Get Gentoo!
gentoo.org sites
gentoo.org Wiki Bugs Forums Packages
Planet Archives Sources
Infra Status
aboutsummaryrefslogtreecommitdiff
Commit message (Collapse)AuthorAgeFilesLines
* dev-python/traits: version bump to 5.1.0Horea Christian2019-04-162-0/+44
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-physics/mc-tester: add missing SLOT (non-maintainer commit)Martin Mokrejs2019-04-131-2/+2
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/chiron: Fix RDEPEND issueMartin Mokrejs2019-04-131-3/+3
| | | | | | | | | | RDEPEND uses the = operator with no revision: '=sci-libs/tensorflow-1.0.1'; if any revision is acceptable, use '~' instead; if only -r0 then please append '-r0' to the dep Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-mathematics/dolfin: Fix RDEPEND.suspectMartin Mokrejs2019-04-132-4/+4
| | | | | | | | | | | | | Non-maintainer commit fixing: RDEPEND.suspect 2 sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild: 'dev-lang/swig:0=' sci-mathematics/dolfin/dolfin-2017.1.0.ebuild: 'dev-lang/swig:0=' All swig ebuilds define only SLOT="0" Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sys-cluster/openmpi: specify external libraries and version bumpJian Cao2019-04-082-4/+4
| | | | | | | Closes: https://bugs.gentoo.org/671510 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Jian Cao <sworden.cao@gmail.com> Signed-off-by: Justin Bronder <jsbronder@gentoo.org>
* sci-biology/behaviopy: new packageHorea Christian2019-04-084-0/+115
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/ncbi-tools++: set -rpath-link to temp build locationMartin Mokrejs2019-04-052-3/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add more regexps specifying which parts of the test suite should not be compiled at all. We have so far problems with say ncbi-tools++-18.0.0 libs installed in ${EPREFIX}/usr/lib64/ncbi-tools++/ which get picked during linking of a currently emerged package, like ncbi-tools++-22.0.0. That happens due to LDPATH being set through ``` echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} doenvd "${S}/99${PN}" ``` which results in ``` $ cat /etc/env.d/99ncbi-tools++ LDPATH=/usr/lib64/ncbi-tools++ $ ``` and later used during linking of a future version. Some symbols will be resolved by ${EPREFIX}/usr/lib64/ncbi-tools++/ from older version, some probably not. It is confusing to debug the errors popping up during compilation/linking. Aaron Ucko from NCBI proposed: To avoid interference from old installations, please try passing `LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib` to configure, no patches (likely) needed. @kiwifb François Bissey commented with: <quote> LDPATH is used to generate the ld.so.conf.d files. So it is important to have it to be able to find the libraries that are not in a standard path. LDPATH is a Gentoo special. You need to regenerate the cache with ldconfig after installing such a library and such a path. ... $ /usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11 -Wl,--verbose -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0 -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -Wl,-O1 -Wl,--as-needed -g speedtest.o -L/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\ ncbi_cxx--22_0_0_build/lib -lprosplign -lxalgoalignutil -ltaxon1 -lxalgoseq -lxcleanup -lxobjedit -ltaxon3 -lvalid -lvalerr -lproteinkmer -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -lxqueryparse -lxregexp -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2 -lncbi_xreader_cache -ldbapi_driver -lncbi_xreader -lxconnect -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -lxcompress -lz -lbz2 -llzo2 -lz -lnsl -ldl -lpcre -llmdb -lpthread -ldw -ldl -lm -lpthread -o speedtest It cannot find libmlacli.so. Note that there isn’t a `-lmlacli` anywhere in the above line. It is searched for because you are compiling an executable and executable cannot have unresolved symbols. It must in the table of needed libraries for libxobjedit.so libmlacli.so needed by /scratch/var/tmp/portage/sci-biology/\ ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib/libxobjedit.so Because there is no path or possibly a final path in libxobjedit.so that library cannot be found. Two solutions here: 1) add -lmlacli in the compilation line above 2) Precede the whole line with LD_LIBRARY_PATH=/scratch/var/tmp/portage/sci-biology/\ ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib The