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584,149 Commits 45 Branches 100 Tags 3.4 GiB
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3354 Commits

Author SHA1 Message Date
Yuri Victorovich
8b4b845a51 biology/py-PySCeS: Update 1.0.1 -> 1.0.2 
Reported by:	portscout
 2022-05-20 15:02:59 -07:00
Yuri Victorovich
5ba960dcdd biology/taxonkit: Update 0.11.0 -> 0.11.1 
Reported by:	portscout
 2022-05-20 15:02:59 -07:00
Yuri Victorovich
a19ac12c2c biology/mothur: Update 1.47.0 -> 1.48.0 
Reported by:	portscout
 2022-05-19 19:10:18 -07:00
Yuri Victorovich
d776c97dcf biology/biosig: Update 2.4.0 -> 2.4.1 2022-05-16 15:09:25 -07:00
Yuri Victorovich
8732b987ed biology/taxonkit: Update 0.10.1 -> 0.11.0 
Reported by:	portscout
 2022-05-16 11:45:25 -07:00
Loïc Bartoletti
2d34c2bfea devel/cmake: Update to 3.23.0 
Update to 3.23.0.
Fix pkg-plist: using the default share/man location

Release Notes:
  https://cmake.org/cmake/help/v3.23/release/3.23.html

PR:		262886
Exp-run by:	antoine
 2022-05-16 08:49:43 +02:00
Po-Chuan Hsieh
bf3c49f70a
devel/grpc: Update to 1.46.0 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
 2022-05-13 19:39:14 +08:00
Kevin Bowling
db78da8f8b devel/libffi: Bump deps PORTREVISION for shlib change 
PR:		263764
Reported by:	VVD <vvd@unislabs.com>
 2022-05-09 12:23:51 -07:00
Jason W. Bacon
dda5e52508 biology/py-dna-features-viewer: Update to 3.1.1 
python 3.9 compatibility

Changes: https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/tags

Reported by:    portscout
 2022-05-08 07:48:38 -05:00
Yuri Victorovich
dda16bd485 biology/checkm: Update 1.1.11 -> 1.2.0 
Reported by:	portscout
 2022-05-01 11:14:09 -07:00
Yuri Victorovich
8db0b60850 biology/py-mrcfile: New port: MRC file I/O library which is used in structural biology 2022-05-01 10:37:04 -07:00
Yuri Victorovich
84de6204b9 biology/py-pysam: Update 0.18.0 -> 0.19.0 
Reported by:	portscout
 2022-04-27 10:38:26 -07:00
Yuri Victorovich
fedffc237c biology/py-resdk: Update 14.0.0 -> 14.1.0 
Reported by:	portscout
 2022-04-27 10:38:25 -07:00
Piotr Kubaj
eaf43a218b biology/pooler: use openmp only when omp.h is present 2022-04-27 13:22:12 +00:00
Piotr Kubaj
1115257612 biology/ncbi-blast+: check for omp.h on all architectures 2022-04-27 13:22:09 +00:00
Piotr Kubaj
74016ad026 biology/cd-hit: check for omp.h on all architectures 2022-04-27 13:22:07 +00:00
Piotr Kubaj
e7af5e32b4 biology/hhsuite: check for omp.h on all architectures 2022-04-27 13:22:04 +00:00
Piotr Kubaj
cf150ef9e2 biology/fasttree: check for omp.h on all architectures 2022-04-27 13:22:02 +00:00
Yuri Victorovich
a47cbfbf39 biology/unikmer: Update 0.18.8 -> 0.19.0 
Reported by:	portscout
 2022-04-26 11:51:57 -07:00
Yuri Victorovich
088dbf75b8 biology/checkm: Update 1.1.10 -> 1.1.11 
Reported by:	portscout
 2022-04-25 13:50:10 -07:00
Piotr Kubaj
b3b6b26431 biology/seqan-apps: remove obsolete USE_GCC 
Instead use USES=compiler.
 2022-04-25 14:12:52 +00:00
Joseph Mingrone
e2c4d38d48
biology/hyphy: Update to 2.5.38 
Upstream changes: https://github.com/veg/hyphy/compare/2.5.36...2.5.38

Sponsored by:	The FreeBSD Foundation
 2022-04-24 15:24:30 -03:00
Joseph Mingrone
d9f5d5d949
biology/diamond: Update to 2.0.15 
https://github.com/bbuchfink/diamond/releases/tag/v2.0.15

