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* Merge remote-tracking branch 'upstream/master'Koop Mast2019-09-1412-79/+84
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| * biology/bedtools: Upgrade to 2.29.0jwb2019-09-135-49/+64
| | | | | | | | | | | | Add test target to run test scripts in dist Reported by: portscout
| * biology/py-cutadapt: Upgrade to 2.5jwb2019-09-132-5/+6
| | | | | | | | Add pigz run depend for parallel gzip/gunzip
| * biology/phyml: update to 3.3.20190909fernape2019-09-112-6/+6
| | | | | | | | | | | | While here, add license. Reported by: portscout
| * Update to 1.007006 (1.7.6)sunpoet2019-09-083-19/+8
| | | | | | | | | | | | - Remove PGTEST and SQLITETEST options: DBD::Pg and DBD::SQLite have been removed from BioPerl by upstream for the move of modules and programs into separate distributions Changes: https://metacpan.org/changes/distribution/BioPerl
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-09-0710-22/+190
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| * Fix after gets(3) retirement using gets_s(3).cy2019-09-021-1/+1
| | | | | | | | | | | | | | Bump PORTREVISION as this is a security issue too. PR: 222796 MFH: 2019Q3
| * Add a patch to remove use of gets(3)lwhsu2019-09-022-0/+169
| | | | | | | | | | | | | | PR: 238685 Submitted by: Walter Schwarzenfeld <w.schwarzenfeld@utanet.at> Reported by: emaste Sponsored by: The FreeBSD Foundation
| * biology/py-pysam: Update 0.15.2 -> 0.15.3yuri2019-08-312-4/+4
| | | | | | | | Reported by: portscout
| * biology/ngs-sdk: Update 2.9.6 -> 2.10.0yuri2019-08-314-13/+13
| | | | | | | | Reported by: portscout
| * biology/iqtree: Update to version 1.6.12jrm2019-08-272-5/+4
| | | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.12
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-08-2413-41/+35
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| * biology/gperiodic: fix NLS and other rough edgespi2019-08-232-30/+22
| | | | | | | | | | | | PR: 239642 Submitted by: Walter Schwarzenfeld <w.schwarzenfeld@utanet.at> Reported by: bapt
| * devel/boost-*: update to 1.71.0jbeich2019-08-199-7/+9
| | | | | | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_71_0.html PR: 238827 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D20774
| * biology/checkm: Update 1.0.17 -> 1.0.18yuri2019-08-192-4/+4
| | | | | | | | Reported by: portscout
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-08-1529-201/+190
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| * Convert to UCL & cleanup pkg-message (categories a-c)mat2019-08-1413-32/+78
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| * biology/bolt-lmm: Upgrade to 2.3.4jwb2019-08-137-120/+63
| | | | | | | | | | | | Remove previously upstreamed patches New Makefile patch that preserves default behavior and should be palatable to upstream
| * biology/checkm: Update 1.0.16 -> 1.0.17yuri2019-08-122-4/+4
| | | | | | | | Reported by: portscout
| * biology/gperiodic: upgrade 2.0.10 -> 3.0.3pi2019-08-123-23/+39
| | | | | | | | | | | | | | | | - new mastersite PR: 239642 Submitted by: Walter Schwarzenfeld <w.schwarzenfeld@utanet.at> Relnotes: https://sourceforge.net/p/gperiodic/code/HEAD/tree/branches/3.0.3/ChangeLog
| * Update to 1.007005 (1.7.5)sunpoet2019-08-123-20/+5
| | | | | | | | | | | | | | - Fix DISTNAME - Bump PORTREVISION for package change Changes: https://metacpan.org/changes/distribution/BioPerl
| * Update WWWsunpoet2019-08-111-1/+1
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| * biology/checkm: Update 1.0.13 -> 1.0.16yuri2019-08-092-5/+4
| | | | | | | | Reported by: portscout
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-08-0760-38/+160
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| * biology/hhsuite: fix build on powerpc64pkubaj2019-08-051-2/+7
| | | | | | | | | | | | | | | | This port can't use Altivec. Instead, it's possible to use GCC's translation layer from SSE. Adjust build flags to do it. PR: 239645 Approved by: yuri (maintainer), tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D21160
| * PR: 239613jwb2019-08-056-1/+94
| | | | | | | | Submitted by: pkubaj
| * biology/diamond: Update to version 0.9.25jrm2019-08-052-4/+4
| | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.25
| * Mark BROKEN: unfetchableantoine2019-08-043-0/+6
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| * Bump PORTREVISION for ports depending on the canonical version of GCCgerald2019-07-2750-32/+50
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330
* | Merge remote-tracking branch 'upstream/master'Koop Mast2019-07-2713-16/+107
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| * biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43yuri2019-07-272-12/+31
| | | | | | | | | | | | | | | | Now it builds with gradle-5. Improvements im Makefile to simplify the port update process, in line with some other gradle-based ports. Reported by: repology
| * - Update WWWamdmi32019-07-251-1/+1
| | | | | | | | Approved by: portmgr blanket
| * Prepare for devel/gradle4 and java/openjfx8-devel updatestobik2019-07-231-2/+2
| | | | | | | | | | | | | | | | openjfx8-devel now requires at least Gradle 4.8. biology/gatk however does not build with Gradle 4.10.3. Preserve Gradle 4.6 for now. PR: 239392
| * biology/treekin: fix build on GCC architecturespkubaj2019-07-191-1/+2
| | | | | | | | | | | | | | Needs C++11 compiler: configure: error: *** A compiler with support for C++11 language features is required. Approved by: mentors (implicit approval)
| * ncbi-blast+: Unbreak build with gcc8 following gcc9 patchjwb2019-07-132-7/+9
| | | | | | | | | | | | | | | | | | | | | | | | GCC 8 and 9 are incompatible in handling const variables with OpenMP default(none). All const variables default to shared even with default(none) present. 8 errors out if a const variable is explicitly defined as shared and 9 requires an explicit definition. Using an upstream trunk patch for now, which checks the compiler version. Also discussing more portable approaches to avoid future issues. Reported by: jrm
| * New port: biology/libbigwig: C library for handling bigWig files (containing ↵yuri2019-07-125-0/+54
| | | | | | | | genomic data)
| * ncbi-blast+: Fix build with gcc9jwb2019-07-111-0/+14
| | | | | | | | | | | | | | | | GCC 9 requires OpenMP variables to be explicitly defined as shared or private where earlier versions fell back on default. New patch sent upstream. PR: 238471 Reported by: gerald
| * Update security/nettle to 3.5.1sunpoet2019-07-102-1/+2
| | | | | | | | | | | | | | | | | | | | - Bump PORTREVISION of dependent ports for shlib change - Fix build of devel/pijul [1] Changes: https://git.lysator.liu.se/nettle/nettle/blob/master/NEWS PR: 238991 Exp-run by: antoine Thanks to: tobik [1]
| * - Update WWWamdmi32019-07-081-1/+1
| | | | | | | | Approved by: portmgr blanket
* | Git and myself don't get along, I messed up the master branch really goodKoop Mast2019-07-27100-352/+1828
|\| | | | | | | attempt to correct this.
| * biology/mothur: Update 1.42.2 -> 1.42.3yuri2019-06-282-4/+4
| | | | | | | | Reported by: portscout
| * Mark this port as not buildable on powerpc64:linimon2019-06-251-0/+2
| | | | | | | | | | | | | | | | | | *** File 'Makefile.config.FreeBSD.powerpc' is missing. Please run ./configure The configuration script may have other problems as well. This needs to be addressed by upstream (if there is interest). Approved by: portmgr (tier-2 blanket)
| * biology/iqtree: Update to version 1.6.11jrm2019-06-252-4/+4
| | | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.11
| * biology/viennarna: Make it less/not prone to failures due to hardcoded C++ ↵yuri2019-06-255-29/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | library name configure and Makefile.in provided in tarballs have -lstdc++ hard-coded in them. The previous version of the port patches these to be -lc++, which still might fail on gcc systems, depending on which C++ library is used. This change adds USES=autoreconf which makes it to regenerate configure and Makefile.in and hopefully have the proper C++ library in these files. GNU libtool links with the C compiler, not with the C++ compiler, in this project. This is what I think triggers link failures due to a wrong C++ library getting into the link lines. GNU libtool likely chooses C compiler because this project has its 'main' functions in .c files, but also includes C++ object modules. This likely causes GNU tools confusion and it uses the C compiler to link and fails due to wrong C++ libraries added there.
