowtie-2.4.4 fails tests

  806067 - Assigned to Gentoo Science Biology related packages
• sci-biology/wise-2.4.0_alpha-r1 calls ar directly

  809725 - Assigned to Gentoo Science Biology related packages
• sci-libs/profnet-1.0.22 installs files with broken symlink

  809734 - Assigned to Gentoo Science Biology related packages
• sci-biology/wise-2.4.0_alpha-r1 - ! LaTeX Error: Bad math environment delimiter.

  818616 - Assigned to Gentoo Science Biology related packages
• sci-libs/dcmtk-3.6.5 - /.../syncpub.h: error: invalid conversion from int to dcmtk::log4cplus::thread::MutexImplBase [-fpermissive

  822171 - Assigned to Gentoo Science Biology related packages
• sci-biology/raxml-7.2.6 fails to compile: pmmintrin.h:86:1: error: inlining failed in call to ‘always_inline’ ‘_mm_hadd_pd’: target specific option mismatch

  822408 - Assigned to Gentoo Science Biology related packages
• dev-libs/igraph-0.9.4 fails to compile: pottsmodel_2.cpp:124:12: error: variable av_k set but not used [-Werror,-Wunused-but-set-variable]

  829664 - Assigned to Gentoo Science Biology related packages
• sci-biology/kallisto-0.46.2 - /.../Bootstrap.h: error: uint has not been declared

  830041 - Assigned to Gentoo musl team
• sci-biology/paml-4.9j fails to compile: clang-13: error: cannot specify -o when generating multiple output files

  831488 - Assigned to Gentoo Science Biology related packages
• sci-biology/raxml-7.2.6 fails to compile: evaluatePartialGenericSpecial.c:136:12: error: always_inline function _mm_hadd_pd requires target feature sse3, but would be inlined into function computeVectorGTRCATPROT that is compiled without support for sse3

  831489 - Assigned to Gentoo Science Biology related packages
• sci-biology/uchime-4.2.40 fails to compile: invalid argument -std=c++14 not allowed with C

  831490 - Assigned to Gentoo Science Biology related packages
• sci-biology/ucsc-genome-browser-260-r1 fails to compile: orthoEvaluate.c:310:2: error: non-void function agxSupportForEdge should return a value [-Wreturn-type]

  831491 - Assigned to Gentoo Science Biology related packages
• sci-biology/mrbayes-3.2.7 fails to compile: avxintrin.h:318:1: error: inlining failed in call to always_inline _mm256_mul_ps: target specific option mismatch

  832184 - Assigned to Gentoo Science Biology related packages
• sci-biology/trf-4.04-r1 installs files with unresolved SONAME dependencies

  832680 - Assigned to Gentoo Science Biology related packages
• sci-biology/gmap-2020.10.27 fails tests on MUSL

  836814 - Assigned to Gentoo Science Biology related packages
• sci-biology/newick-utils-1.6-r1 fails tests on MUSL: FAIL: test_nw_gen.sh

  836856 - Assigned to Gentoo Science Biology related packages
• sci-biology/t-coffee-11.00-r3 - io_lib/io_func.c: error: cannot convert std::nullptr_t to int in return

  842387 - Assigned to Gentoo musl team
• sci-biology/abyss-2.3.4 fails to compile (lto): museq.c:58:13: error: type of [-Werror=lto-type-mismatch]

  862252 - Assigned to Gentoo Science Biology related packages
• sci-biology/bwa-0.7.17 fails to compile (lto): bwamem.c:1207:21: error: type of [-Werror=lto-type-mismatch]

  862255 - Assigned to Gentoo Science Biology related packages
• sci-biology/embassy-esim4-1.0.0.660-r1 fails to compile (lto): encoding.h:3:28: error: type of dna_complement does not match original declaration [-Werror=lto-type-mismatch]

  862258 - Assigned to Gentoo Science Biology related packages
• sci-biology/embassy-phylipnew-3.69.660-r1 fails to compile (lto): draw.c:213:13: error: type of pltfilename does not match original declaration [-Werror=lto-type-mismatch]

  862261 - Assigned to Gentoo Science Biology related packages
• sci-biology/exonerate-2.2.0-r3 fails to compile (lto): c4_model_archive.h:225:10: error: type of [-Werror=lto-type-mismatch]

  862264 - Assigned to Gentoo Science Biology related packages
• sci-biology/fasta-36.3.8h-r1 fails to compile (lto): compacc2e.c:954:1: error: type of [-Werror=lto-type-mismatch]

  862267 - Assigned to Gentoo Science Biology related packages
• sci-biology/glimmerhmm-3.0.1-r1 fails to compile (lto): oc1.h:52:6: error: [-Werror=odr]

  862270 - Assigned to Gentoo Science Biology related packages
• sci-biology/mothur-1.27.0-r1 fails to compile (lto): linearalgebra.cpp:1191:18: error: dereferencing type-punned pointer will break strict-aliasing rules [-Werror=strict-aliasing]

