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Ukraine
Some details on the 2023-01-16 website outage.
We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
non port: biology/bowtie2/Makefile
SVNWeb

Number of commits found: 33

Sat, 21 Jan 2023
[ 22:30 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:65ce3f1684bc6a0457bfc55feb059baf76bbee2a  commit hash:65ce3f1684bc6a0457bfc55feb059baf76bbee2a  commit hash:65ce3f1684bc6a0457bfc55feb059baf76bbee2a  65ce3f1 
biology/bowtie2: Update to 2.5.1

A few minor fixes and enhancements

Changes:    https://github.com/BenLangmead/bowtie2/tags

Reported by:    portscout
Fri, 4 Nov 2022
[ 23:49 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa  commit hash:f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa  commit hash:f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa  f2f8bd7 
biology/bowtie2: Update to 2.5.0

Performance improvements and minor improvements
Changes:    https://github.com/BenLangmead/bowtie2/tags

Reported by:    portscout
Wed, 7 Sep 2022
[ 21:10 Stefan E├čer (se) search for other commits by this committer ]    commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52  commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52  commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52  b7f0544  (Only the first 10 of 27931 ports in this commit are shown above. View all ports for this commit)
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Wed, 20 Jul 2022
[ 14:20 Tobias C. Berner (tcberner) search for other commits by this committer ]    commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671  commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671  commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671  37526bb  (Only the first 10 of 82 ports in this commit are shown above. View all ports for this commit)
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Fri, 21 Jan 2022
[ 14:33 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:bfdda4387466c93127ca47424f61e03c94aae8bb  commit hash:bfdda4387466c93127ca47424f61e03c94aae8bb  commit hash:bfdda4387466c93127ca47424f61e03c94aae8bb  bfdda43 
biology/bowtie2: Update to 2.4.5

A few bug fixes

Changes:        https://github.com/BenLangmead/bowtie2/tags
Reported by:    portscout
Mon, 24 May 2021
[ 16:35 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:4521502b9bd34932d3547b69cd5aea3c221fad88  commit hash:4521502b9bd34932d3547b69cd5aea3c221fad88  commit hash:4521502b9bd34932d3547b69cd5aea3c221fad88  4521502 
biology/bowtie2: Update to 2.4.4

Fix deadlock issue in multithreaded execution

Reported by:    portscout
Mon, 17 May 2021
[ 23:40 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef  commit hash:1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef  commit hash:1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef  1effaac 
biology/bowtie2: Update to 2.4.3

Drop tbb dependency (upstream switched to C++ threads)
Add support for powerpc64

Reported by:    portscout
Tested by:      pkubaj (powerpc64*)
Sun, 18 Apr 2021
[ 15:53 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6d  commit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6d  commit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6d  48ddc73 
biology/bowtie2: Add support for powerpc64le

PR:             255092
Submitted by:   pkubaj
Wed, 14 Apr 2021
[ 10:08 Ganael LAPLANCHE (martymac) search for other commits by this committer ]    commit hash:9ee84848094757a07a41aefc97967e6ae1a43039  commit hash:9ee84848094757a07a41aefc97967e6ae1a43039  commit hash:9ee84848094757a07a41aefc97967e6ae1a43039  9ee8484  (Only the first 10 of 17 ports in this commit are shown above. View all ports for this commit)
devel/onetbb: Update to 2021.2.0 and bump dependencies

Changelog:
https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html
Wed, 7 Apr 2021
[ 08:09 Mathieu Arnold (mat) search for other commits by this committer ]    commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  cf118cc  (Only the first 10 of 8873 ports in this commit are shown above. View all ports for this commit)
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
Tue, 6 Apr 2021
[ 14:31 Mathieu Arnold (mat) search for other commits by this committer ]    commit hash:305f148f482daf30dcf728039d03d019f88344eb  commit hash:305f148f482daf30dcf728039d03d019f88344eb  commit hash:305f148f482daf30dcf728039d03d019f88344eb  305f148  (Only the first 10 of 29333 ports in this commit are shown above. View all ports for this commit)
Remove # $FreeBSD$ from Makefiles.
Fri, 19 Feb 2021
[ 15:14 martymac search for other commits by this committer ] Original commit   Revision:566074 (Only the first 10 of 38 ports in this commit are shown above. View all ports for this commit)
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
Sat, 30 Jan 2021
[ 17:43 jwb search for other commits by this committer ] Original commit   Revision:563428
biology/bowtie2: Reverse switch to devel/onetbb

Mistakenly believed onetbb was already committed

PR:             252683
[ 17:39 jwb search for other commits by this committer ] Original commit   Revision:563427
biology/bowtie2: Switch to devel/onetbb

PR:             252683
Submitted by:   martymac
Sat, 7 Nov 2020
[ 13:47 jwb search for other commits by this committer ] Original commit   Revision:554390
biology/bowtie2: Upgrade to 2.4.2

Minor bug fix release

Reported by:    portscout
Fri, 17 Jul 2020
[ 10:12 martymac search for other commits by this committer ] Original commit   Revision:542423 (Only the first 10 of 37 ports in this commit are shown above. View all ports for this commit)
Update devel/tbb to 2020.3 and bump dependent ports' revisions

