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SVNWeb
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Number of commits found: 33 |
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Sat, 21 Jan 2023
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[ 22:30 Jason W. Bacon (jwb)  ]    65ce3f1
biology/bowtie2: Update to 2.5.1
A few minor fixes and enhancements
Changes: https://github.com/BenLangmead/bowtie2/tags
Reported by: portscout
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Fri, 4 Nov 2022
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[ 23:49 Jason W. Bacon (jwb) ] f2f8bd7
biology/bowtie2: Update to 2.5.0
Performance improvements and minor improvements
Changes: https://github.com/BenLangmead/bowtie2/tags
Reported by: portscout
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Wed, 7 Sep 2022
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[ 21:10 Stefan Eßer (se) ] b7f0544 (Only the first 10 of 27931 ports in this commit are shown above.  )
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 )
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Wed, 20 Jul 2022
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[ 14:20 Tobias C. Berner (tcberner) ] 37526bb (Only the first 10 of 82 ports in this commit are shown above. )
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 )
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Fri, 21 Jan 2022
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[ 14:33 Jason W. Bacon (jwb) ] bfdda43
biology/bowtie2: Update to 2.4.5
A few bug fixes
Changes: https://github.com/BenLangmead/bowtie2/tags
Reported by: portscout
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Mon, 24 May 2021
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[ 16:35 Jason W. Bacon (jwb) ] 4521502
biology/bowtie2: Update to 2.4.4
Fix deadlock issue in multithreaded execution
Reported by: portscout
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Mon, 17 May 2021
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[ 23:40 Jason W. Bacon (jwb) ] 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*)
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Sun, 18 Apr 2021
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[ 15:53 Jason W. Bacon (jwb) ] 48ddc73
biology/bowtie2: Add support for powerpc64le
PR: 255092
Submitted by: pkubaj
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Wed, 14 Apr 2021
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[ 10:08 Ganael LAPLANCHE (martymac) ] 9ee8484 (Only the first 10 of 17 ports in this commit are shown above. )
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
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Wed, 7 Apr 2021
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[ 08:09 Mathieu Arnold (mat) ] cf118cc (Only the first 10 of 8873 ports in this commit are shown above. )
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
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Tue, 6 Apr 2021
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[ 14:31 Mathieu Arnold (mat) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
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Fri, 19 Feb 2021
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[ 15:14 martymac ]   (Only the first 10 of 38 ports in this commit are shown above. )
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
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Sat, 30 Jan 2021
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[ 17:43 jwb ]
biology/bowtie2: Reverse switch to devel/onetbb
Mistakenly believed onetbb was already committed
PR: 252683
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[ 17:39 jwb ]
biology/bowtie2: Switch to devel/onetbb
PR: 252683
Submitted by: martymac
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Sat, 7 Nov 2020
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[ 13:47 jwb ]
biology/bowtie2: Upgrade to 2.4.2
Minor bug fix release
Reported by: portscout
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Fri, 17 Jul 2020
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[ 10:12 martymac ] (Only the first 10 of 37 ports in this commit are shown above. )
Update devel/tbb to 2020.3 and bump dependent ports' revisions
Changelog: https://github.com/oneapi-src/oneTBB/blob/v2020.3/CHANGES
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Wed, 1 Apr 2020
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[ 14:14 martymac ] (Only the first 10 of 34 ports in this commit are shown above. )
Update devel/tbb to 2020.2 and bump dependent port's revisions
Changelog: https://github.com/oneapi-src/oneTBB/blob/tbb_2020/CHANGES
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Sun, 1 Mar 2020
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[ 16:01 jwb ]
biology/bowtie2: Upgrade to 2.4.1
Numerous bugfixes and enhancements
Enable experimental support for aarch64
Reported by: portscout
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Thu, 26 Dec 2019
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[ 16:25 martymac ] (Only the first 10 of 34 ports in this commit are shown above. )
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
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Wed, 25 Sep 2019
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[ 10:03 martymac ] (Only the first 10 of 24 ports in this commit are shown above. )
Update devel/tbb to 2019.8 and bump dependent ports' revisions
Changelog: https://github.com/intel/tbb/blob/tbb_2019/CHANGES
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Wed, 24 Apr 2019
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[ 17:41 jwb ]
biology/bowtie2: Clarify CPU-specificity
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Sun, 21 Apr 2019
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[ 15:23 jwb ]
biology/bowtie2: Upgrade to 2.3.5.1
Disable aarch64. Upstream support has changed and I lack the resources
to develop new patches.
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Fri, 29 Mar 2019
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[ 22:13 linimon ]
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)
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Mon, 18 Mar 2019
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[ 17:30 jwb ]
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)
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Thu, 11 Oct 2018
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[ 14:47 martymac ] (Only the first 10 of 17 ports in this commit are shown above. )
Update devel/tbb to version 2019.1 and bump dependent ports' revisions
Also, reintegrate HTML documentation that was removed in previous version.
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Thu, 4 Oct 2018
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[ 10:03 martymac ] (Only the first 10 of 19 ports in this commit are shown above. )
Update devel/tbb to version 2019 and bump dependent port's revisions
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Thu, 30 Nov 2017
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[ 02:59 jwb ]
biology/bowtie2: Upgrade to 2.3.3.1
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D13300
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Sun, 17 Sep 2017
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[ 07:03 martymac ]
Update tbb to 2018 and bump dependent ports' revisions
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Tue, 7 Mar 2017
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[ 12:44 martymac ]
Update devel/tbb to 2017.5
Also bring the following changes:
- Fetch distfiles from Github
- Bump dependent ports' PORTREVISIONs
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Mon, 27 Feb 2017
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[ 14:08 jbeich ]
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)
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Tue, 20 Dec 2016
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[ 17:01 jrm ]
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
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Fri, 13 May 2016
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[ 20:12 pi ]
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)
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Wed, 23 Mar 2016
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[ 11:22 rakuco ]
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>
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Number of commits found: 33 |
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