Gentoo Project

Biology Project

Bug Reports

• sci-biology/bioperl: tests require several perl modules not in portage yet

  145580 - Assigned to Gentoo Science Biology related packages
• sci-biology/ucsc-genome-browser-260-r2 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/bioperl-1.6.9 dev-perl/Bio-ASN1-EntrezGene-1.91.0-r1 circular dependencies

  547018 - 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/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-260-r2 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/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/kallisto-0.46.2 - /.../Bootstrap.h: error: uint has not been declared

  830041 - Assigned to Gentoo musl team
• 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/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/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/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/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/fasta-36.3.8i 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: The SDSL library is required, but wasn't found

  894622 - 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/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/gmap-2020.10.27 has implicit function declarations in configure logs (GCC-13-SYSTEM)

  900549 - 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
• sci-biology/bedtools-2.30.0 fails to compile (MUSL-SYSTEM): BamAux.h:10:17: error: int32_t does not name a type

  907971 - Assigned to Gentoo Science Biology related packages
• sci-biology/kallisto-0.46.2-r1 fails to compile (MUSL-SYSTEM): common.h:132:24: error: std::string pretty_num redeclared as different kind of entity

  907972 - Assigned to Gentoo Science Biology related packages
• sci-libs/dcmtk-3.6.7-r1 fails to compile (MUSL-SYSTEM): offile.h:359:16: error: ::fopen64 has not been declared

  908398 - Assigned to Gentoo Science Biology related packages
• sci-biology/pysam-0.22.1: needs to use PEP517 build (DistutilsNonPEP517Build)

  910017 - Assigned to Gentoo Science Biology related packages
• sci-biology/clustalw-2.1-r2 - [clang] ./.../FileReader.h: error: no template named auto_ptr

  913591 - Assigned to Gentoo Science Biology related packages
• sci-biology/mosaik-2.2.30 - [clang] JumpDnaHash.cpp: error: use of undeclared identifier random_shuffle

  913592 - Assigned to Gentoo Science Biology related packages
• sci-biology/iedera-1.05-r2 - [clang] ./automaton.h: fatal error: ext/slist file not found

  913632 - Assigned to Gentoo Science Biology related packages
• sci-biology/yass-1.14-r3 - assemble.c: error: implicit declaration of function hashVerifie [-Wimplicit-function-declaration]

  919215 - Assigned to Gentoo Science Biology related packages
• sci-biology/clustalw-mpi-0.13-r3 - interface.c: error: return with no value, in function returning non-void [-Wreturn-mismatch]

  919251 - Assigned to Gentoo Science Biology related packages
• sci-biology/bfast-0.7.0a - RGMatch.c: error: passing argument 1 of feof from incompatible pointer type [-Wincompatible-pointer-types]

  919254 - Assigned to Gentoo Science Biology related packages
• sci-biology/amap-2.2-r5 - [clang] ./MultiSequenceDag.h: error: no template named binary_function; did you

  919473 - Assigned to Gentoo Science Biology related packages
• sci-biology/iqpnni-3.3.2-r2 - [clang] brent.cpp: error: reference to vector is ambiguous

  919851 - Assigned to Gentoo Science Biology related packages
• sci-biology/emboss-6.6.0-r3 - ajreg.c: error: assignment to struct real_pcre from incompatible pointer type pcre {aka struct real_pcre8_or_16 } [-Winc

  920917 - Assigned to Gentoo Science Biology related packages
• sci-biology/t-coffee-11.00-r3 - [clang] util_lib/util_make_tree.c: error: ISO C++17 does not allow register

  921101 - Assigned to Gentoo Science Biology related packages
• sci-biology/stride-20060723 fails to fetch (GCC-14-SYSTEM)

  921260 - Assigned to Gentoo Science Biology related packages
• sci-biology/unafold-3.8-r1 fails tests: Cant locate Parser.pm in @INC

  924694 - Assigned to Gentoo Science Biology related packages
• sci-biology/glimmerhmm-3.0.4 does not respect LDFLAGS

  926804 - Assigned to Gentoo Science Biology related packages
• sci-biology/glimmerhmm-3.0.4 does not respect CFLAGS

  926805 - Assigned to Gentoo Science Biology related packages
• sci-biology/muscle-5.1.0 - x86_64-pc-linux-gnu-g++: fatal error: cannot read spec file libgomp.spec: No such file or directory