Changelog: https://github.com/oneapi-src/oneTBB/blob/v2020.3/CHANGES
Wed, 1 Apr 2020
[ 14:14 martymac search for other commits by this committer ] Original commit   Revision:530219 (Only the first 10 of 34 ports in this commit are shown above. View all ports for this commit)
Update devel/tbb to 2020.2 and bump dependent port's revisions

Changelog: https://github.com/oneapi-src/oneTBB/blob/tbb_2020/CHANGES
Sun, 1 Mar 2020
[ 16:01 jwb search for other commits by this committer ] Original commit   Revision:527560
biology/bowtie2: Upgrade to 2.4.1

Numerous bugfixes and enhancements
Enable experimental support for aarch64

Reported by:    portscout
Thu, 26 Dec 2019
[ 16:25 martymac search for other commits by this committer ] Original commit   Revision:520935 (Only the first 10 of 34 ports in this commit are shown above. View all ports for this commit)
Update devel/tbb to 2020.0 and bump dependent ports' revisions [1]

Also, while here, re-generate patches using the makepatch target

[1] Changelog: https://github.com/intel/tbb/blob/v2020.0/CHANGES
Wed, 25 Sep 2019
[ 10:03 martymac search for other commits by this committer ] Original commit   Revision:512777 (Only the first 10 of 24 ports in this commit are shown above. View all ports for this commit)
Update devel/tbb to 2019.8 and bump dependent ports' revisions

Changelog: https://github.com/intel/tbb/blob/tbb_2019/CHANGES
Wed, 24 Apr 2019
[ 17:41 jwb search for other commits by this committer ] Original commit   Revision:499873
biology/bowtie2: Clarify CPU-specificity
Sun, 21 Apr 2019
[ 15:23 jwb search for other commits by this committer ] Original commit   Revision:499544
biology/bowtie2: Upgrade to 2.3.5.1

Disable aarch64.  Upstream support has changed and I lack the resources
to develop new patches.
Fri, 29 Mar 2019
[ 22:13 linimon search for other commits by this committer ] Original commit   Revision:497212
Mark as broken on aarch64:

  usage: dirname string [...]

My guess is that some parameter is being passed the empty string.

Approved by:	portmgr (tier-2 blanket)
Mon, 18 Mar 2019
[ 17:30 jwb search for other commits by this committer ] Original commit   Revision:496155
biology/bowtie2: Upgrade to 2.3.5

-   Add bowtie2-test script
-   Separate Makefile patches into a static patch for upstream and reinplace
    for ports-specifics
-   Allow aarch64 per upstream Makefile (untested)
Thu, 11 Oct 2018
[ 14:47 martymac search for other commits by this committer ] Original commit   Revision:481833 (Only the first 10 of 17 ports in this commit are shown above. View all ports for this commit)
Update devel/tbb to version 2019.1 and bump dependent ports' revisions

Also, reintegrate HTML documentation that was removed in previous version.
Thu, 4 Oct 2018
[ 10:03 martymac search for other commits by this committer ] Original commit   Revision:481215 (Only the first 10 of 19 ports in this commit are shown above. View all ports for this commit)
Update devel/tbb to version 2019 and bump dependent port's revisions
Thu, 30 Nov 2017
[ 02:59 jwb search for other commits by this committer ] Original commit   Revision:455161
biology/bowtie2: Upgrade to 2.3.3.1

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13300
Sun, 17 Sep 2017
[ 07:03 martymac search for other commits by this committer ] Original commit   Revision:449986
Update tbb to 2018 and bump dependent ports' revisions
Tue, 7 Mar 2017
[ 12:44 martymac search for other commits by this committer ] Original commit   Revision:435599
Update devel/tbb to 2017.5

Also bring the following changes:
- Fetch distfiles from Github
- Bump dependent ports' PORTREVISIONs
Mon, 27 Feb 2017
[ 14:08 jbeich search for other commits by this committer ] Original commit   Revision:434940
biology/bowtie2: update to 2.3.0

- Unbreak with Clang 4.0

Changes:	https://github.com/BenLangmead/bowtie2/releases/tag/v2.3.0
PR:		216619
Submitted by:	Jason Bacon <bacon4000@gmail.com> (maintainer)
Tue, 20 Dec 2016
[ 17:01 jrm search for other commits by this committer ] Original commit   Revision:429003
biology/bowtie2: Update to version 2.2.9

- Update license information.
- Add python to USES (bowtie2-build bowtie2-inspect need python)
- Add DOCS and EXAMPLES options

Approved by:	AMDmi3 (mentor) swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8182
Fri, 13 May 2016
[ 20:12 pi search for other commits by this committer ] Original commit   Revision:415148
biology/bowtie2: 2.2.7 -> 2.2.8

- Various website updates
- Fixed the bowtie2-build issue that made TBB compilation fail

PR:		208943
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	Jason Bacon <bacon4000@gmail.com> (maintainer)
Wed, 23 Mar 2016
[ 11:22 rakuco search for other commits by this committer ] Original commit   Revision:411698
New port: biology/bowtie2.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.

This is Bowtie version 2, which will need to coexists with Bowtie 1 for the
foreseeable future. Both are required by certain genomics pipelines, in some
cases (e.g. Trinity) by the same pipeline.

WWW: https://github.com/BenLangmead/bowtie2

PR:		207908
Submitted by:	Jason Bacon <bacon4000@gmail.com>

Number of commits found: 33