| * New port: biology/viennarna: Alignment tools for the structural analysis of RNAyuri2019-06-249-0/+331
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| * Use USES=pathfixsunpoet2019-06-231-21/+14
| | | | | | | | | | | | | | | | - Add USES=gnome - Use = instead of += for PLIST_SUB - Use CMAKE_BOOL - Cosmetic change - Take maintainership
| * biology/abyss: fix build on big-endian architecturespkubaj2019-06-213-2/+20
| | | | | | | | | | | | | | | | | | | | | | | | Use new GCC from ports on GCC architectures. Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC architectures. Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at https://github.com/bcgsc/abyss/pull/287 ). PR: 238737 Approved by: yuri (maintainer), mat (mentor) Differential Revision: https://reviews.freebsd.org/D20717
| * Enable workaround for building on powerpc64.linimon2019-06-211-2/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | Autoconf reports that HAVE_ASM_BSR is true (1). However, it's a false positive. I do not have enough knowledge of autoconf to fix this problem correctly, so fix src/config.h in post-configure. Patches welcome. A proper fix will most likely also fix the build on other tier-2 archs, but I have not taken the time to test that yet. Approved by: portmgr (tier-2 blanket)
| * biology/mothur: Update 1.42.1-3 -> 1.42.2yuri2019-06-202-6/+5
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| * biology/py-bx-python: Update 0.8.2 -> 0.8.4yuri2019-06-192-5/+4
| | | | | | | | Reported by: pirtscout
| * New port: biology/treekin: Efficient computation of RNA folding dynamicsyuri2019-06-164-0/+37
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| * biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pljwb2019-06-141-4/+10
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| * biology/ncbi-blast+: Upgrade to 2.9.0jwb2019-06-133-6/+78
| | | | | | | | | | | | | | Fixes build issue with gcc9 PR: 238471 Reported by: gerald
| * biology/kallisto: Upgrade to 0.46.0jwb2019-06-122-4/+4
| | | | | | | | Reported by: portscout
| * biology/tRNAscan-SE: Update to 2.0.3swills2019-06-083-15/+8
| | | | | | | | | | PR: 238253 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
| * biology/igv: Update 2.5.2 -> 2.5.3yuri2019-06-022-6/+6
| | | | | | | | Reported by: portscout
| * biology/tRNAscan-SE: fix build with GCC-based architecturspkubaj2019-05-301-1/+3
| | | | | | | | | | | | | | | | | | | | Add MAKE_JOBS_UNSAFE=yes to fix build. Remove USES=compiler:c11, it's not necessary. PR: 237848 Approved by: mzaki@niid.go.jp (maintainer), linimon (mentor) Differential Revision: https://reviews.freebsd.org/D20439
| * biology/cufflinks: Fix build on i386 by removing the hard-coded -m64yuri2019-05-291-0/+16
| | | | | | | | Reported by: fallout
| * biology/bolt-lmm: Mixed model association testing and variance component ↵jwb2019-05-269-0/+228
| | | | | | | | | | | | | | | | | | analysis The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations).
| * New port: biology/cufflinks: Cufflinks assembles transcripts, estimates ↵yuri2019-05-266-0/+80
| | | | | | | | their abundance, etc
| * biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't ↵yuri2019-05-222-0/+36
| | | | | | | | | | | | | | | | exist or isn't detected. It forces it to default to SSE2 on amd64/i386 and relaxes the SIMD requirement on all other platforms. Reported by: fallout
| * biology/fastp: Remove redundant USE_GCCjwb2019-05-211-8/+1
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| * biology/mothur: Add USES=compiler:c++11-langyuri2019-05-211-1/+1
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| * New port: biology/mothur: Software for bioinformatics of the microbial ↵yuri2019-05-214-0/+41
| | | | | | | | ecology community
| * - Update to 3.3.20190321wen2019-05-202-5/+4
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| * - Update to 5.18.0wen2019-05-203-29/+22
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| * New port: biology/hhsuite: Remote protein homology detection suiteyuri2019-05-198-0/+128
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| * biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCCjwb2019-05-191-9/+3
| | | | | | | | Reported by: danfe, Gerald Pfeifer
| * biology/gemma: Genome-wide Efficient Mixed Model Associationjwb2019-05-178-0/+431
| | | | | | | | | | | | GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.
| * biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64jwb2019-05-148-16/+79
| | | | | | | | | | PR: 237868 Submitted by: pkubaj
| * biology/vsearch: Update to 2.13.4jwb2019-05-114-91/+4
| | | | | | | | | | | | FreeBSD patches incorporated into new upstream release Reported by: portscout
| * biology/igv: Update 2.5.0 -> 2.5.2yuri2019-05-112-6/+6
| | | | | | | | Reported by: portscout
| * biology/trimadap: Mark only for amd64 and i386jwb2019-05-111-3/+2
| | | | | | | | Contains hard-coded SSE instructions
| * biology/stacks: Remove obsolete pkg-message regarding web interfacejwb2019-05-111-16/+0
| | | | | | | | PHP code no longer included in dist as of v2.4
| * biology/stacks: Upgrade to 2.4jwb2019-05-113-52/+6
| | | | | | | | | | | | Improve check to avoid outdated GCC on 2nd tier platforms Reported by: portscout
| * biology/vsearch: Remove powerpc64 supportjwb2019-05-101-1/+1
| | | | | | | | Requires little endian mode and FreeBSD currently does not support it
| * biology/vsearch: Versatile open-source tool for metagenomicsjwb2019-05-108-0/+163
| | | | | | | | | | | | | | | | | | | | | | VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010).
| * devel/openmp: phase outjbeich2019-05-092-1/+2
| | | | | | | | | | | | | | | | | | - Expire after the last version without /usr/lib/libomp.so - Drop SOVERSION for seamless transition (i.e., avoid conditionals) PR: 236907 Approved by: bapt (maintainer) Differential Revision: https://reviews.freebsd.org/D19767
| * biology/tRNAscan-SE: fix build with GCC-based architecturespkubaj2019-05-081-1/+1
| | | | | | | | | | | | Add USES=compiler:c11 to fix build. Approved by: mentors (implicit approval)
| * biology/minimap2: Upgrade to 2.17jwb2019-05-053-7/+9
| | | | | | | | Reported by: portscout
| * biology/ddocent: Upgrade to 2.7.8jwb2019-05-046-152/+86
| | | | | | | | Reported by: portscout
| * biology/fastp: Respect WITH_DEBUG - do not strip binaryjwb2019-05-041-1/+3
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| * These ports now build on aarch64.linimon2019-05-041-3/+1
| | | | | | | | | | | | | | Where necessary, pet portlint. Approved by: portmgr Obtained from: aarch64 TRYBROKEN run
| * biology/fastp: Ultra-fast all-in-one FASTQ preprocessorjwb2019-05-035-0/+73
| | | | | | | | | | | | fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
| * biology/star: Force newer GCC on platforms with GCC 4.2 basejwb2019-05-021-1/+8
|/ | | | | PR: 237700 Submitted by: pkubaj
* biology/py-cutadapt: Upgrade to 2.3jwb2019-04-272-5/+4
| | | | Numerous bugfixes and enhancements since 2.1
* Clean up plistantoine2019-04-251-1/+1
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* biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequencesjwb2019-04-255-0/+87
| | | | | Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
* biology/bowtie2: Clarify CPU-specificityjwb2019-04-251-1/+2
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* biology/star: Modify PKGBASE to avoid conflict with archivers/starjwb2019-04-231-0/+1
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* Fix typosunpoet2019-04-231-2/+2
| | | | | | - Bump PORTREVISION for dependency change Notified by: mat
* Sort PLISTsunpoet2019-04-232-23/+23
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* Related to revision 499061 bump ports with USES=fortran to have themgerald2019-04-224-4/+4
| | | | | | | benefit from the improved situation where libgcc_s is only used when absolutely necessary. Suggested by: tijl
* biology/star: Spliced Transcripts Alignment to a Referencejwb2019-04-226-0/+70
| | | | | STAR is an extremely fast RNA-seq aligner, an alternative to tophat2, hisat2, bowtie, subread, etc.
* biology/bowtie2: Upgrade to 2.3.5.1jwb2019-04-214-13/+42
| | | | | Disable aarch64. Upstream support has changed and I lack the resources to develop new patches.
