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Port details
plinkseq Toolset for working with human genetic variation data
0.10_1 biology Deleted on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.10_1Version of this port present on the latest quarterly branch.
Broken BROKEN: unfetchable
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2020-05-05
Ignore IGNORE: is marked as broken: unfetchable
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2012-09-27 10:00:09
Last Update: 2020-05-05 15:38:12
SVN Revision: 534093
Also Listed In: science
License: GPLv2
WWW:
http://atgu.mgh.harvard.edu/plinkseq/
Description:
PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package. WWW: http://atgu.mgh.harvard.edu/plinkseq/
Homepage    cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (13 items)
Collapse this list.
  1. /usr/local/share/licenses/plinkseq-0.10_1/catalog.mk
  2. /usr/local/share/licenses/plinkseq-0.10_1/LICENSE
  3. /usr/local/share/licenses/plinkseq-0.10_1/GPLv2
  4. bin/behead
  5. bin/browser
  6. bin/gcol
  7. bin/mm
  8. bin/mongoose
  9. bin/pdas
  10. bin/pseq
  11. bin/smp
  12. bin/tab2vcf
  13. lib/libplinkseq.a
Collapse this list.
Dependency lines:
  • plinkseq>0:biology/plinkseq
No installation instructions:
This port has been deleted.
PKGNAME: plinkseq
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (plinkseq-src-0.10.tgz) = e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58 SIZE (plinkseq-src-0.10.tgz) = 6090698

No package information for this port in our database
Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link: pkg-fallout
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
N/A
USES:
libtool gmake
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/
Collapse this list.

Number of commits found: 19

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.10_1
05 May 2020 15:38:12
Revision:534093Original commit files touched by this commit
rene search for other commits by this committer
Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.10_1
04 Apr 2020 20:51:41
Revision:530719Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
0.10_1
06 Nov 2019 12:48:32
Revision:516880Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
0.10_1
31 Jan 2018 01:07:08
Revision:460452Original commit files touched by this commit
jwb search for other commits by this committer
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128
0.10_1
13 May 2017 03:35:51
Revision:440746Original commit files touched by this commit
linimon search for other commits by this committer
Mark some ports failing on power64.  In cases where the error message
was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
0.10_1
27 Feb 2017 14:09:25
Revision:434941Original commit files touched by this commit
jbeich search for other commits by this committer
biology/plinkseq: unbreak with clang 4.0

PR:		216618
Submitted by:	Jason Bacon <bacon4000@gmail.com> (maintainer)
0.10
11 Nov 2016 09:31:03
Revision:425879Original commit files touched by this commit
linimon search for other commits by this committer
Mark various leaf ports broken on aarch64, and, where appropriate, other
tier-2 archs.

Approved by:	portmgr (tier-2 blanket)
0.10
21 Apr 2016 16:43:15
Revision:413746Original commit files touched by this commit
swills search for other commits by this committer
many ports: mark broken on powerpc64
0.10
11 Dec 2015 08:48:57
Revision:403506Original commit files touched by this commit
miwi search for other commits by this committer
- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
0.10
12 Oct 2014 03:16:10
Revision:370680Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.10

PR:		194309
Submitted by:	jwbacon@tds.net(maintainer)
0.08_3
04 Oct 2014 15:12:45
Revision:369969Original commit files touched by this commit
sunpoet search for other commits by this committer
- Update to 2.6.0
- Update MASTER_SITES
- Add my LOCAL to MASTER_SITES
- Use USE_CSTD
- Use MAKE_CMD
- Reformat pkg-descr
- Update WWW
- Take maintainership
- Bump PORTREVISION for devel/protobuf shlib change

Changes:	https://code.google.com/p/protobuf/source/browse/trunk/CHANGES.txt
0.08_2
22 Jul 2014 22:12:15
Revision:362596Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Switch to USES=libtool, drop .la files
- Fix shebangs

Approved by:	portmgr blanket
0.08_1
07 Mar 2014 11:37:35
Revision:347367Original commit files touched by this commit
bapt search for other commits by this committer
Convert to dos2unix
0.08_1
31 Jan 2014 12:33:12
Revision:341988Original commit files touched by this commit
miwi search for other commits by this committer
- Stage support
0.08_1
11 Dec 2013 14:43:51
Revision:336171Original commit files touched by this commit
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
0.08_1
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
0.08_1
21 Mar 2013 14:09:23
Revision:314843Original commit files touched by this commit
vanilla search for other commits by this committer
Fix build with protobuf-2.5.0

Obtained from:	miwi@
0.08_1
18 Mar 2013 15:14:28
Revision:314580Original commit files touched by this commit
vanilla search for other commits by this committer
1: Upgrade protobuf to 2.5.0.
2: bump revision.
3: document UPDATING.
0.08
27 Sep 2012 09:59:25
Revision:304954Original commit files touched by this commit
makc search for other commits by this committer
Add new ports biology/plink [1] and biology/plinkseq [2]:

PLINK is a free, open-source whole genome association analysis toolset.
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data.

PR:		ports/171918 [1]
PR:		ports/171922 [2]
Submitted by:	Jason Bacon <jwbacon at tds.net>

Number of commits found: 19