| Commit message (Collapse) | Author | Age | Files | Lines |
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PR: 276530
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Numerous bug fixes and enhancements since 3.3
Changes: https://github.com/marcelm/cutadapt/tags
PR: 276814
Reported by: wen
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Numerous bug fixes and enhancements since 0.5.1
Changes: https://github.com/marcelm/dnaio/tags
PR: 276814
Reported by: wen
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Changelog: https://github.com/bbuchfink/diamond/releases/tag/v2.1.9
Sponsored by: The FreeBSD Foundation
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Reported by: fallout
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statement
Reported by: fallout
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PR: 275494
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A python module to read and write the Newick format.
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Update to 0.10.0. This release adds support for python 3.11
Changes: https://github.com/bxlab/bx-python/releases/tag/v0.10.0
PR: 276683
PR: 275494
Approved by: yuri (maintainer)
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Approved by: portmgr (blanket)
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Approved by: portmgr (blanket)
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Add FASTQ support to usearch_global and search_exact
Code cleanup and manual clarifications
Reported by: portscout
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Reported by: portscout
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PR: 275494
Approved by: portmgr@(blanket, fix build)
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Reported by: fallout
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Reported by: portscout
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A few bug fixes
Add option for faster indexing of small indexes
Reported by: portscout
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2024-01-17 biology/recombine: Upstream advises to use biology/lamarc
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2024-01-17 biology/seqio: Upstream last release was in 2000
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2024-01-17 biology/sim4: Upstream last update was in 2005
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is fixed
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Reported by: https://portsfallout.com/
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While here move manpages to share/man
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metaeuk produces wrong results there.
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Reported by: https://portsfallout.com/
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Until the breakage is fixed by the upstream.
Reported by: https://portsfallout.com/
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Add biology/py-macs3 dep to metaport
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MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying
transcription factor (TF) binding sites. Such sites are generated
by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq
(Assay for Transposase Accessible Chromatin Sequencing). MACS
identifies "peaks" in the genome sequence, which are areas enriched
in bound TFs or accessible chromatin.
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PR: 275860
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Changes: https://ziglang.org/download/0.11.0/release-notes.html
PR: 273124
Approved by: dch (maintainer)
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- Remove all references to defunct ARCH arm
- Remove all references to defunct ARCH sparc64
- Remove x11-drivers/xf86-video-sunffb which requires defunct sparc64
ARCH
- Remove sysutils/afbinit requires defunct sparc64 ARCH
- Remove all references to bktr driver
- Remove all references to defunct FreeBSD_12
- Remove all references to OSVERSION/OSREL corresponding to 12
- Remove conditionals in Mk/Uses/cabal.mk
- Remove sparc reference from Mk/Uses/qt-dist.mk
- Remove BROKEN_sparc64/NOT_FOR_ARCH=sparc64
- Remove BROKEN_FreeBSD_12* from:
- Remove OpenSSL patches from:
- Remove conditional flags for OSVERSION >= 1300000 to fixed flags.
Also move conditional flags for non sparc64/arm ARCH to fixed flags.
Reviewed by: brooks, jbeich, rene, salvadore
Differential Revision: https://reviews.freebsd.org/D42068
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Currently their is a hardcoded dependency on mysql57-client which is
about to be removed. Ports depending on mysql should always use
USES=mysql rather than hardcoded *_DEPENDS. As I do not have a licensed
version of this application for now switch to USES=mysql. This should
not affect the cluster build at all as this is a RESTRICTED ports.
Approved by: portmgr (blanket)
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- There are multiple ports which has MYSQL options and are non-DEFAULT.
Most of the time committers actually forget to check with the OPTION
enabled and in some cases they are BROKEN with newr versions of mysql.
So test with different versions of mysql and mark IGNOPRE_WITH_MYSQL
appropriately. Due to the EOL of 5.7 this has not been checked.
- Unbreak sysutils/cfengine* with MySQL 8.0 and later
- The primary purpose of running this check is having statistics of the
MySQL usability over MariaDB to explore the future possibility of
shifting to MariaDB as the default as major ports upstream have moved
their codebase to support MariaDB over MySQL.
- The following actions will also be taken after the sunset of MySQL 5.7
If a port is broken on all instances of MySQL/MariaDB:
- If a port has the option of multiple DB backends and MySQL is the
default then the DEFAULT will be changed to PGSQL/SQLITE before
2024Q1. And the OPTION will be removed before 2024Q2. If a
MAINTAINER is aware about such cases and want to prefer PGSQL over
SQLITE or vice versa please do so at your own accord. Otherwise
PGSQL will be preferred over SQLITE.
- If a port has the option of multiple DB backends and MySQL is not
the default then the the OPTION will be removed before 2024Q1.
Approved by: portmgr (blanket)
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Rename the roundup method defined in bwValues.c as it clashes with the
roundup macro defined in sys/param.h
/wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:9:35:
error: too few arguments provided to function-like macro invocation
static uint32_t roundup(uint32_t v) {
^
/usr/include/sys/param.h:300:9: note: macro 'roundup' defined here
^
/wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:9:24:
error: expected ';' after top level declarator
static uint32_t roundup(uint32_t v) {
^
;
/wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:350:30:
error: too few arguments provided to function-like macro invocation
o->m = roundup(o->l+1);
^
/usr/include/sys/param.h:300:9: note: macro 'roundup' defined here
^
/wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:370:30:
error: too few arguments provided to function-like macro invocation
o->m = roundup(o->l+1);
^
/usr/include/sys/param.h:300:9: note: macro 'roundup' defined here
^
4 errors generated.
Approved by: portmgr (blanket)
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- Update LICENSE_FILE
Changes: https://metacpan.org/dist/Bio-DB-NCBIHelper/changes
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Changes: https://github.com/veg/hyphy/releases/tag/2.5.58
Sponsored by: The FreeBSD Foundation
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Reported by: portscout
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Reported by: portscout
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ChangeLog: https://github.com/broadinstitute/gatk/releases/tag/4.5.0.0
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