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Current status

The server has been repaired, with a new power supply, for $23. I am waiting for lower COVID rates before visiting the datacenter to return it.
non port: biology/bowtie2/Makefile
SVNWeb

Number of commits found: 26

Sun, 18 Apr 2021
[ 15:53 jwb (Jason W. Bacon) ]    commit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6d  48ddc73 
biology/bowtie2: Add support for powerpc64le

PR:             255092
Submitted by:   pkubaj
Wed, 14 Apr 2021
[ 10:08 martymac (Ganael LAPLANCHE) ]    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 mat (Mathieu Arnold) ]    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 mat (Mathieu Arnold) ]    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 ] 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 ] Original commit   Revision:563428
biology/bowtie2: Reverse switch to devel/onetbb

Mistakenly believed onetbb was already committed

PR:             252683
[ 17:39 jwb ] Original commit   Revision:563427
biology/bowtie2: Switch to devel/onetbb

PR:             252683
Submitted by:   martymac
Sat, 7 Nov 2020
[ 13:47 jwb ] 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 ] 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 ] 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 ] 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 ] 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 ] 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 ] Original commit   Revision:499873
biology/bowtie2: Clarify CPU-specificity
Sun, 21 Apr 2019
[ 15:23 jwb ] 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 ] 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 ] 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 ] 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 ] 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 ] 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 ] Original commit   Revision:449986
Update tbb to 2018 and bump dependent ports' revisions
Tue, 7 Mar 2017
[ 12:44 martymac ] 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 ] 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 ] 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 ] 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 ] 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: 26