* biology/canu: Fix build on powerpc64 and aarch64jwb2019-04-184-20/+141
| | | | | | | Should also work on powerpc and arm*, but unable to test PR: 237105 Reported by: pkubaj
* New port: biology/py-xenaPython: API for Xena Hub to access genetic ↵yuri2019-04-134-0/+32
| | | | information shared through the hub
* devel/boost-*: update to 1.70.0jbeich2019-04-127-3/+7
| | | | | | | Changes: http://www.boost.org/users/history/version_1_70_0.html PR: 235956 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D19303
* Bump a few PORTREVISIONs after r498529antoine2019-04-105-1/+5
| | | | With hat: portmgr
* Update devel/readline to 8.0sunpoet2019-04-091-1/+1
| | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://tiswww.case.edu/php/chet/readline/CHANGES PR: 236156 Exp-run by: antoine
* Use real PORTVERSION of devel/p5-Parse-RecDescentsunpoet2019-04-061-1/+1
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* biology/igv: Update 2.4.19 -> 2.5.0yuri2019-04-042-6/+6
| | | | Reported by: portscout
* - Fix build in head i386danilo2019-04-021-0/+1
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* biology/py-fastTSNE: Add the PORTSCOUT lineyuri2019-04-011-0/+2
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* biology/ngs-sdk: Update 2.9.4 -> 2.9.6yuri2019-03-313-5/+5
| | | | Reported by: portscout
* - Add LICENSEamdmi32019-03-301-4/+4
| | | | | | - Switch to USES=localbase Approved by: portmgr blanket
* Mark as broken on aarch64:linimon2019-03-301-0/+2
| | | | | | | | usage: dirname string [...] My guess is that some parameter is being passed the empty string. Approved by: portmgr (tier-2 blanket)
* biology/p5-TrimGalore: Upgrade to 0.6.1jwb2019-03-254-11/+39
| | | | Add test script
* biology/py-cutadapt: Upgrade to 2.1jwb2019-03-252-7/+13
| | | | Add do-test target
* Unbreakantoine2019-03-252-2/+2
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* biology/py-dnaio: Read and write FASTQ and FASTAjwb2019-03-254-0/+27
| | | | | | Factored out of py-cutadapt Reviewed by: jrm
* biology/bowtie2: Upgrade to 2.3.5jwb2019-03-195-41/+111
| | | | | | | - Add bowtie2-test script - Separate Makefile patches into a static patch for upstream and reinplace for ports-specifics - Allow aarch64 per upstream Makefile (untested)
* Qt4 deprecation: Remove Qt4 and its consumes.tcberner2019-03-175-62/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2019-03-15 accessibility/qt4-accessible: Qt4 has been EOL since december 2015 2019-03-15 astro/qlandkartegt: Qt4 has been EOL since december 2015 2019-03-15 astro/stellarium-qt4: Qt4 has been EOL since december 2015 2019-03-15 astro/xglobe: Qt4 has been EOL since december 2015 2019-03-15 audio/acoustid-fingerprinter: Qt4 has been EOL since december 2015 2019-03-15 audio/cueplayer: Qt4 has been EOL since december 2015 2019-03-15 audio/esperanza: Qt4 has been EOL since december 2015 2019-03-15 audio/lastfm-desktop: Qt4 has been EOL since december 2015 2019-03-15 audio/minitunes: Qt4 has been EOL since december 2015 2019-03-15 audio/mixxx20: Qt4 has been EOL since december 2015 2019-03-15 audio/mumble: Qt4 has been EOL since december 2015 2019-03-15 audio/murmur: Qt4 has been EOL since december 2015 2019-03-15 audio/puddletag: Qt4 has been EOL since december 2015 2019-03-15 audio/qmpdclient: Qt4 has been EOL since december 2015 2019-03-15 audio/skype-call-recorder: Qt4 has been EOL since december 2015 2019-03-15 audio/virtual_oss_ctl: Qt4 has been EOL since december 2015 2019-03-15 biology/clustalx: Qt4 has been EOL since december 2015 2019-03-15 cad/klayout: Qt4 has been EOL since december 2015 2019-03-15 cad/layouteditor: Qt4 has been EOL since december 2015 2019-03-15 cad/leocad: Qt4 has been EOL since december 2015 2019-03-15 cad/meshlab: Qt4 has been EOL since december 2015 2019-03-15 cad/qfsm: Qt4 has been EOL since december 2015 2019-03-15 cad/qucs: Qt4 has been EOL since december 2015 2019-03-15 chinese/gcin-qt4: Qt4 has been EOL since december 2015 2019-03-15 chinese/qt4-codecs-cn: Qt4 has been EOL since december 2015 2019-03-15 chinese/qt4-codecs-tw: Qt4 has been EOL since december 2015 2019-03-15 chinese/qterm: Qt4 has been EOL since december 2015 2019-03-15 comms/dabstick-radio: Qt4 has been EOL since december 2015 2019-03-15 comms/hamfax: Qt4 has been EOL since december 2015 2019-03-15 comms/linpsk: Qt4 has been EOL since december 2015 2019-03-15 databases/py-qt4-sql: Qt4 has been EOL since december 2015 2019-03-15 databases/qt4-ibase-plugin: Qt4 has been EOL since december 2015 2019-03-15 databases/qt4-mysql-plugin: Qt4 has been EOL since december 2015 2019-03-15 databases/qt4-odbc-plugin: Qt4 has been EOL since december 2015 2019-03-15 databases/qt4-pgsql-plugin: Qt4 has been EOL since december 2015 2019-03-15 databases/qt4-sql: Qt4 has been EOL since december 2015 2019-03-15 databases/qt4-sqlite-plugin: Qt4 has been EOL since december 2015 2019-03-15 databases/qt4-sqlite3-plugin: Qt4 has been EOL since december 2015 2019-03-15 databases/sqliteman: Qt4 has been EOL since december 2015 2019-03-15 databases/tora: Qt4 has been EOL since december 2015 2019-03-15 deskutils/cdcat: Qt4 has been EOL since december 2015 2019-03-15 deskutils/fbreader: Qt4 has been EOL since december 2015 2019-03-15 deskutils/launchy: Qt4 has been EOL since december 2015 2019-03-15 deskutils/qorganizer: Qt4 has been EOL since december 2015 2019-03-15 deskutils/qrfcview: Qt4 has been EOL since december 2015 2019-03-15 deskutils/qtm: Qt4 has been EOL since december 2015 2019-03-15 deskutils/tuxcards: Qt4 has been EOL since december 2015 2019-03-15 deskutils/vym: Qt4 has been EOL since december 2015 2019-03-15 devel/apiextractor: Qt4 has been EOL since december 2015 2019-03-15 devel/automoc4: Qt4 has been EOL since december 2015 2019-03-15 devel/edb: Qt4 has been EOL since december 2015 2019-03-15 devel/generatorrunner: Qt4 has been EOL since december 2015 2019-03-15 devel/grantlee: Qt4 has been EOL since december 2015 2019-03-15 devel/gwenhywfar-qt4: Qt4 has been EOL since december 2015 2019-03-15 devel/kaptain: Qt4 has been EOL since december 2015 2019-03-15 devel/ninja-ide: Qt4 has been EOL since december 2015 2019-03-12 devel/physfs-devel: is the same as devel/physfs, serving no purpose 2019-03-15 devel/piklab: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-assistant: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-core: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-dbus: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-dbussupport: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-declarative: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-designer: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-designerplugin: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-help: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-qscintilla2: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-script: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-scripttools: Qt4 has been EOL since december 2015 2019-03-15 devel/py-qt4-test: Qt4 has been EOL since december 2015 2019-03-15 devel/pyside: Qt4 has been EOL since december 2015 2019-03-15 devel/pyside-tools: Qt4 has been EOL since december 2015 2019-03-15 devel/qbzr: Qt4 has been EOL since december 2015 2019-03-15 devel/qct: Qt4 has been EOL since december 2015 2019-03-15 devel/qdevelop: Qt4 has been EOL since december 2015 2019-03-15 devel/qprog: Qt4 has been EOL since december 2015 2019-03-15 devel/qross: Qt4 has been EOL since december 2015 2019-03-15 devel/qscintilla2: Qt4 has been EOL since december 2015 2019-03-15 devel/qscintilla2-designerplugin: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-assistant: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-assistant-adp: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-corelib: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-dbus: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-designer: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-help-tools: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-libqtassistantclient: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-linguist: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-linguisttools: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-makeqpf: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-moc: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-porting: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-qdbusviewer: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-qdoc3: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-qmake: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-qmlviewer: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-qt3support: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-qtsolutions-singleapplication: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-qtsolutions-soap: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-qvfb: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-rcc: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-script: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-scripttools: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-testlib: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-uic: Qt4 has been EOL since december 2015 2019-03-15 devel/qt4-uic3: Qt4 has been EOL since december 2015 2019-03-15 devel/qtscriptgenerator: Qt4 has been EOL since december 2015 2019-03-15 devel/shiboken: Qt4 has been EOL since december 2015 2019-03-15 devel/subcommander2: Qt4 has been EOL since december 2015 2019-03-15 devel/universalindentgui: Qt4 has been EOL since december 2015 2019-03-15 editors/leo: Qt4 has been EOL since december 2015 2019-03-15 editors/lfhex: Qt4 has been EOL since december 2015 2019-03-15 editors/plume-creator-devel: Qt4 has been EOL since december 2015 2019-03-15 editors/textroom: Qt4 has been EOL since december 2015 2019-03-15 editors/yzis: Qt4 has been EOL since december 2015 2019-03-15 emulators/dboxfe: Qt4 has been EOL since december 2015 2019-03-15 emulators/q4wine: Qt4 