LDPATH setting probably enabled you to find a previously installed version of the library. François PS: You can pass that analysis upstream because -lmlacli should probably be added by right. </quote> Later François also wrote: <quote> rpath are usually the preferred solution but it is not the end all solution. Looking for LDPATH in your /etc/env.d/ may shock you. In the case of ncbi, adding path is only one of the solution I would consider. I don’t see why they need to install in /usr/lib{,64}/ncbi-tools++ rather than just /usr/lib{,64} in the first place. It is not even versioned to allow several versions installed in parallel. It is not plugins or “modules” or other special kinds of shared objects. Possibly it is some language runtime - at best. Does it use names that could collide easily with something else? May be some of them should be prefixed then. </quote> make[3]: Entering directory '/scratch/var/tmp/portage/sci-biology/\ ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/build/app/speedtest' Updating dependency information for /scratch/var/tmp/portage/sci-biology/\ ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/app/speedtest/speedtest.cpp. /usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -fPIC -g -D_DEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_MT -D_REENTRANT -D_THREAD_SAFE -I/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\ ncbi_cxx--22_0_0_build/inc -I/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\ ncbi_cxx--22_0_0/include /scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\ ncbi_cxx--22_0_0/src/app/speedtest/speedtest.cpp -o speedtest.o /usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11 -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0 -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -Wl,-O1 -Wl,--as-needed -g speedtest.o -L/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\ ncbi_cxx--22_0_0_build/lib -lprosplign -lxalgoalignutil -ltaxon1 -lxalgoseq -lxcleanup -lxobjedit -ltaxon3 -lvalid -lvalerr -lproteinkmer -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -lxqueryparse -lxregexp -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2 -lncbi_xreader_cache -ldbapi_driver -lncbi_xreader -lxconnect -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -lxcompress -lz -lbz2 -llzo2 -lz -lnsl -ldl -lpcre -llmdb -lpthread -ldw -ldl -lm -lpthread -o speedtest /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/\ bin/ld: warning: libmlacli.so, needed by /scratch/var/tmp/portage/\ sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib/\ libxobjedit.so, not found (try using -rpath or -rpath-link) The problem here is that the rpath would have to be provided when you link libxobjedit.so. I checked the log and it wasn’t done. And you definitely don’t want to do that unless you re-link without the rpath (or the correct final rpath) at install time. For information cmake does exactly that. But in the end adding a path in this case is no substitute to providing the libraries you need. When building stuff with libtool, libtool produces test scripts that set LD_LIBRARY_PATH properly for running the tests before install. So the test executables don’t have to be linked with rpath to the build folder. Or the objects that you want to ship either. </quote> This change will ensure `LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib` is passed to `bash ./src/build-system/configure` in `src_configure()` and at least helps to get symbols resolved during linking although it is probably still far from ideal. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-libs/trilinos: version bump to 12.14.1Matthias Maier2019-04-034-1/+1181
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-libs/itk: version bump 5.0_rc1Horea Christian2019-04-022-2/+154
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* dev-cpp/castxml: no keywords for live packagewHorea Christian2019-04-011-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* dev-cpp/castxml: corrected EGIT REPOHorea Christian2019-04-012-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* dev-cpp/castxml: new packageHorea Christian2019-03-313-0/+79
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/velvetk: drop faulty software per its authorMartin Mokrejs2019-03-313-37/+0
| | | | | | From: Torsten S. The velvetk.pl is faulty and should not be used. Try `kmergenie` instead, or use the SPades Assembler.
