Ganael LAPLANCHE 34fdd4dc58 Introduce devel/onetbb and mark devel/tbb as legacy ... Intel oneAPI tbb 2021.1 (onetbb) has been released[1][2] and has deprecated several interfaces over tbb 2020, breaking most dependent ports. Old tbb 2020 will be kept for a certain time to allow transition but will be removed in a near future as it CONFLICTS with devel/onetbb. New ports should now use devel/onetbb instead of devel/tbb. We tried to move a maximum number of dependent ports to devel/onetbb (or disable dependency when not possible), but some of them still remain stuck to devel/tbb. Remaining ones have not been identified as major dependencies themselves and will be fixed as soon as updates are available from upstream. PR: 252648, 252688 [3], 252683 [4], 252651 [5], 252690 [3], 252693 [3], 252695 [3], 252696 [3], 252786 [3], 252649, 252868 [6], 252870 [5], 252684 [7], 252785 [7] Approved by: yuri [3], jwb [4], thierry [5], FreeBSD@Shaneware.biz [6], maintainer timeout [7] [1] https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html [2] https://software.intel.com/content/www/us/en/develop/articles/tbb-revamp.html		2021-02-19 15:14:46 +00:00
..
abyss	biology/abyss: Update 2.2.4 -> 2.2.5	2020-09-27 06:59:05 +00:00
artemis	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
avida	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
babel
bamtools	Bump devel/jsoncpp consumers after r540853.	2020-06-30 17:46:18 +00:00
bcftools	biology/bcftools: Upgrade to 1.11	2020-11-05 20:34:03 +00:00
bedtools	biology/bedtools: Upgrade to 2.30.0	2021-01-24 18:25:39 +00:00
bioawk	biology/bioawk: BWK awk modified for biological data	2020-06-05 02:45:33 +00:00
biococoa	Update a few GNUstep ports:	2021-02-14 23:21:02 +00:00
bioparser	biology/bioparser: Update 3.0.12 -> 3.0.12-2	2021-02-03 19:08:28 +00:00
biosoup	New port: biology/biosoup: Collection of C++ header-only data structures for bioinformatics	2021-01-19 09:01:41 +00:00
bolt-lmm	Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.	2020-09-27 07:41:33 +00:00
bowtie	biology/bowtie: Unbreak build with GCC 10	2020-07-04 10:46:08 +00:00
bowtie2	Introduce devel/onetbb and mark devel/tbb as legacy	2021-02-19 15:14:46 +00:00
bwa	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
canu	biology/canu: Drop dependency on gcc	2021-01-11 16:51:15 +00:00
cd-hit	biology/cd-hit: Drop dependency on gcc	2021-01-11 16:55:15 +00:00
cdbfasta
checkm	scipy 1.5.4 is only compatible with python 3.6+	2020-12-24 09:03:39 +00:00
clustal-omega
clustalw
cufflinks	- Upgrade math/eigen3 to 3.3.8;	2020-12-12 17:04:37 +00:00
cytoscape	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
ddocent	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
diamond	biology/diamond: Update to 2.0.7	2021-02-17 16:43:27 +00:00
dsr-pdb	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
edlib	Fix build on GCC-based systems by adding compiler:c++14-lang to USES:	2021-01-20 02:31:33 +00:00
emboss	- update libgd to 2.3.0	2020-05-04 21:31:39 +00:00
exonerate
fasta	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
fasta3	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
fastahack	biology/fastahack: Upgrade to 1.0.0	2019-10-06 21:34:32 +00:00
fastdnaml
fastool
fastp	biology/fastp: Upgrade to 0.20.1	2020-04-09 16:17:02 +00:00
fastqc	biology/fastqc: Update to 0.11.9	2021-02-04 15:56:33 +00:00
fasttree	biology/fasttree: Drop dependency on gcc	2021-01-11 16:58:13 +00:00
fastx-toolkit
figtree	Add education virtual category	2020-11-20 07:16:06 +00:00
fluctuate
freebayes	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
garlic	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
gatk	biology/gatk: Add the WITH_LARGE_FILES option.	2021-01-22 02:50:38 +00:00
gcta	biology/gcta: Drop dependency on gcc	2021-01-11 17:09:37 +00:00
gemma	biology/gemma: Upgrade to 0.98.3	2021-01-02 22:05:58 +00:00
gff2ps
gmap	biology/gmap: enable on powerpc64le	2020-10-09 13:23:12 +00:00
gperiodic	- Update WWW	2020-01-19 09:30:22 +00:00
graphlan	biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed	2020-08-14 04:59:29 +00:00
grappa	Extend expiration of ports broken with -fno-common	2020-08-30 09:47:49 +00:00