has been EOL since december 2015 2019-03-15 emulators/qtemu: Qt4 has been EOL since december 2015 2019-03-15 emulators/swine: Qt4 has been EOL since december 2015 2019-03-15 finance/alkimia-qt4: Qt4 has been EOL since december 2015 2019-03-15 finance/bitcoin-armory: Qt4 has been EOL since december 2015 2019-03-15 finance/qhacc: Qt4 has been EOL since december 2015 2019-03-15 ftp/scythia: Qt4 has been EOL since december 2015 2019-03-15 games/bubble-chains: Qt4 has been EOL since december 2015 2019-03-15 games/capicity: Qt4 has been EOL since december 2015 2019-03-15 games/capitalism: Qt4 has been EOL since december 2015 2019-03-15 games/flukz: Qt4 has been EOL since december 2015 2019-03-15 games/goldencheetah: Qt4 has been EOL since december 2015 2019-03-15 games/jag: Qt4 has been EOL since december 2015 2019-03-15 games/kardsgt: Qt4 has been EOL since december 2015 2019-03-15 games/kcheckers: Qt4 has been EOL since december 2015 2019-03-15 games/openpref: Qt4 has been EOL since december 2015 2019-03-15 games/pokerth: Qt4 has been EOL since december 2015 2019-03-15 games/qgo: Qt4 has been EOL since december 2015 2019-03-15 games/qtads: Qt4 has been EOL since december 2015 2019-03-15 games/quackle: Qt4 has been EOL since december 2015 2019-03-15 games/spellathon: Qt4 has been EOL since december 2015 2019-03-15 games/sudoku-sensei: Qt4 has been EOL since december 2015 2019-03-15 games/tbe: Qt4 has been EOL since december 2015 2019-03-15 games/xptools: Qt4 has been EOL since december 2015 2019-03-15 german/tipp10: Qt4 has been EOL since december 2015 2019-03-15 graphics/appleseed: Qt4 has been EOL since december 2015 2019-03-15 graphics/aqsis: Qt4 has been EOL since december 2015 2019-03-15 graphics/autoq3d: Qt4 has been EOL since december 2015 2019-03-15 graphics/burplex: Qt4 has been EOL since december 2015 2019-03-15 graphics/darknock: Qt4 has been EOL since december 2015 2019-03-15 graphics/djview4-qt4: Qt4 has been EOL since december 2015 2019-03-15 graphics/easypaint: Qt4 has been EOL since december 2015 2019-03-15 graphics/eos-movrec: Qt4 has been EOL since december 2015 2019-03-15 graphics/gle-graphics: Qt4 has been EOL since december 2015 2019-03-15 graphics/lprof-devel: Qt4 has been EOL since december 2015 2019-03-15 graphics/luminance: Qt4 has been EOL since december 2015 2019-03-15 graphics/luxrender: Qt4 has been EOL since december 2015 2019-03-15 graphics/luxrender14: Qt4 has been EOL since december 2015 2019-03-15 graphics/meshviewer: Qt4 has been EOL since december 2015 2019-03-15 graphics/natron: Qt4 has been EOL since december 2015 2019-03-15 graphics/oyranos: Qt4 has been EOL since december 2015 2019-03-15 graphics/pencil: Qt4 has been EOL since december 2015 2019-03-15 graphics/prison: Qt4 has been EOL since december 2015 2019-03-15 graphics/py-qt4-svg: Qt4 has been EOL since december 2015 2019-03-15 graphics/qt4-iconengines: Qt4 has been EOL since december 2015 2019-03-15 graphics/qt4-imageformats: Qt4 has been EOL since december 2015 2019-03-15 graphics/qt4-opengl: Qt4 has been EOL since december 2015 2019-03-15 graphics/qt4-pixeltool: Qt4 has been EOL since december 2015 2019-03-15 graphics/qt4-svg: Qt4 has been EOL since december 2015 2019-03-15 graphics/qxv: Qt4 has been EOL since december 2015, qxv is unmaintained 2019-03-15 graphics/scantailor: Qt4 has been EOL since december 2015 2019-03-15 graphics/seexpr: Qt4 has been EOL since december 2015 2019-03-15 graphics/smillaenlarger: Qt4 has been EOL since december 2015 2019-03-15 graphics/structuresynth: Qt4 has been EOL since december 2015 2019-03-15 graphics/yagf: Qt4 has been EOL since december 2015 2019-03-15 japanese/qt4-codecs-jp: Qt4 has been EOL since december 2015 2019-03-15 korean/qt4-codecs-kr: Qt4 has been EOL since december 2015 2019-03-15 mail/qgmailnotifier: Qt4 has been EOL since december 2015 2019-03-15 math/qtiplot: Qt4 has been EOL since december 2015 2019-03-15 math/qtoctave: Qt4 has been EOL since december 2015 2019-03-15 math/qwtplot3d-qt4: Qt4 has been EOL since december 2015 2019-03-15 misc/py-qt4-demo: Qt4 has been EOL since december 2015 2019-03-15 misc/py-qt4-doc: Qt4 has been EOL since december 2015 2019-03-15 misc/qmetro: Qt4 has been EOL since december 2015 2019-03-15 misc/qt4-doc: Qt4 has been EOL since december 2015 2019-03-15 misc/qt4-l10n: Qt4 has been EOL since december 2015 2019-03-15 misc/qt4-qtconfig: Qt4 has been EOL since december 2015 2019-03-15 misc/qt4-qtdemo: Qt4 has been EOL since december 2015 2019-03-15 misc/saaghar: Qt4 has been EOL since december 2015 2019-03-15 multimedia/2mandvd: Qt4 has been EOL since december 2015 2019-03-15 multimedia/abby: Qt4 has been EOL since december 2015 2019-03-15 multimedia/avidemux-qt4: Qt4 has been EOL since december 2015 2019-03-15 multimedia/gstreamer-qt4: Qt4 has been EOL since december 2015 2019-03-15 multimedia/mediadownloader: Qt4 has been EOL since december 2015 2019-03-15 multimedia/mlt-qt4: Qt4 has been EOL since december 2015 2019-03-15 multimedia/phonon-xine: Qt4 has been EOL since december 2015 2019-03-15 multimedia/py-qt4-multimedia: Qt4 has been EOL since december 2015 2019-03-15 multimedia/py-qt4-phonon: Qt4 has been EOL since december 2015 2019-03-15 multimedia/qmmp: Qt4 has been EOL since december 2015 2019-03-15 multimedia/qmmp-plugin-pack: Qt4 has been EOL since december 2015 2019-03-15 multimedia/qt4-mobility: Qt4 has been EOL since december 2015 2019-03-15 multimedia/qt4-multimedia: Qt4 has been EOL since december 2015 2019-03-15 multimedia/umplayer: Qt4 has been EOL since december 2015 2019-03-15 net/avahi-qt4: Qt4 has been EOL since december 2015 2019-03-15 net/cagibi: Qt4 has been EOL since december 2015 2019-03-15 net/hupnp: Qt4 has been EOL since december 2015 2019-03-15 net/ostinato: Qt4 has been EOL since december 2015 2019-03-15 net/py-qt4-network: Qt4 has been EOL since december 2015 2019-03-15 net/qjsonrpc: Qt4 has been EOL since december 2015 2019-03-15 net/qoauth: Qt4 has been EOL since december 2015 2019-03-15 net/qt4-network: Qt4 has been EOL since december 2015 2019-03-15 net/qtweetlib: Qt4 has been EOL since december 2015 2019-03-15 net-im/libjreen: Qt4 has been EOL since december 2015 2019-03-15 net-im/psimedia: Qt4 has been EOL since december 2015 2019-03-15 net-im/ramblercontacts: Qt4 has been EOL since december 2015 2019-03-15 net-im/telepathy-logger-qt4: Qt4 has been EOL since december 2015 2019-03-15 net-im/turpial: Qt4 has been EOL since december 2015 2019-03-15 net-im/vacuum-im: Qt4 has been EOL since december 2015 2019-03-15 net-mgmt/nagiosagent: Qt4 has been EOL since december 2015 2019-03-15 net-mgmt/qkismet: Qt4 has been EOL since december 2015 2019-03-15 net-p2p/bitmessage: Qt4 has been EOL since december 2015 2019-03-15 net-p2p/eiskaltdcpp-qt: Qt4 has been EOL since december 2015 2019-03-15 net-p2p/valknut: Qt4 has been EOL since december 2015 2019-03-15 polish/qfaktury: Qt4 has been EOL since december 2015 2019-03-15 print/kpdftool: Qt4 has been EOL since december 2015 2019-03-15 print/scribus: Qt4 has been EOL since december 2015 2019-03-15 science/MOOSE-neural-simulator: Qt4 has been EOL since december 2015 2019-03-15 science/avogadro: Qt4 has been EOL since december 2015 2019-03-15 science/openstructure: Qt4 has been EOL since december 2015 2019-03-15 science/py-veusz: Qt4 has been EOL since december 2015 2019-03-15 science/qtresistors: Qt4 has been EOL since december 2015 2019-03-15 security/keepassx2: Qt4 has been EOL since december 2015 2019-03-15 security/kqoauth: Qt4 has been EOL since december 2015 2019-03-15 security/tpmmanager: Qt4 has been EOL since december 2015 2019-03-15 sysutils/android-file-transfer-qt4: Qt4 has been EOL since december 2015 2019-03-15 sysutils/bacula9-bat: Qt4 has been EOL since december 2015 2019-03-15 sysutils/bareos-traymonitor: Qt4 has been EOL since december 2015 2019-03-15 sysutils/bareos16-bat: Qt4 has been EOL since december 2015 2019-03-15 sysutils/bareos16-traymonitor: Qt4 has been EOL since december 2015 2019-03-15 sysutils/policykit-qt: Qt4 has been EOL since december 2015 2019-03-15 sysutils/qpxtool: Qt4 has been EOL since december 2015 2019-03-15 sysutils/qsynergy: Qt4 has been EOL since december 2015 2019-03-15 sysutils/qzeitgeist: Qt4 has been EOL since december 2015 2019-03-15 sysutils/searchmonkey: Qt4 has been EOL since december 2015 2019-03-15 sysutils/unetbootin: Qt4 has been EOL since december 2015 2019-03-15 textproc/beediff: Qt4 has been EOL since december 2015 2019-03-15 textproc/dixit: Qt4 has been EOL since december 2015 2019-03-15 textproc/goldendict: Qt4 has been EOL since december 2015 2019-03-15 textproc/ibus-qt: Qt4 has been EOL since december 2015 2019-03-15 textproc/py-qt4-xml: Qt4 has been EOL since december 2015 2019-03-15 textproc/py-qt4-xmlpatterns: Qt4 has been EOL since december 2015 2019-03-15 textproc/qt4-clucene: Qt4 has been EOL since december 2015 2019-03-15 textproc/qt4-xml: Qt4 has been EOL since december 2015 2019-03-15 textproc/qt4-xmlpatterns: Qt4 has been EOL since december 2015 2019-03-15 textproc/qt4-xmlpatterns-tool: Qt4 has been EOL since december 2015 2019-03-15 textproc/scim-bridge-qt4: Qt4 has been EOL since december 2015 2019-03-15 textproc/uim-qt4: Qt4 has been EOL since december 2015 2019-03-15 textproc/xxdiff: Qt4 has been EOL since december 2015 2019-03-15 www/aria2fe: Qt4 has been EOL since december 2015 2019-03-15 www/cutycapt: Qt4 has been EOL since december 2015 2019-03-15 www/py-qt4-webkit: Qt4 has been EOL since december 2015 2019-03-15 www/qt4-webkit: Qt4 has been EOL since december 2015 2019-03-15 www/qupzilla-qt4: Qt4 has been EOL since december 2015 2019-03-15 x11/leechcraft: Qt4 has been EOL since december 2015 2019-03-15 x11/py-qt4-opengl: Qt4 has been EOL since december 2015 2019-03-15 x11/qimageblitz: Qt4 has been EOL since december 2015 2019-03-15 x11/qt4-graphicssystems-opengl: Qt4 has been EOL since december 2015 2019-03-15 x11/qt4-inputmethods: Qt4 has been EOL since december 2015 2019-03-15 x11/qxkb: Qt4 has been EOL since december 2015 2019-03-15 x11-fonts/fontmatrix: Qt4 has been EOL since december 2015 2019-03-15 x11-themes/qt4-style-float: Qt4 has been EOL since december 2015 2019-03-15 x11-themes/qt4-style-phase: Qt4 has been EOL since december 2015 2019-03-15 x11-themes/qt4-style-quantumstyle: Qt4 has been EOL since december 2015 2019-03-15 x11-themes/qtcurve-qt4: Qt4 has been EOL since december 2015 2019-03-15 x11-toolkits/attica: Qt4 has been EOL since december 2015 2019-03-15 x11-toolkits/py-qt4-gui: Qt4 has been EOL since december 2015 2019-03-15 x11-toolkits/qt4-declarative: Qt4 has been EOL since december 2015 2019-03-15 x11-toolkits/qt4-gui: Qt4 has been EOL since december 2015 2019-03-15 x11-toolkits/qt4pas: Qt4 has been EOL since december 2015 2019-03-15 x11-toolkits/qwt5: Qt4 has been EOL since december 2015 2019-03-15 x11-toolkits/qwt5-designerplugin: Qt4 has been EOL since december 2015 2019-03-15 x11-toolkits/soqt: Qt4 has been EOL since december 2015 2019-03-15 x11-wm/qlwm: Qt4 has been EOL since december 2015 Approved by: portmgr (implicit)