* sci-biology/ncbi-tools++: document possible issue with buildsMartin Mokrejs2019-03-303-5/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | I have the following defined due to ncbi-tools++-18.0.0 installed on my system: /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32: /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0: /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/32: /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0: /usr/lib/llvm/7/lib32: /usr/lib/llvm/7/lib64: /usr/lib64/itcl4.1.1: /usr/lib64/itk4.1.0: /lib64: /usr/lib64: /usr/local/lib64: /lib32: /usr/lib32: /usr/lib64/rust-1.29.2: /usr/lib64/R/lib: /usr/lib64/fltk: /usr/lib64/ncbi-tools++: /usr/lib64/staden: grep: /etc: No such file or directory grep: /etc/env.d: No such file or directory /etc/env.d/99ncbi-tools++:LDPATH=/usr/lib64/ncbi-tools++ ... That in turn makes linker pick "${WORKDIR}"/ncbi_cxx--22_0_0_build/lib/* files but later overrides some of them with /usr/lib64/ncbi-tools++/*, depending on the ordering of -lXXXXXX arguments. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/ncbi-tools++: version bumpMartin Mokrejs2019-03-302-0/+381
| | | | | | | | | | | | | | | | It does not link if older version is installed because linker picks up older version of libraries and obviously does not find newly added functions. Upstream says: Please try either supplying an LD_RUN_PATH environment setting or a -Wl,-rpath-link,... flag pointing at your build tree's lib directory. Also, please bear in mind that adding the old installation's library directory to the central search path largely defeats the purpose of making it a separate directory. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/KaKs_Calculator: and rewrite the checksum of courseMartin Mokrejs2019-03-301-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/KaKs_Calculator: another attempt at SRC_URIMartin Mokrejs2019-03-301-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/KaKs_Calculator: fix download URLMartin Mokrejs2019-03-301-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bowtie: add another upstream patchMartin Mokrejs2019-03-303-1/+19
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/repeatmasker: rewamp configuration codeMartin Mokrejs2019-03-296-224/+292
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The changes are partly based on https://github.com/gentoo/sci/pull/580 from Michael Schubert but it seems we could figure out the paths to binaries automatically using `which`. Block between the USE options and allow only a single to be enabled, that is what configure requires, otherwise it enters a loop. The hmmer is the default in configure and preferred. Tested with `USE="hmmer -wublast -phrap -rmblast"` and other combinations while only one is allowed. If users have wublast/abblast/rmblast/crossmatch in the PATHS we just pick it. `which` returns a '.' (dot) if a binary was not found, we need to zap it otherwise configure enters a loop. In the end, one can get: Add a Search Engine: 1. CrossMatch: [ Configured ] 2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured ] 3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ] 4. HMMER3.1 & DFAM: [ Configured, Default ] 5. Done properly written into /usr/lib64/perl5/vendor_perl/5.28.0/RepeatMaskerConfig.pm Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/repeatmasker-libraries: dohtml has been banned for EAPI 7Martin Mokrejs2019-03-292-2/+2
| | | | | | | This slipped through repoman checks. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/augustus: fix typo in a comment lineMartin Mokrejs2019-03-291-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/augustus: adjust to current LICENSE, use ${PV}Martin Mokrejs2019-03-291-3/+3
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/augustus: version bump, fix awful Makefile'sMartin Mokrejs2019-03-294-71/+120
| | | | | | | | | | | | | | | | | | | | | | | | | | Do not require static libraries. Only bamtools are really needed. htslib is not needed. For bam2wig samtools-0.2 series is needed. I decided to blindly install some of the binaries created but not copied into `./bin/`. `src/Makefile` will gladly define mysql and sqlite together, probably a non-sense. We force mysql as we check for it first. Not sure if sqlite should be preferred. I documented in the augustus-3.3.2.ebuild other "forgotten" files, like gbrowse.conf and a template for gff2ps. I dropped `-O3` but left in `-ggdb` in the `CXXFLAGS`. https://github.com/Gaius-Augustus/Augustus/issues/14 https://github.com/Gaius-Augustus/Augustus/issues/50 https://github.com/Gaius-Augustus/Augustus/issues/51 https://github.com/Gaius-Augustus/Augustus/issues/52 https://github.com/Gaius-Augustus/Augustus/issues/53 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-libs/bids-validator: new packageHorea Christian2019-03-294-0/+59