groopm	scipy 1.5.4 is only compatible with python 3.6+	2020-12-24 09:03:39 +00:00
haplohseq	biology/haplohseq: Fix example scripts for python 3	2021-01-23 19:31:49 +00:00
hhsuite	biology/hhsuite: Update 3.2.0 -> 3.3.0	2020-08-27 04:28:24 +00:00
hisat2
hmmer	Also enable on powerpc64le.	2020-09-24 20:29:35 +00:00
htslib	biology/htslib: Upgrade to 1.11.0	2020-11-05 20:30:50 +00:00
hyphy	biology/hyphy: Update to version 2.5.27	2021-01-27 11:33:53 +00:00
igv	biology/igv: Fix fetch by fixing a small left-over mistake	2020-11-30 17:29:48 +00:00
infernal	Also enable on powerpc64le.	2020-09-24 20:38:59 +00:00
iolib
iqtree	biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ build	2021-01-12 18:12:12 +00:00
jalview	Restrict to Java 8, since this doesn't compile with Java 11	2020-12-26 23:01:20 +00:00
jellyfish	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
kallisto	biology/kallisto: Add -lz for pending hdf5 upgrade	2021-01-26 01:34:20 +00:00
lagan	Extend expiration of ports broken with -fno-common	2020-08-30 09:47:49 +00:00
lamarc
libbigwig	New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)	2019-07-11 17:05:22 +00:00
libgtextutils
libsbml	Set CMAKE options explicitly	2020-12-20 15:23:50 +00:00
linux-foldingathome	Update to 7.6.13	2020-05-09 13:21:29 +00:00
mafft
mapm3	biology/mapm3: Reformat patches.	2020-09-04 12:24:23 +00:00
migrate	Mark BROKEN on riscv64 the same as armv*:	2021-01-19 02:26:53 +00:00
minimap2
molden	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
mopac	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
mothur	biology/mothur: fix build on powerpc64le	2020-10-19 10:30:11 +00:00
mrbayes	- Swap back from net/openmpi3 to net/openmpi	2020-04-21 21:47:57 +00:00
mummer	biology/mummer: fix build on powerpc64 elfv2 and powerpc64le	2020-10-25 23:03:14 +00:00
muscle	biology/muscle: unbreak in -CURRENT	2020-01-17 16:49:03 +00:00
ncbi-blast+	biology/ncbi-blast+: Drop dependency on gcc	2021-01-11 17:17:35 +00:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: Fix build on 13	2020-09-27 04:57:44 +00:00
ncbi-toolkit	Chase security/p11-kit update	2020-08-30 03:10:23 +00:00
ngs-sdk	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene	Update *_DEPENDS	2020-01-08 18:36:30 +00:00
p5-Bio-Cluster	Update *_DEPENDS	2019-12-08 16:57:18 +00:00
p5-Bio-Coordinate	Cosmetic change	2020-04-02 12:01:30 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL	Add p5-Bio-DB-EMBL 1.7.4	2019-12-08 16:49:19 +00:00
p5-Bio-DB-NCBIHelper	Add p5-Bio-DB-NCBIHelper 1.7.6	2019-12-08 16:49:25 +00:00
p5-Bio-FeatureIO	Cosmetic change	2020-04-02 12:01:35 +00:00
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-Bio-Variation	Update to 1.7.5	2020-01-08 18:36:35 +00:00
p5-BioPerl	Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113	2020-06-26 11:55:23 +00:00
p5-BioPerl-Run	Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago	2020-01-08 18:36:40 +00:00
p5-transdecoder	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
p5-TrimGalore	biology/p5-TrimGalore: Upgrade to 0.6.5	2019-11-26 16:20:12 +00:00
paml	biology/paml: fix the build with LLVM 11	2020-08-20 17:07:03 +00:00
pbbam	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
pbseqan	biology/unanimity and dependencies: Flag as no longer open source	2019-11-24 15:53:00 +00:00
pear-merger	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
phrap	Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).	2020-05-27 11:59:13 +00:00
phred	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
phylip	Extend expiration of ports broken with -fno-common	2020-08-30 09:47:49 +00:00
phyml	biology/phyml: fix build on recent current	2020-08-29 08:34:27 +00:00
picard-tools	biology/picard-tools: Remove extraneous file	2020-08-30 14:06:54 +00:00
plink	Allow building on powerpc64le.	2020-09-27 07:44:15 +00:00
pooler	biology/pooler: Upgrade to 1.76	2021-01-08 22:44:13 +00:00
primer3
prodigal	biology/prodigal: Eliminate a very old version from the portscout discovery process	2019-10-12 15:40:21 +00:00
prodigy-lig	Unbreak bulk -a	2020-06-13 15:05:44 +00:00
protomol	Add USES=xorg USES=gl, ports categories b	2019-11-04 21:08:20 +00:00