  927355 - Assigned to Gentoo Science Biology related packages
• sci-biology/embassy-topo-2.0.660-r1 fails to compile: topo.c:1900:33: error: passing argument 2 of ajGraphicsDrawsetPoly from incompatible pointer type [-Wincompatible-pointer-types]

  927867 - Assigned to Gentoo Science Biology related packages
• sci-biology/gmap-2020.10.27 fails to compile: genome128_hr.c:3782:12: error: implicit declaration of function _mm256_extract_epi64 [-Wimplicit-function-declaration]

  927868 - Assigned to Gentoo Science Biology related packages
• sci-biology/mcl-14.137 fails to compile: mcxquery.c:1237:58: error: passing argument 4 of get_cls_id from incompatible pointer type [-Wincompatible-pointer-types]

  927869 - Assigned to Gentoo Science Biology related packages
• sci-biology/glimmerhmm-3.0.4 installs files with unresolved SONAME dependencies

  927871 - Assigned to Gentoo Science Biology related packages
• sci-libs/htslib-1.17 has implicit function declarations in configure logs

  927873 - Assigned to Gentoo Science Biology related packages
• sci-biology/yass-1.14-r3 - /.../ld: final link failed: bad value

  928064 - Assigned to Gentoo Science Biology related packages
• sci-biology/bedtools: needs upgrade to Python 3.12 (PythonCompatUpdate)

  929751 - Assigned to Gentoo Science Biology related packages
• sci-biology/eugene-4.1d-r1 - OptiAlgorithm.cc: error: use of undeclared identifier setiosflags; did

  930438 - Assigned to Gentoo Science Biology related packages
• sci-biology/embassy-mse-3.0.0.660-r1 - mse.c: error: invalid use of incomplete typedef WINDOW {aka struct _win_st}

  932136 - Assigned to Gentoo Science Biology related packages
• sci-libs/dcmtk-3.6.8 fails to builld with gcc:15 : error: ‘const struct OFrvalue_storage<T, <anonymous> >’ has no member named ‘pt’

  936681 - Assigned to Gentoo Science Biology related packages
• sci-biology/muscle-5.1.0 - Fatal error: cant create Linux/efabestcols.o: No such file or directory

  938273 - Assigned to Gentoo musl team
• sci-biology/fasta-36.3.8i - mm_file.h: error: implicit declaration of function ftello

  938324 - Assigned to Gentoo musl team
• sci-biology/ucsc-genome-browser-260-r2 - [llvm] orthoEvaluate.c: error: non-void function agxSupportForEdge should

  938456 - Assigned to Gentoo Science Biology related packages
• sci-biology/amap: treeclean request

  938872 - Assigned to Gentoo Science Biology related packages
• sci-biology/abyss-2.3.4 - [gcc-15] Timer.cpp: error: m_start was not declared in this scope

  939044 - Assigned to Gentoo musl team
• sci-biology/seaview-4.6-r1 - [ncurses-6.5] [meson] [libtool] [gcc-15] treedraw.cxx: error: type struct branche violates the C++ One Definition Rule [-Werror=odr]

  940561 - Assigned to Gentoo Science Biology related packages
• sci-biology/augustus-2.5.5 - [ncurses-6.5] [libtool] [gcc-15] list.c: error: implicit declaration of function FatalError [-Wimplicit-function-declaration]

  940693 - Assigned to Gentoo Science Biology related packages
• sci-biology/seqan-3.1.0 - [libtool] [gcc-15] -- Configuring incomplete, errors occurred!

  940694 - Assigned to Gentoo Science Biology related packages
• sci-biology/dialign-tx-1.0.2-r2 - [libtool] [gcc-15] museq.c: error: type of simple_aligner does not match original declaration [-Werror=lto-type-mismatch]

  941102 - Assigned to Gentoo Science Biology related packages
• sci-biology/vcftools-0.1.16 - [libtool] [llvm] variant_file_filters.cpp: error: use of undeclared identifier random_shuffle

  941490 - Assigned to Gentoo Science Biology related packages
• sci-biology/unafold-3.8-r1 - [meson] [libtool] [gcc-15] Failed running aclocal!

  941896 - Assigned to Gentoo Science Biology related packages
• sci-biology/raxml-8.2.13 fails to compile: evaluatePartialGenericSpecial.c:110:9: error: unknown type name __m128d

  941996 - Assigned to Gentoo Science Biology related packages

Stabilization Bug Reports

• sci-biology/augustus-3.4.0-r3 and friends: stablereq

  920140 - Assigned to Gentoo Science Biology related packages