  862273 - Assigned to Gentoo Science Biology related packages
• sci-biology/muscle-3.8.31 fails to compile (lto): globalslinux.cpp:17:24: error: dereferencing type-punned pointer will break strict-aliasing rules [-Werror=strict-aliasing]

  862276 - Assigned to Gentoo Science Biology related packages
• sci-biology/newick-utils-1.6-r1 fails to compile (lto): svg_graph_radial.h:43:6: error: type of display_svg_tree_radial does not match original declaration [-Werror=lto-type-mismatch]

  862279 - Assigned to Gentoo Science Biology related packages
• sci-biology/poa-2-r1 fails to compile (lto): fasta_format.c:48:9: error: type of [-Werror=lto-type-mismatch]

  862282 - Assigned to Gentoo Science Biology related packages
• sci-biology/qrna-2.0.3c-r3 fails to compile (lto): evolscorewithmodelscanfast.c:307:15: error: type of [-Werror=lto-type-mismatch]

  862285 - Assigned to Gentoo Science Biology related packages
• sci-biology/t-coffee-11.00-r3 fails to compile (lto): evaluate_dirichlet.c:499:14: error: dereferencing type-punned pointer will break strict-aliasing rules [-Werror=strict-aliasing]

  862327 - Assigned to Gentoo Science Biology related packages
• sci-libs/dcmtk-3.6.7 fails to compile (lto): oftest.h:140:7: error: type struct OFTestManager violates the C++ One Definition Rule [-Werror=odr]

  862699 - Assigned to Gentoo Science Biology related packages
• sci-libs/libmuscle-3.7-r3 fails to compile (lto): globalslinux.cpp:20:24: error: dereferencing type-punned pointer will break strict-aliasing rules [-Werror=strict-aliasing]

  862897 - Assigned to Gentoo Science Biology related packages
• sci-libs/profnet-1.0.22 fails to compile (lto): phd.f:2139:72: error: type of [-Werror=lto-type-mismatch]

  862921 - Assigned to Gentoo Science Biology related packages
• sci-biology/STAR-2.7.10a - SharedMemory.cpp: error: _key was not declared in this scope

  863080 - Assigned to Gentoo musl team
• sci-biology/velvet-1.2.10 - x86_64-pc-linux-gnu-gcc: fatal error: cannot read spec file libgomp.spec: No such file or directory

  864987 - Assigned to Gentoo Science Biology related packages
• sci-biology/augustus-3.4.0-r3 calls g++ directly

  868363 - Assigned to Gentoo Science Biology related packages
• sci-biology/STAR-2.7.10a fails to compile (MUSL): SharedMemory.h:142:27: error: expected ) before key

  873019 - Assigned to Gentoo Science Biology related packages
• sci-biology/abyss-2.3.4 fails to compile (MUSL): Timer.h:17:17: error: clock_t does not name a type

  873022 - Assigned to Gentoo Science Biology related packages
• sci-biology/augustus-3.4.0-r2 fails tests (MUSL)

  873025 - Assigned to Gentoo Science Biology related packages
• sci-biology/trf-4.04-r2 fails to fetch

  873034 - Assigned to Gentoo Science Biology related packages
• sci-libs/dcmtk-3.6.7-r1 installs pkg-config files that fail validation

  873268 - Assigned to Gentoo Science Biology related packages
• sci-biology/clustalw-mpi-0.13-r3 - interface.c: error: non-void function check_param should return a value

  875461 - Assigned to Gentoo Science Biology related packages
• sci-biology/kallisto-0.46.2 fails to compile (lto): main.cpp:2:10: fatal error: catch.hpp: No such file or directory

  877887 - Assigned to Gentoo Science Biology related packages
• sci-biology/hmmer-2.3.2-r5 - cp: cannot stat src/hmmalign: No such file or directory

  878613 - Assigned to Gentoo Science Biology related packages
• sci-biology/biopandas: still depends on dev-python/nose

  878721 - Assigned to Gentoo Science Biology related packages
• dev-libs/igraph-0.9.4 - /.../gss.h: error: a function declaration without a prototype is deprecated in all versions of C [-Werror,

  880815 - Assigned to Gentoo Science Biology related packages
• sci-biology/velvet-1.2.10 - Fatal error: cant create obj/concatenatedPreGraph.o: No such file or directory

  880981 - Assigned to Gentoo Science Biology related packages
• sci-biology/bedtools-2.30.0 - src/.../version.cpp: fatal error: version_git.h: No such file or directory

  881783 - Assigned to Gentoo Science Biology related packages
• sci-biology/hmmer-3.1_beta2-r1 leaves trace of segfault in dmesg

  882355 - Assigned to Gentoo Science Biology related packages
• sci-biology/clustalw-mpi-0.13-r3 - stupid.c: error: implicit declaration of function pforward_pass [-Werror=implicit-function-decl

  883663 - Assigned to Gentoo Science Biology related packages
• sci-biology/wise-2.4.0_alpha-r1 - int (const char , const char ); ISO C99 and later do not support