* biology/cd-hit: Upgrade to 4.8.1jwb2019-03-154-14/+106
| | | | Convert Makefile REINPLACE to patch for sending upstream
* biology/bedtools: unbreak with libc++ 8jbeich2019-03-041-0/+5
| | | | | | | | | | | | | | | | | | | In file included from FileReader.cpp:1: In file included from /usr/include/c++/v1/iostream:38: In file included from /usr/include/c++/v1/ios:216: In file included from /usr/include/c++/v1/__locale:15: In file included from /usr/include/c++/v1/string:505: In file included from /usr/include/c++/v1/string_view:176: In file included from /usr/include/c++/v1/__string:57: In file included from /usr/include/c++/v1/algorithm:640: In file included from /usr/include/c++/v1/initializer_list:47: In file included from /usr/include/c++/v1/cstddef:38: ../../../utils//gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ PR: 236192 Approved by: portmgr blanket
* biology/paml: Update to version 4.9ijrm2019-02-263-4/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Upstream changes as described by the author: - mcmctree: I have added an option (duplication = 1) for dating a tree with both speciations and gene duplications, so that some nodes on the tree share divergence times. Nodes sharing ages are identified using labels in the tree file: #1, #2, .... I have yet to update the document about specification of the model. - mcmctree: The TipDate option was written for one locus or partition and never worked for more than two loci/partitions. I have edited the code so that it works for multiple partitions, some of which may be molecular and the others morphological. - codeml: The option estFreq = 0 when codonFreq = 6 (FMutSel0) and 7 (FMutSel) is not working in versions 4.9g and 4.9h. This is fixed now. This option uses the observed codon or amino acid frequencies for the mutation-selection models of codon usage. Instead the program estimates the frequencies using maximum likeihood, which is what the option estFreq = 1 does. Look at the README file in the examples/mtCDNAape/ folder. - codeml clade model D: The bounds for the w (dN/dS) ratios in the first site classes are set tp (0.0001, 0.5) for w0 and (0.5, 1.5) for w1, in versions 4.9b,c,d,e,f,g, since I added the BEB calculation for clade model D in 4.9b. The motivation for the bounds is that site class 0 represents strong purifying selection with a small w0, while site class 1 should include sites under weak purifying selection with a larger w1. However the bounds are arbitrary. In some datasets, the MLEs are found to be at the bounds, making the interpretation awkward. I have changed the bounds to the following: w0b[]={0.0001, 1.0}, w1b[]={0.01, 1.5}. This means that the user should swap the estimates of w0 and w2 if w0 > w1.
* New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end ↵yuri2019-02-256-0/+116
| | | | sequence assembler
* kallisto: Upgrade to 0.45.1, unbundle hstlibjwb2019-02-255-16/+65
|
* biology/unanimity: Upgrade to 3.4.1jwb2019-02-253-5/+5
| | | | Minor fixes and enhancements upstream.
* biology/ngs-sdk: Update 2.9.3 -> 2.9.4yuri2019-02-243-5/+5
| | | | Reported by: portscout
* biology/igv: Update 2.4.16 -> 2.4.19yuri2019-02-242-6/+6
| | | | Reported by: portscout
* biology/unanimity is not compatible with python 3.xantoine2019-02-232-2/+2
| | | | PR: 234633
* Update to 1.007005 (1.7.5)sunpoet2019-02-233-17/+2
| | | | Changes: https://metacpan.org/changes/distribution/BioPerl
* biology/iqtree: Update to version 1.6.10jrm2019-02-212-5/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.10
* Update to 1.007003sunpoet2019-02-214-67/+16
| | | | | | - Take maintainership Changes: https://metacpan.org/changes/distribution/BioPerl-Run
* Update to 1.007004 (1.7.4)sunpoet2019-02-215-998/+189
| | | | | | | | | - Add LICENSE_FILE - Use USES=shebangfix - Use COPYTREE_SHARE instead of CP -R - Take maintainership Changes: https://metacpan.org/changes/distribution/BioPerl
* Add p5-Bio-Cluster 1.7.3sunpoet2019-02-215-0/+55
| | | | | | | Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe the basic structure for a cluster of BioPerl objects. WWW: https://metacpan.org/release/Bio-Cluster
* biology/pbseqan: Mark deprecatedjwb2019-02-201-0/+2
| | | | Upstream was merged into the SeqAn project represented by biology/seqan.
* biology/unanimity: Upgrade to 3.4.0jwb2019-02-2010-70/+133
| | | | | Switch from cmake to new meson build system Tests disabled for now pending work on unbundling googletest
* biology/pbbam: Upgrade to 0.18.0 releasejwb2019-02-204-23/+47
| | | | In preparation for unanimity upgrade
* biology/pbcopper: Upgrade to 0.4.1 releasejwb2019-02-205-38/+26
| | | | In preparation for biology/unanimity upgrade
* vec_splats function is not supported by base GCC. Add USES=compiler:c11linimon2019-02-181-2/+2
| | | | | | | | to fix build on powerpc platforms. PR: 235514 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* biology/pbseqan: Minor upgrade to latest commitjwb2019-02-182-6/+6
| | | | In preparation for biology/unanimity upgrade
* Update dns/libidn2 to 2.1.1sunpoet2019-02-102-2/+2
| | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://gitlab.com/libidn/libidn2/blob/master/NEWS
* biology/checkm: Update 1.0.12 -> 1.0.13yuri2019-02-102-5/+4
| | | | Reported by: portscout
* - Update WWWamdmi32019-02-071-1/+1
| | | | Approved by: portmgr blanket
* biology/dsr-pdb: Correct typoyuri2019-02-061-1/+1
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* biology/dsr-pdb: Add c++11 flags because boost isn't found without ityuri2019-02-063-2/+25
| | | | | | | Also add patches for missing includes that only gcc complains about. PR: 235519 Reported by: Piotr Kubaj <pkubaj@anongoth.pl>
* New port: biology/figtree: Graphical viewer of phylogenetic treesyuri2019-02-044-0/+49
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* New port: biology/graphlan: High-quality circular representations of ↵yuri2019-02-045-0/+127
| | | | taxonomic, phylogenetic trees
* New port: biology/prodigy-lig: Prediction of protein-small molecule binding ↵yuri2019-02-044-0/+34
| | | | affinities
* New port: biology/prodigal: Protein-coding gene prediction for prokaryotic ↵yuri2019-02-044-0/+51
| | | | genomes
* Move Objective-C ports to the v2 GNUstep ABI.theraven2019-02-031-1/+1
| | | | | | | | | | | | | | | | | | | | | | * Bump the LLVM revision used for GNUstep to 7, the minimum to support the new ABI. * GNUstep-back does not work with lld, so mark it to use Gold (BFD LD doesn't seem able to link Objective-C things). * Turn off some annoying debug logs in GNUstep back, which generate several messages per second when you move the mouse. These should never have been enabled in a release build anyway. * Downgrade Cenon to 4.0.2. This was the last version to actually work with GNUstep (the later ones use XCode >= 5 .xib files, which GNUstep can't parse). * Update gorm to git head. The current release doesn't work with the new Objective-C ABI, but -head has the patches to fix it. * Update PikoPixel and add it to the gnustep-app meta-package. * Update the three core GNUstep packages to the latest release. * Update gnumail and pantomime to the latest release and fix a linking error with the new ABI. * Update GNUstep FTP to the latest version. Reviewed by: bapt (previous version)
* biology/py-loompy: Update 2.0.16 -> 2.0.17yuri2019-02-032-5/+5
| | | | Reported by: portscout
* New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein ↵yuri2019-01-299-0/+122
| | | | description format)
* biology/py-pysam: Update 0.15.1 -> 0.15.2yuri2019-01-262-4/+4
| | | | Reported by: portscout
* Sort categories Makefiles.mat2019-01-231-1/+1
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* Fix Qt5 symbol version scripts to put the catch-all clause first. Whentijl2019-01-163-2/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | a symbol matches multiple clauses the last one takes precedence. If the catch-all is last it captures everything. In the case of Qt5 libraries this caused all symbols to have a Qt_5 label while some should have Qt_5_PRIVATE_API. This only affects lld because GNU ld always gives the catch-all lowest priority. Older versions of Qt5Webengine exported some memory allocation symbols from the bundled Chromium. Version 5.9 stopped exporting these [1] but the symbols were kept as weak wrappers for the standard allocation functions to maintain binary compatibility. [2][3] The problem is that the call to the standard function in these weak wrappers is only resolved to the standard function if there's a call to this standard function in other parts of Qt5Webengine, because only then is there a non-weak symbol that takes precedence over the weak one. If there's no such non-weak symbol the call in the weak wrapper resolves to the weak wrapper itself creating an infinite call loop that overflows the stack and causes a crash. Some of the allocation functions are variants of C++ new and delete and it probably depends on the compiler whether these variants are used in other parts of Qt5Webengine. Remove the weak wrappers (make them Linux specific). This isn't binary compatible but we are already breaking that with the changes to the symbol versions. [1] https://github.com/qt/qtwebengine/commit/5c2cbfccf9aafb547b0b30914c4056abd25942a4 [2] https://github.com/qt/qtwebengine/commit/2ed5054e3a800fa97c2c9e920ba1e6ea4b6ef2a5 [3] https://github.com/qt/qtwebengine/commit/009f5ebb4bd6e50188671e0815a5dae6afe39db5 Bump all ports that depend on Qt5. PR: 234070 Exp-run by: antoine Approved by: kde (adridg)