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/tablet: fix indentationMartin Mokrejs2019-03-281-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* media-libs/avbin-bin: non-maintainer commitMartin Mokrejs2019-03-282-6/+7
| | | | | | | | | | | | | Trying to get rids of FATAL errors reported by Travis.CI. Use `if [ "${ABI}" == "amd64" ]; then` instead of `if use amd64; then` Also bump to EAPI7. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/ncbi-blast+: emphasize alternative building from sourcesMartin Mokrejs2019-03-281-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/repeatmasker-libraries: finish version bump, EAPI7, add KEYWORDSMartin Mokrejs2019-03-283-7/+7
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/maker: some progress with the ebuild, empty KEYWORDSMartin Mokrejs2019-03-283-6/+167
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/NGSTools: renamed into NGSEPcore and NGSEPpluginMartin Mokrejs2019-03-283-36/+0
|
* sci-biology/bowtie: patch --interleaved, add KEYWORDSMartin Mokrejs2019-03-272-3/+15
| | | | | | | | | | | | | | | Do not unset contents of CFLAGS and CXXFLAGS. Thanks to ch4rr0 at https://github.com/BenLangmead/bowtie2/issues/239 Add deemed patch from https://github.com/BenLangmead/bowtie2/issues/240 Added KEYWORDS. Closes: https://bugs.gentoo.org/649824 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/NGSEPplugin: some progress with the packageMartin Mokrejs2019-03-273-0/+51
| | | | | | | Still does not work. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/NGSEPcore: some improvements with the packageMartin Mokrejs2019-03-273-0/+56
| | | | | | | Still unfinished work. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bamql: switch to `$(use_enable ...)`Martin Mokrejs2019-03-262-8/+4
| | | | | | | https://github.com/gentoo/sci/issues/907#issuecomment-476420962 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bamql: remove dependency on llvm static libsMartin Mokrejs2019-03-263-10/+37
| | | | | | | | Thanks for the patch and guidance to François Bissey: https://github.com/gentoo/sci/issues/907 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/ncbi-blast+: EAPI7 bump, remove unused variableMartin Mokrejs2019-03-255-11/+372
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/tablet: still installs a mix of our and bundled jarsMartin Mokrejs2019-03-252-11/+35
| | | | | | | | | | | We have only dev-java/htdjdk-2.3.0 in the tree as newer versions use gradle. The tablet-1.17.08.17 lacks the lib/htsjdk-2.0.11.jar so we cannot install it. Use sci-biology/tablet-bin instead. https://github.com/cropgeeks/tablet/issues/6 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* dev-java/htsjdk: drop old 2.1.0 versionMartin Mokrejs2019-03-251-47/+0
|
* sci-biology/gffread: bump to 0.11.0, drop old patch, use sed hackeryMartin Mokrejs2019-03-253-46/+22
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bowtie: update SRC_URI and hash for 2.3.5Martin Mokrejs2019-03-252-1/+2
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* dev-java/htsjdk: 2.3.0 which was the last using Apache antMartin Mokrejs2019-03-255-12/+14
| | | | | | | | | | | | | | | | | Bump to EAPI7 Building does not work since sandbox has now no network access. Downloading https://services.gradle.org/distributions/gradle-5.2.1-bin.zip Exception in thread "main" java.net.SocketException: Network is unreachable (connect failed) htsjdk calls some `gradlew` wrapper so the recent ebuilds need more work to use dev-java/gradle-bin package. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* Drop BSD-2 license of sci-biology/tabletMartin Mokrejs2019-03-251-10/+0
|
* sci-biology/tablet-bin: update licenseMartin Mokrejs2019-03-251-13/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/tablet-bin: use https for the new homepageMartin Mokrejs2019-03-251-1/+1
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/tablet: update ebuildMartin Mokrejs2019-03-253-27/+26
| | | | | | | | | | New homepage, switch from svn to github, new license, switch from picard to htsjdk There is no ./classes/ so `ant build` does not work for me. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/tablet: drop old versionMartin Mokrejs2019-03-251-51/+0
|
* sci-biology/tablet-bin: version bump, ebuild cleanupMartin Mokrejs2019-03-252-5/+6
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/MolBioLib: fix RDEPEND.suspect at leastMartin Mokrejs2019-03-251-9/+10
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/bamql: bump to EAPI7Martin Mokrejs2019-03-252-2/+2
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>