  883891 - Assigned to Gentoo Science Biology related packages
• sci-biology/qrna-2.0.3c-r3 - EvolScoreWithRNA; ISO C99 and later do not support implicit function

  884283 - Assigned to Gentoo Science Biology related packages
• sci-biology/wise-2.4.0_alpha-r1 fails to compile (CLANG-STRICTER-SYSTEM): compressed_protein_index.dy:223:10: error: incompatible pointer to integer conversion returning void from a function with result type boolean (aka int) [-Wint-conversion]

  886065 - Assigned to Gentoo Science Biology related packages
• sci-biology/embassy-signature-0.1.660-r1 - file collision with app-admin/tripwire-2.4.3.7

  886478 - Assigned to Gentoo Science Biology related packages
• sci-biology/velvet-1.2.10 - Fatal error: cant create obj/readCoherentGraph.o: No such file or directory

  890344 - Assigned to Gentoo Science Biology related packages
• sci-biology/fasta-36.3.8h-r1 fails to compile (DASH-SYSTEM): comp_lib9.c:(.text+0xad6): undefined reference to adler32

  890417 - Assigned to Gentoo Science Biology related packages
• sci-biology/seqan-3.1.0 - -- Configuring incomplete, errors occurred!

  894622 - Assigned to Gentoo Science Biology related packages
• dev-libs/igraph-0.10.4 adds -Werror flag on its own (MUSL-CLANG-SYSTEM)

  895066 - Assigned to Gentoo Science Biology related packages
• sci-biology/augustus-3.4.0-r3 - ../.../sqliteDB.hh: error: uint64_t has not been declared

  895204 - Assigned to Gentoo Science Biology related packages
• sci-biology/t-coffee-11.00-r3 - io_lib/tree_util.c: error: invalid operands of types long unsigned int and std::nullptr_t to binar

  896062 - Assigned to Gentoo musl team
• sci-biology/bedtools-2.30.0 fails tests (HARDENED-SYSTEM)

  896172 - Assigned to Gentoo Science Biology related packages
• sci-biology/STAR-2.7.10a fails to compile (MUSL-CLANG-SYSTEM): SharedMemory.h:142:22: error: unknown type name key_t

  898110 - Assigned to Gentoo Science Biology related packages
• sci-biology/abyss-2.3.4 calls commands that do not exist (MUSL-CLANG-SYSTEM): :

  898112 - Assigned to Gentoo Science Biology related packages
• sci-biology/clustalw-2.1-r2 fails to compile (MUSL-CLANG-SYSTEM): FileParser.cpp:37:5: error: ISO C++17 does not allow register storage class specifier [-Wregister]

  898114 - Assigned to Gentoo Science Biology related packages
• sci-biology/elph-1.0.1-r2 fails to compile (MUSL-CLANG-SYSTEM): GBase.cpp:211:3: error: ISO C++17 does not allow register storage class specifier [-Wregister]

  898116 - Assigned to Gentoo Science Biology related packages
• sci-biology/primer3-2.3.7-r1 fails to compile (MUSL-CLANG-SYSTEM): dpal.cdpal.c::368368::55:: error: error: ISO C++17 does not allow register storage class specifier [-Wregister]

  898118 - Assigned to Gentoo Science Biology related packages
• sci-biology/mosaik-2.2.30 fails to compile (MUSL-CLANG-SYSTEM): SHA1.cpp:76:2: error: ISO C++17 does not allow register storage class specifier [-Wregister]

  898120 - Assigned to Gentoo Science Biology related packages
• sci-biology/pals-1.0-r2 fails to compile (MUSL-CLANG-SYSTEM): comp.cpp:31:5: error: ISO C++17 does not allow register storage class specifier [-Wregister]

  898122 - Assigned to Gentoo Science Biology related packages
• sci-biology/pilercr-1.0-r2 fails to compile (MUSL-CLANG-SYSTEM): comp.cpp:31:5: error: ISO C++17 does not allow register storage class specifier [-Wregister]

  898124 - Assigned to Gentoo Science Biology related packages
• sci-biology/gmap-2020.10.27 has implicit function declarations in configure logs (GCC-13-SYSTEM)

  900549 - Assigned to Gentoo Science Biology related packages
• sci-biology/hmmer-2.3.2-r5 has implicit function declarations in configure logs (GCC-13-SYSTEM)

  900551 - Assigned to Gentoo Science Biology related packages
• sci-biology/kalign-2.03-r3 has implicit function declarations in configure logs (GCC-13-SYSTEM)

  900553 - Assigned to Gentoo Science Biology related packages
• sci-biology/mcl-14.137 has implicit function declarations in configure logs (GCC-13-SYSTEM)

  900555 - Assigned to Gentoo Science Biology related packages
• sci-biology/unafold-3.8-r1 has implicit function declarations in configure logs (GCC-13-SYSTEM)

  900557 - Assigned to Gentoo Science Biology related packages