* biology/stacks: Upgrade to 2.3jwb2019-01-124-38/+14
| | | | Approved by: jrm (mentor, implicit)
* New port: biology/hisat2: Program for mapping next-generation sequencing readsjwb2019-01-127-0/+577
| | | | Approved by: jrm (mentor, implicit)
* Fixup bulk -a errors with BUILD_ALL_PYTHON_FLAVORS=yes.mat2019-01-111-1/+2
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* biology/seqtools: fix build on current, if lld is lld7pi2019-01-081-0/+1
| | | | | | | - fixed by LLD_UNSAFE=yes PR: 230609 Submitted by: jbeich
* biology/groopm fails to build with python3antoine2019-01-071-1/+1
| | | | PR: 234633
* Update dns/libidn2 to 2.1.0sunpoet2019-01-072-0/+2
| | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://gitlab.com/libidn/libidn2/blob/master/NEWS
* Update science/hdf5 to 1.10.4sunpoet2019-01-061-1/+1
| | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes PR: 233070 Submitted by: wen
* biology/ncbi-blast+: Upgrade to 2.8.1jwb2019-01-024-32/+244
| | | | | | | Remove hacks that are no longer needed New patch for endian.h location Approved by: jrm (mentor, implicit)
* biology/diamond: Update to version 0.9.24jrm2019-01-014-27/+12
| | | | | | | Port changes: Tune for package building based on the author's recommendation. Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.24
* biology/iqtree: switch to outsource cmake buildjrm2018-12-281-2/+2
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* Update math/eigen3 to 3.3.7tcberner2018-12-261-0/+1
| | | | | - http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6 - http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7
* Change cmake default behaviour to outsource.tcberner2018-12-268-8/+8
| | | | | | | | | | | Ports that build out of source now simply can use "USES=cmake" instead of "USES=cmake:outsource". Ports that fail to build out of source now need to specify "USES=cmake:insource". I tried to only set insource where explictely needed. PR: 232038 Exp-run by: antoine
* biology/iqtree: Update to version 1.6.9jrm2018-12-232-5/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9
* - Update to 1.73wen2018-12-222-5/+4
| | | | | | PR: 234154 Submitted by: wenheping2000@hotmail.com(myself) Approved by: maintainer
* Remove expired ports:rene2018-12-214-57/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2018-12-19 net/py-libstorj: Broken for more than 6 months 2018-12-20 net/xferstats: Uses obsolete glib12 2018-12-20 net/wmlj: Uses obsolete glib12 2018-12-20 net/ipsorc: Uses obsolete glib12 2018-12-20 net/bsdproxy: Uses obsolete glib12 2018-12-20 net/gini: Uses obsolete glib12 2018-12-21 net/netatalk: Outdated branch of netatalk; use net/netatalk3 instead 2018-12-20 net/nocatsplash: Uses obsolete glib12 2018-12-20 net/jags: Uses obsolete glib12 2018-12-19 net/scribe: Broken for more than 6 months 2018-12-20 net/libnetdude: Uses obsolete glib12 2018-12-20 net/nepim: Uses obsolete glib12 2018-12-20 emulators/generator: Uses obsolete glib12 2018-12-19 emulators/py-nova: Broken for more than 6 months 2018-12-20 emulators/generator-cbiere: Uses obsolete glib12 2018-12-20 x11-toolkits/p5-Gtk-Perl: Uses obsolete glib12 2018-12-20 deskutils/ithought: Uses obsolete glib12 2018-12-20 deskutils/gaddr: Uses obsolete glib12 2018-12-20 x11-fonts/gfe: Uses obsolete glib12 2018-12-20 graphics/graphopt: Uses obsolete glib12 2018-12-19 graphics/fotoxx: Broken for more than 6 months 2018-12-20 graphics/gcolor: Uses obsolete glib12 2018-12-20 graphics/danpei: Uses obsolete glib12 2018-12-20 graphics/chbg: Uses obsolete glib12 2018-12-20 mail/pop3lite: Uses obsolete glib12 2018-12-20 mail/gbuffy: Uses obsolete glib12 2018-12-20 security/gtk-knocker: Uses obsolete glib12 2018-12-20 security/gpasman: Uses obsolete glib12 2018-12-20 security/crank: Uses obsolete glib12 2018-12-20 security/stegdetect: Uses obsolete glib12 2018-12-20 devel/liboop: Uses obsolete glib12 2018-12-20 devel/gcvs: Uses obsolete glib12 2018-12-20 print/lpr-wrapper: Uses obsolete glib12 2018-12-20 print/libppd: Uses obsolete glib12 2018-12-20 net-p2p/napshare: Uses obsolete glib12 2018-12-20 net-p2p/gnewtellium: Uses obsolete glib12 2018-12-20 editors/gnotepad+: Uses obsolete glib12 2018-12-20 editors/manedit: Uses obsolete glib12 2018-12-20 misc/gtkfind: Uses obsolete glib12 2018-12-20 games/mindguard: Uses obsolete glib12 2018-12-20 games/xbattle: Uses obsolete glib12 2018-12-20 games/xbill: Uses obsolete glib12 2018-12-20 games/corewars: Uses obsolete glib12 2018-12-20 games/dopewars: Uses obsolete glib12 2018-12-20 games/garith: Uses obsolete glib12 2018-12-20 games/wmquake: Uses obsolete glib12 2018-12-20 games/znibbles: Uses obsolete glib12 2018-12-20 games/xpuyopuyo: Uses obsolete glib12 2018-12-19 games/kajongg: Broken for more than 6 months 2018-12-20 games/netspades: Uses obsolete glib12 2018-12-20 games/gtklife: Uses obsolete glib12 2018-12-20 biology/xmolwt: Uses obsolete glib12 2018-12-20 x11-clocks/wmclockmon: Uses obsolete glib12 2018-12-20 x11-clocks/asclock-gtk: Uses obsolete glib12 2018-12-20 net-im/gale: Uses obsolete glib12 2018-12-20 audio/xmms-ahx: Uses obsolete glib12 2018-12-20 audio/xmms-curses: Uses obsolete glib12 2018-12-20 audio/scrobbler: Uses obsolete glib12 2018-12-20 audio/xmms-nsf: Uses obsolete glib12 2018-12-20 audio/xmms-nas: Uses obsolete glib12 2018-12-20 audio/xmms-gbsplay: Uses obsolete glib12 2018-12-20 audio/xmms-wavpack: Uses obsolete glib12 2018-12-20 audio/xmms-shn: Uses obsolete glib12 2018-12-20 audio/xmms-volnorm: Uses obsolete glib12 2018-12-20 audio/xmms-faad: Uses obsolete glib12 2018-12-20 audio/xmms-scrobbler: Uses obsolete glib12 2018-12-20 audio/mcplay: Uses obsolete glib12 2018-12-20 audio/gmixer: Uses obsolete glib12 2018-12-20 audio/soundtracker: Uses obsolete glib12 2018-12-20 audio/xmms-sapplug: Uses obsolete glib12 2018-12-20 audio/rio500: Uses obsolete glib12 2018-12-20 audio/xmmsctrl: Uses obsolete glib12 2018-12-20 audio/xmms-xf86audio: Uses obsolete glib12 2018-12-20 audio/xmms-mailnotify: Uses obsolete glib12 2018-12-20 audio/xmms-sexypsf: Uses obsolete glib12 2018-12-20 audio/gqmpeg: Uses obsolete glib12 2018-12-20 audio/wmalbum: Uses obsolete glib12 2018-12-20 audio/xmms-xymms: Uses obsolete glib12 2018-12-20 audio/xmms-flac: Uses obsolete glib12 2018-12-20 audio/xmms-festalon: Uses obsolete glib12 2018-12-20 audio/gkrellmms2: Uses obsolete glib12 2018-12-20 audio/xmms-ladspa: Uses obsolete glib12 2018-12-19 math/octave-forge-engine: Broken for more than 6 months 2018-12-20 math/surf: Uses obsolete glib12 2018-12-19 math/msieve: Broken for more than 6 months 2018-12-19 math/octave-forge-fl-core: Broken for more than 6 months 2018-12-19 math/octave-forge-pdb: Broken for more than 6 months 2018-12-19 math/octave-forge-audio: Broken for more than 6 months 2018-12-20 math/geg: Uses obsolete glib12 2018-12-20 math/grpn: Uses obsolete glib12 2018-12-20 x11/gdkxft: Uses obsolete glib12 2018-12-20 x11/gtk-theme-switch: Uses obsolete glib12 2018-12-19 x11/xpyb: Broken for more than 6 months 2018-12-20 x11/gtk-launch: Uses obsolete glib12 2018-12-19 x11/xpra: Broken for more than 6 months 2018-12-20 palm/pilrc: Uses obsolete glib12 2018-12-20 x11-fm/mtoolsfm: Uses obsolete glib12 2018-12-20 german/steak: Uses obsolete glib12 2018-12-20 multimedia/xmms-skins-huge: Uses obsolete glib12 2018-12-20 multimedia/openquicktime: Uses obsolete glib12 2018-12-20 multimedia/xmms-skins: Uses obsolete glib12 2018-12-20 multimedia/oqtplayer: Uses obsolete glib12 2018-12-20 multimedia/oqtencoder: Uses obsolete glib12 2018-12-20 multimedia/p5-Video-OpenQuicktime: Uses obsolete glib12 2018-12-20 multimedia/xtheater: Uses obsolete glib12 2018-12-20 multimedia/dv2jpg: Uses obsolete glib12 2018-12-20 comms/hf: Uses obsolete glib12 2018-12-20 comms/gscmxx: Uses obsolete glib12 2018-12-20 sysutils/wmcube-gdk: Uses obsolete glib12 2018-12-20 sysutils/gcombust: Uses obsolete glib12 2018-12-20 sysutils/xlogmaster: Uses obsolete glib12 2018-12-20 sysutils/mount.app: Uses obsolete glib12 2018-12-20 sysutils/bbapm: Uses obsolete glib12
* biology/gff2ps: update 0.98d to 0.98legypcio2018-12-202-5/+5
| | | | | | | adopt port. Approved by: araujo (mentor) Differential Revision: https://reviews.freebsd.org/D18591
* biology/diamond: Update to 0.9.23 plus fixes after releasejrm2018-12-183-10/+11
| | | | | | | | | Also: - update license since upstream changed to GPLv3 - only build/package for amd64, since it is untested on other architectures and currently does not build on i386 Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.23
* Update Qt5 to 5.12.0tcberner2018-12-161-0/+11
| | | | | | | | | http://blog.qt.io/blog/2018/12/06/qt-5-12-lts-released/ - This breaks support for libressl again. Patches are welcome. PR: 233705 Exp-run by: antoine
* New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNEyuri2018-12-155-0/+47
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* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2018-12-1237-20/+37
| | | | | | | | | | | | | | | defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590
* devel/boost-*: update to 1.69.0jbeich2018-12-125-3/+5
| | | | | | | Changes: http://www.boost.org/users/history/version_1_69_0.html PR: 232525 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D17645
* Remove biology/njplotjrm2018-12-115-111/+0
| | | | | The author of both NJplot and SeaView says that NJplot can be considered deprecated and replaced by SeaView.