psi88	biology/psi88: Unbreak build with GCC 10	2020-07-04 12:15:58 +00:00
py-biom-format	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-biopython	biology/py-biopython: Upgrade to 1.78	2020-10-16 19:12:43 +00:00
py-bx-python	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-cutadapt	biology/py-cutadapt: Update to 3.2	2021-02-02 20:39:09 +00:00
py-dnaio	biology/py-cutadapt: Update to 3.2	2021-02-02 20:39:09 +00:00
py-ete3	Update PyQt5 to 5.15.2, sip to 5.5.0, py-qtbuilder to 1.6.0 and py-qt5-sip to 12.8.1	2020-12-15 17:56:00 +00:00
py-fastTSNE	Drop dependency on devel/openmp	2020-03-08 21:56:36 +00:00
py-Genesis-PyAPI	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-gffutils	Unbreak bulk -a	2020-07-14 07:59:28 +00:00
py-gtfparse	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-hits	New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments	2020-05-16 03:11:05 +00:00
py-loompy	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-macs2	biology/py-macs2: Upgrade to 2.2.7.1	2020-04-14 12:13:55 +00:00
py-multiqc	biology/py-multiqc: Update to 1.9	2021-02-05 01:37:04 +00:00
py-orange3-bioinformatics	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-orange3-single-cell	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-pandas-charm	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-pyfaidx	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-pysam	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-scikit-bio	Add education virtual category	2020-11-20 07:16:06 +00:00
py-xenaPython	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
pyfasta	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
python-nexus	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
rainbow	Update WWW	2020-03-31 23:18:09 +00:00
rampler	Add compiler:c++11-lang to USES to fix build on GCC-based systems:	2021-01-20 02:30:13 +00:00
recombine	Fix after gets(3) retirement using gets_s(3).	2019-09-02 05:00:43 +00:00
ruby-bio	biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser	2020-05-05 14:22:09 +00:00
rubygem-bio	Update to 2.0.1	2020-07-24 07:49:43 +00:00
rubygem-bio-executables	Add rubygem-bio-executables 1.0.0	2020-07-24 07:08:00 +00:00
rubygem-bio-old-biofetch-emulator	Add rubygem-bio-old-biofetch-emulator 1.0.0	2020-07-24 07:08:05 +00:00
rubygem-bio-shell	Add rubygem-bio-shell 1.0.0	2020-07-24 07:08:11 +00:00
samtools	biology/samtools: Upgrade to 1.11	2020-11-05 20:32:39 +00:00
scrm	Add compiler:c++11-lang to USES to fix build on GCC-based systems:	2020-05-15 07:30:34 +00:00
seaview	Mark BROKEN in 13/14 (via latest llvm update).	2021-02-17 21:59:47 +00:00
seqan
seqan1	Fix some misspelled or duplicated LICENSE_*	2019-09-17 19:21:45 +00:00
seqan-apps	devel/boost-*: update to 1.72.0	2019-12-11 17:53:48 +00:00
seqio
seqtk
sim4
slclust
smithwaterman
spoa	biology/spoa: Fix build after recent devel/cereal update; Fix LIB_DEPENDS	2021-02-19 09:22:30 +00:00
stacks	biology/stacks: Drop dependency on gcc	2021-01-11 17:27:30 +00:00
star	biology/star: Drop dependency on gcc	2021-01-11 17:39:52 +00:00
stringtie	biology/stringtie: fix build on GCC architectures	2020-02-23 10:52:44 +00:00
subread	biology/subread: Add -fcommon for clang 11	2020-09-18 00:57:35 +00:00
tabixpp	biology/tabixpp: fix build on GCC architectures	2020-11-23 16:13:15 +00:00
treekin	Fix math/openblas and bump dependent ports	2020-01-30 14:17:44 +00:00
treepuzzle
trimadap
trimmomatic	Clean up after java/openjdk6 and java/openjdk6-jre removal	2019-11-26 21:46:12 +00:00
tRNAscan-SE	biology/tRNAscan-SE: update to 2.0.5	2020-01-13 17:36:57 +00:00
ugene	Mark BROKEN on riscv64 the same as on aarch64.	2021-01-19 02:29:16 +00:00
vcflib	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
vcftools
velvet
viennarna	biology/viennarna: Update 2.4.16 -> 2.4.17	2020-12-06 20:14:53 +00:00
vsearch	biology/vsearch: Update to 2.15.2	2021-01-30 15:31:11 +00:00
vt	biology/vt: Fix build with htslib 1.11	2020-11-09 00:35:58 +00:00
wise	a-b: Add missing USES={gnome,php,sdl,xorg}	2019-11-08 09:27:56 +00:00
Makefile	New port: biology/rampler: Standalone module for sampling genomic sequences	2021-01-19 09:49:53 +00:00