Sponsored by:	The FreeBSD Foundation
 2022-04-24 14:50:21 -03:00
Yuri Victorovich
2d70d2a28e biology/{,py-}libnuml: Update 1.1.5 -> 1.1.6 
Reported by:	portscout
 2022-04-23 18:36:56 -07:00
Yuri Victorovich
1c92a5a1da biology/{,py-}libsedml: Update 2.0.30 -> 2.0.31 
Reported by:	portscout
 2022-04-22 11:04:38 -07:00
Yuri Victorovich
d0a1dad5c4 biology/checkm: Update 1.1.9 -> 1.1.10 
Reported by:	portscout
 2022-04-22 11:04:37 -07:00
Piotr Kubaj
8a75ffbc9f biology/hhsuite: drop HAVE_POWER8 on powerpc64 
powerpc64 uses PPC970 as a baseline.
 2022-04-21 17:11:16 +00:00
Piotr Kubaj
52e46764cf biology/py-scikit-bio: drop unnecessary USE_GCC on powerpc64 2022-04-21 17:11:15 +00:00
Piotr Kubaj
6812895caa biology/bolt-lmm: remove unnecessary CFLAGS_powerpc64 2022-04-21 17:11:13 +00:00
Yuri Victorovich
44210d2f50 biology/seqkit: Update 2.1.0 -> 2.2.0 
Reported by:	portscout
 2022-04-19 20:44:55 -07:00
Piotr Kubaj
a3f5e20929 biology/py-scikit-bio: build with clang on powerpc64le 2022-04-19 14:09:20 +02:00
Piotr Kubaj
b48c8810a8 biology/bolt-lmm: remove unnecessary flags for powerpc64le 2022-04-17 13:05:53 +02:00
Yuri Victorovich
f7875ce1de biology/checkm: Update 1.1.8 -> 1.1.9 
Reported by:	portscout
 2022-04-15 12:09:58 -07:00
Yuri Victorovich
1aa4b19950 biology/py-scikit-bio: Update 0.5.6 -> 0.5.7 
Reported by:	portscout
 2022-04-15 12:09:57 -07:00
Yuri Victorovich
350d96226d biology/checkm: Update 1.0.18 -> 1.1.8 
Reported by:	portscout
 2022-04-11 20:22:30 -07:00
Yuri Victorovich
0fe062bee9 biology/gatk: Update 4.2.0.0 -> 4.2.6.0 2022-04-10 16:21:50 -07:00
Charlie Li
d63665f7cd
textproc/libxml2: bump all LIB_DEPENDS consumers 
This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)
 2022-04-10 15:11:41 -04:00
Yuri Victorovich
53aca1ad84 biology/{,py-}libsedml: Update 2.0.28 -> 2.0.30 
Reported by:	portscout
 2022-04-07 13:19:03 -07:00
Yuri Victorovich
0ba58a1a6f biology/{,py-}libnuml: Update 1.1.4 -> 1.1.5 
Reported by:	portscout
 2022-04-07 13:19:03 -07:00
Dmitry Marakasov
ff5a2c36cc biology/py-cutadapt: fix tests by adding missing test depend 
Approved by:	portmgr blanket
 2022-04-07 21:59:32 +03:00
Dmitry Marakasov
7b4d1f0b36 */*: fix trailing whitespace in pkg-descr's 
Approved by:	portmgr blanket
 2022-04-01 18:09:49 +03:00
Po-Chuan Hsieh
a478c75844
devel/grpc: Update to 1.45.0 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
 2022-03-31 06:02:45 +08:00
Guangyuan Yang
d690b5102f */*: Bump PORTREVISION after lang/go 1.18 update 2022-03-30 03:01:44 -04:00
Matthias Fechner
247c7db751 textproc/libxml2: bump all dependencies 
This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd7
 2022-03-26 09:27:27 +01:00
Jason W. Bacon
fad5d1754c biology/py-ont-fast5-api: Update to 4.0.2 
Minor bug fix release

Also disabled install of test directory, which was not properly
installed under the package subdir and caused a conflict as a result

PR:             262759
 2022-03-25 11:37:29 -05:00
Po-Chuan Hsieh
d1c57dce04
biology/python-nexus: Fix build with setuptools 58.0.0+ 
With hat:	python
 2022-03-25 21:38:05 +08:00
Po-Chuan Hsieh
0ffe3e7936
biology/py-crossmap: Fix build with setuptools 58.0.0+ 
With hat:	python
 2022-03-25 21:38:04 +08:00
Po-Chuan Hsieh
dab6c99caa
biology/groopm: Fix build with setuptools 58.0.0+ 
With hat:	python
 2022-03-25 21:38:04 +08:00
Po-Chuan Hsieh
c750cbac58
biology/checkm: Fix build with setuptools 58.0.0+ 
With hat:	python
 2022-03-25 21:38:04 +08:00
Yuri Victorovich
929ed69936 biology/dsr-pdb: Remove -pg (mcount instrumentation) flag 
This causes failure on aarch64: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=262709
 2022-03-21 17:07:11 -07:00