* biology/mummer: Add USES=compiler:c++11-langyuri2018-12-111-1/+1
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* biology/mummer: Update 3.23 -> 4.0.0beta2-2yuri2018-12-113-47/+61
| | | | | | | Port changes: * Moved to github * It now installs itself * It uses yaggo during build
* biology/mummer: Take maintainershipyuri2018-12-111-1/+1
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* New port: math/checkm: Quality assessment tool for the microbial genomesyuri2018-12-074-0/+43
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* New port: math/groopm: Metagenomic binning suiteyuri2018-12-074-0/+35
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* devel/gradle: Update to 5.0yuri2018-12-052-4/+4
| | | | | | | Change biology/igv and biology/gatk to gradle4 due to build failures with gradle5. PR: 233623 Approved by: gasol.wu@gmail.com (maintainer)
* biology/gatk: Change gradle4->gradle because it builds fine with both gradle ↵yuri2018-12-041-2/+2
| | | | 4 and 5
* biology/gatk: Correct the targetyuri2018-12-031-1/+1
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* New port: biology/gatk: Variant discovery in high-throughput sequencing datayuri2018-12-036-0/+118
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* Mark QT4 ports/functionality for removal on 2019-03-15rene2018-12-021-0/+3
| | | | | | | | | | | While here, chase some KDE4 ports and functionality, these are scheduled for removal on 2018-12-31. Change the default option/flavor to QT5 where applicable or use alternative toolkits like GTK. Submitted by: tcberner Reviewed by: adridg, jhale, rene, tcberner Approved by: portmgr (implicit, flavor hook) Differential Revision: https://reviews.freebsd.org/D17741
* biology/igv: Update 2.4.15 -> 2.4.16yuri2018-11-192-6/+6
| | | | Reported by: portscout
* biology/molden: update to 5.8.2jmd2018-11-133-10/+45
| | | | | | | Also add do-install-{option}-on targets and shadow ${MKDIR} commands. PR: 233060 Submitted by: yuri
* biology/seqan-apps: fix build with GCC-based architecturesswills2018-11-101-2/+4
| | | | | | PR: 232045 Submitted by: Piotr Kubaj <pkubaj@anongoth.pl> Approved by: maintainer timeout (h2+fbsdports@fsfe.org >1 month)
* biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gccyuri2018-11-071-1/+2
| | | | | | | Add $(LDFLAGS) to makefile. While here, add USES=gl. Approved by: portmgr
* Fix build failure with base GCC because of double typedefs.linimon2018-11-061-0/+48
| | | | | | PR: 232457 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* Remove the incorrect typedefs to fix build on tier-2.linimon2018-11-062-0/+29
| | | | | | PR: 232390 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* Remove the inccorrect typedefs to fix build on tier-2.linimon2018-11-061-4/+0
| | | | | | PR: 232390 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* biology/igv: Update 2.4.10 -> 2.4.15yuri2018-11-053-24/+21
| | | | | | | Port changes: * Change to gradle, corresponding updates in build, install, environment, etc. Reported by: portscout
* biology/canu: Upgrade to 1.8, add experimental SLURM integrationjwb2018-11-045-31/+102
| | | | | | | | Solves build issue with gcc8. PR: 232930 Reported by: gerald Approved by: jrm (mentor, implicit)
* biology/bowtie: Patch for gcc8 and clean upjwb2018-11-042-6/+17
| | | | | | PR: 232929 Reported by: gerald Approved by: jrm (mentor, implicit)
* biology/bowtie: Revert previous commit with missing log messagejwb2018-11-042-17/+5
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* biology/bowtie: Patchjwb2018-11-042-5/+17
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* biology/py-loompy: Update 2.0.15 -> 2.0.16yuri2018-10-302-4/+4
| | | | Reported by: portscout
* biology/iqtree: Update to version 1.6.8jrm2018-10-292-4/+4
| | | | | Upstream release notes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8
* Fix build with tier-2 arches.linimon2018-10-281-1/+7
| | | | | | PR: 231448 Submitted by: Piotr Kubaj Approved by: maintainer
* biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2yuri2018-10-282-4/+4
| | | | Reported by: portscout
* biology/p5-transdecoder: Upgrade to 5.4.0jwb2018-10-234-30/+44
| | | | | Minor clean up to silence portlint Approved by: jrm (mentor, implicit)
* biology/hyphy: Update to version 2.3.14.16jrm2018-10-203-5/+11
| | | | | | | | | | | | | | | | This pulls in fixes after the 2.3.14 release. Upstream changes for version 2.3.14: https://github.com/veg/hyphy/releases/tag/2.3.14 Subsequent fixes: https://github.com/veg/hyphy/commit/1ecac31 https://github.com/veg/hyphy/commit/bec6833 https://github.com/veg/hyphy/commit/9847438 https://github.com/veg/hyphy/commit/02dcedd https://github.com/veg/hyphy/commit/8f44d3c https://github.com/veg/hyphy/commit/5297c30 https://github.com/veg/hyphy/commit/3d88d3e
* biology/py-loompy: Update 2.0.14 -> 2.0.15yuri2018-10-192-4/+4
| | | | Reported by: portscout
* New port: biology/py-gffutils: Work with GFF and GTF files in a flexible ↵yuri2018-10-194-0/+36
| | | | database framework
* New port: biology/py-pyfaidx: Efficient pythonic random access to fasta ↵yuri2018-10-194-0/+38
| | | | subsequences
* New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) ↵yuri2018-10-194-0/+32
| | | | files
* biology/ngs-sdk: Update 2.9.2 -> 2.9.3yuri2018-10-193-5/+5
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* biology/py-orange3-single-cell: Update 0.8.1 -> 0.8.2yuri2018-10-172-4/+4
| | | | Reported by: portscout
* biology/iqtree: Update to version 1.6.7.1jrm2018-10-162-4/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1
* biology/py-orange3-single-cell: Update 0.8.0 -> 0.8.1yuri2018-10-142-6/+11
| | | | Reported by: portscout
* biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2yuri2018-10-142-4/+4
| | | | Reported by: portscout
* Deprecate most glib12 consumersantoine2018-10-121-0/+3
| | | | With hat: portmgr
* Update devel/tbb to version 2019.1 and bump dependent ports' revisionsmartymac2018-10-111-1/+1
| | | | Also, reintegrate HTML documentation that was removed in previous version.
* Update to 1.73sunpoet2018-10-102-6/+10
| | | | Changes: https://metacpan.org/changes/distribution/Bio-ASN1-EntrezGene
* New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkityuri2018-10-085-0/+70
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* biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06yuri2018-10-086-175/+87
| | | | | | | | Port changes: * Take maintainership * Add to LIB_DEPENDS and USExx * Remove lists of executables and manpages, use file listing instead (*) * Update WWW
* biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/yuri2018-10-0713-1004/+0
| | | | | | | | | | Port changes: * Take maintainership * Implement the 'benchmarks' target, and stop installing benchmarks * Add USES=gmake * Update license * Change MASTER_SITES and WWW to https * Silence some commands
* biology/py-biom-format: Update to version 2.1.7jrm2018-10-062-16/+14
| | | | Reported by: portscout
* Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, exceptdes2018-10-0615-30/+30
| | | | | | | for where it resulted in a change in output from build-depends-list or run-depends-list. Approved by: portmgr (adamw)
* Update devel/tbb to version 2019 and bump dependent port's revisionsmartymac2018-10-041-0/+1
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* - Update to 1-14-10danilo2018-09-294-8/+9
| | | | - Move USES to make portlint happy
* - Unbreak by adding missing pkg-plistwen2018-09-282-2/+136
| | | | | PR: 228758 Submitted by: mzaki@niid.go.jp(maintainer)
* Allow building on powerpc64.linimon2018-09-281-1/+1
| | | | | | PR: 231759 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket)
* Update Objective-C LLVM version to 6.0.brooks2018-09-261-1/+1
| | | | | | | | | Fixes aarch64 build. Reduces depends on obsolete LLVM 4.0. PR: 230116 Submitted by: mikael.urankar@gmail.com Approved by: theraven (prior version) Sponsored by: DARPA, AFRL
* Change 4 ports from net/mpich2 to net/mpichyuri2018-09-231-3/+5
| | | | | | | mpich2 is the obsolete version 2.x, mpich is at the current version 3.x Ports: biology/phyml benchmarks/mdtest benchmarks/imb math/parmetis
* - Update to 1.63wen2018-09-222-4/+4
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* Fix build on gcc-based archs by updating USES.linimon2018-09-221-1/+1
| | | | | | | | Tested on powerpc64 and amd64 (for no regression). While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* Update to 1.5.2sunpoet2018-09-222-6/+7
| | | | Changes: https://github.com/bioruby/bioruby/blob/bioruby-1.5/RELEASE_NOTES.rdoc
* New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq datayuri2018-09-214-0/+44
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* biology/py-cutadapt: Upgrade to 1.18jwb2018-09-203-50/+9
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D17099
* biology/ngs-sdk: Update 2.9.1 -> 2.9.2yuri2018-09-203-5/+5
| | | | Reported by: portscout
* Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-basedlinimon2018-09-181-1/+1
| | | | | | | | | | archs such as powerpc64. Tested for no effect on amd64. While here, pet portlint. Approved by: portgmr (tier-2 blanket)
* More precisely specify USES=compiler to fix build on gcc-basedlinimon2018-09-183-3/+3
| | | | | | | | platforms such as powerpc64. Tested on powerpc64, amd64. Approved by: portmgr (tier-2 blanket)
* biology/py-pysam: Update 0.15.0 -> 0.15.1yuri2018-09-182-4/+4
| | | | Reported by: portscout
* Add DOCS options to ports that should have one.mat2018-09-103-0/+6
| | | | | | | | Also various fixes related to said option. PR: 230864 Submitted by: mat exp-runs by: antoine
* biology/seaview: Fix build with Clang 6tobik2018-09-083-0/+65
| | | | | | | | | | | | seaview.cxx:3352:24: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] strcat(suggested, "."PDF_OR_PS_EXT); ^ http://beefy12.nyi.freebsd.org/data/head-amd64-default/p479076_s338486/logs/errors/seaview-4.7,1.log PR: 230881 Submitted by: tobik Approved by: bofh (maintainer timeout, 2 weeks)
* Update science/hdf5 to 1.10.2sunpoet2018-09-061-1/+1
| | | | | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://portal.hdfgroup.org/display/support/HDF5%201.10.2#releasenotes https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt PR: 231009 Exp-run by: antoine
* Update to 1.31.0jhale2018-09-0317-181/+201
| | | | | PR: 229463 Approved by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
* biology/stacks: Enable OpenMP (oversight in previous commit)jwb2018-09-011-2/+2
| | | | | | | Upgrade to latest release will follow, after testing Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D16973
* biology/iqtree: Update to version 1.6.7jrm2018-08-272-5/+4
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7
* biology/py-bx-python: Update 0.8.1 -> 0.8.2yuri2018-08-262-5/+5
| | | | Reported by: portscout
* biology/unanimity: Upgrade to latest release, soften dep version requirementsjwb2018-08-262-11/+10
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D16902
* biology/protomol: Fix doubled USES overwriting the old valuetobik2018-08-251-3/+2
| | | | - Make sure shebangfix is actually used
* biology/protomol: Fix build with Clang 6tobik2018-08-251-0/+1
| | | | | | | | | | | | Report.cpp:208:12: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const std::__1::ostream' (aka 'const basic_ostream<char>')) *myStream << a; ~~~~~~~~~ ^ ~ /usr/include/c++/v1/ostream:218:20: note: candidate function not viable: no known conversion from 'const std::__1::ostream' (aka 'const basic_ostream<char>') to 'const void *' for 1st argument; take the address of the argument with & basic_ostream& operator<<(const void* __p); ^ ... and so on ... http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/protomol-2.0.3_13.log
* biology/primer3: Fix build with Clang 6tobik2018-08-251-0/+24
| | | | | | | | | | | thal.c:426:13: error: comparison between pointer and integer ('int' and 'const unsigned char *') if ('\0' == oligo_f) { ~~~~ ^ ~~~~~~~ thal.c:431:13: error: comparison between pointer and integer ('int' and 'const unsigned char *') if ('\0' == oligo_r) { ~~~~ ^ ~~~~~~~ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/primer3-2.3.6.log
* biology/libsbml: Fix build with Clang 6tobik2018-08-251-9/+2
| | | | | | | | | | | | | In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129: In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207: /usr/include/c++/v1/map:629:15: error: object of type 'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' cannot be assigned because its copy assignment operator is implicitly deleted {__nc = __v.__cc; return *this;} ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/libsbml-5.17.0.log
* biology/avida: Fix build with Clang 6tobik2018-08-251-0/+1
| | | | | | | | | | | | | | | | | | avida-core/source/main/cPopulation.cc:2916:20: error: no matching member function for call to 'push_back' track_founders.push_back(make_pair(organism->GetBioGroup("genotype")->GetID(), new_genome.AsString())); ~~~~~~~~~~~~~~~^~~~~~~~~ /usr/include/c++/v1/vector:688:36: note: candidate function not viable: no known conversion from 'pair<[...], typename __make_pair_return<cString>::type>' to 'const pair<[...], std::__1::basic_string<char>>' for 1st argument _LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x); ^ /usr/include/c++/v1/vector:691:36: note: candidate function not viable: no known conversion from 'pair<[...], typename __make_pair_return<cString>::type>' to 'pair<[...], std::__1::basic_string<char>>' for 1st argument _LIBCPP_INLINE_VISIBILITY void push_back(value_type&& __x); ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/avida-2.12.4.log libs/tcmalloc-1.4/src/sysinfo.cc:832:88: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] "%08"PRIx64"-%08"PRIx64" %c%c%c%c %08"PRIx64" %02x:%02x %-11"PRId64" %s\n", ^
* biology/lamarc: Fix build with Clang 6tobik2018-08-251-0/+2
| | | | | | | | | | | src/tools/mathx.cpp:781:12: error: no matching function for call to 'make_pair' return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/utility:639:1: note: candidate function not viable: no known conversion from 'DoubleVec1d' (aka 'vector<double>') to 'std::__1::vector<double, std::__1::allocator<double> > &&' for 1st argument make_pair(_T1&& __t1, _T2&& __t2) ^ http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/lamarc-2.1.8_1,1.log
* Mark as broken with clang6 after r473289.linimon2018-08-241-1/+9
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* - Update to 1.72wen2018-08-242-5/+4
| | | | | | PR: 230723 Submitted by: wen@(myself) Approved by: maintainer
* Remove expired ports:rene2018-08-176-104/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2018-08-16 net/traceroute: Upstream gone 2018-08-15 net/e169-stats: unknown license 2018-08-15 net/l4ip: unknown license 2018-08-15 net/dhcprelay: unknown license 2018-08-15 emulators/m2000: unknown license 2018-08-15 textproc/ant-xinclude-task: unknown license 2018-08-15 textproc/bomstrip: unknown license 2018-08-15 x11-fonts/ecofont: unknown license 2018-08-15 mail/roundcube-groupvice: unknown license 2018-08-15 security/pft: unknown license 2018-08-15 devel/kickassembler: unknown license 2018-08-15 devel/gdbmods: unknown license 2018-08-15 devel/as31: unknown license 2018-08-15 databases/dbf2mysql: unknown license 2018-08-15 misc/xpns: unknown license 2018-08-15 misc/amfm: unknown license 2018-08-15 games/smashbattle: unknown license 2018-08-15 games/syobon: unknown license 2018-08-15 games/optimax: unknown license 2018-08-15 games/xgospel: unknown license 2018-08-15 biology/blat: unknown license 2018-08-15 x11-clocks/swisswatch: unknown license 2018-08-15 palm/ppmtoTbmp: unknown license 2018-08-15 dns/ghtool: unknown license 2018-08-15 x11-themes/beastie: unknown license 2018-08-15 converters/uudx: unknown license 2018-08-15 sysutils/areca-cli: unknown license
* biology/cytoscape: Fix licenseyuri2018-08-122-3/+5
| | | | Reported by: linimon
* Mark as broken on arm.linimon2018-08-121-0/+4
| | | | Approved by: portmgr (tier-2 blanket)
* devel/boost-*: update to 1.68.0jbeich2018-08-095-2/+5
| | | | | | | | | - Switch to C++14 for libboost_system to support C++14 consumers Changes: http://www.boost.org/users/history/version_1_68_0.html PR: 229569 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D16165
generated by cgit (git 2.34.1) at 2025-02-28 21:38:01 +0800