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Port details
plink Whole genome association analysis toolset
1.90.b6.17_3 biology 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 1.90.b6.17_3Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: 2012-09-27 10:00:09
Last Update: 2023-12-31 00:37:05
Commit Hash: bbab7f5
License: GPLv3
WWW:
https://www.cog-genomics.org/plink/
Description:
PLINK is a widely used toolset for genome-wide association studies (GWAS) and research in population genetics. Citation: Chang et al. (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4(1) doi:10.1186/s13742-015-0047-8
Homepage    cgit ¦ Codeberg ¦ 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 (10 items)
Collapse this list.
  1. /usr/local/share/licenses/plink-1.90.b6.17_3/catalog.mk
  2. /usr/local/share/licenses/plink-1.90.b6.17_3/LICENSE
  3. /usr/local/share/licenses/plink-1.90.b6.17_3/GPLv3
  4. bin/plink
  5. bin/prettify
  6. share/examples/plink/toy.map
  7. share/examples/plink/toy.ped
  8. @owner
  9. @group
  10. @mode
Collapse this list.
Dependency lines:
  • plink>0:biology/plink
Conflicts:
CONFLICTS_INSTALL:
  • putty
  • putty-nogtk
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/plink/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/plink
  • pkg install plink
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: plink
Flavors: there is no flavor information for this port.
NOT_FOR_ARCHS: aarch64 mips64 powerpc64 powerpc64le
distinfo:
TIMESTAMP = 1588630386 SHA256 (chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz) = 1207dcabb4bf3f3f4ec5b0e4e5d66ec14075e2cd6d45dd318f13dfb8b4e57116 SIZE (chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz) = 3013121

Packages (timestamps in pop-ups are UTC):
plink
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-1.90.b6.17_31.90.b6.17_11.90.b6.17_31.90.b6.17_3---
FreeBSD:13:quarterly-1.90.b6.17_3-1.90.b6.17_31.90.b6.17_3---
FreeBSD:14:latest-1.90.b6.17_3-1.90.b6.17_31.90.b6.17_3---
FreeBSD:14:quarterly-1.90.b6.17_3-1.90.b6.17_31.90.b6.17_3---
FreeBSD:15:latest-1.90.b6.17_3n/a1.90.b6.17_3n/a---
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. gfortran12 : lang/gcc12
  3. as : devel/binutils
Runtime dependencies:
  1. gfortran12 : lang/gcc12
Library dependencies:
  1. libopenblas.so : math/openblas
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for plink-1.90.b6.17_3: EXAMPLES=on: Build and/or install examples ====> BLAS/LAPACK implementation: you have to select exactly one of them NETLIB=off: Netlib's reference OPENBLAS=on: OpenBLAS BLAS implementation ===> Use 'make config' to modify these settings
Options name:
biology_plink
USES:
gmake fortran blaslapack:openblas
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/chrchang/plink-ng/tar.gz/79b2df8c?dummy=/
Collapse this list.

Number of commits found: 30

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.90.b6.17_3
31 Dec 2023 00:37:05
commit hash: bbab7f59e9630416397189df70ec133bdd690e38commit hash: bbab7f59e9630416397189df70ec133bdd690e38commit hash: bbab7f59e9630416397189df70ec133bdd690e38commit hash: bbab7f59e9630416397189df70ec133bdd690e38 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree

- 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
1.90.b6.17_3
12 Dec 2023 19:03:50
commit hash: ab1713728d621e7b57d276ef27de37a8754e6ee0commit hash: ab1713728d621e7b57d276ef27de37a8754e6ee0commit hash: ab1713728d621e7b57d276ef27de37a8754e6ee0commit hash: ab1713728d621e7b57d276ef27de37a8754e6ee0 files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
*/*: bump PORTREVISION after the upgrade of OpenBLAS

PR:		273219
1.90.b6.17_2
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.90.b6.17_1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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)
1.90.b6.17_1
06 Feb 2022 18:36:07
commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
1.90.b6.17_1
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
1.90.b6.17_1
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.90.b6.17_1
27 Sep 2020 07:44:15
Revision:550249Original commit files touched by this commit
linimon search for other commits by this committer
Allow building on powerpc64le.

Approved by:	portmgr (tier-2 blanket)
1.90.b6.17_1
06 May 2020 16:39:12
Revision:534190Original commit files touched by this commit
yuri search for other commits by this committer
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas
because after the recent math/openblas update the library name changed in
openblas
1.90.b6.17
04 May 2020 23:01:58
Revision:533993Original commit files touched by this commit
jwb search for other commits by this committer
biology/plink: Whole genome association analysis toolset

Reversed removal, commit r471892 2018/06/07
Upgraded to 1.90 beta 6.17

PR:             ports/243733
Submitted by:   mzaki@e-mail.ne.jp
1.07_8
07 Jun 2018 00:34:18
Revision:471892Original commit files touched by this commit
rene search for other commits by this committer
Remove expired ports:
2018-06-06 biology/ssaha: Broken for more than 6 months
2018-06-06 biology/crux: Broken for more than 6 months
2018-06-06 biology/ariadne: Broken for more than 6 months
2018-06-06 cad/sceptre: Broken for more than 6 months
2018-06-06 cad/cider: Broken for more than 6 months
2018-06-06 chinese/scim-array: Broken for more than 6 months
2018-06-06 chinese/xpdf: Broken for more than 6 months
2018-06-06 chinese/telnet: Broken for more than 6 months
2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring
comms/java-commapi
2018-06-06 comms/soundmodem: Broken for more than 6 months
2018-06-06 comms/jsdr: Broken for more than 6 months
2018-06-06 comms/java-commapi: Broken for more than 6 months
2018-06-06 converters/pdf2djvu: Broken for more than 6 months
2018-06-06 databases/rdb: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.07_8
05 May 2018 10:49:36
Revision:469100Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
1.07_8
10 Mar 2018 17:46:06
Revision:464084Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
1.07_7
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
1.07_7
13 Oct 2017 11:14:53
Revision:451982Original commit files touched by this commit Sanity Test Failure
bapt search for other commits by this committer
Mark as broken ports with no public distfiles
1.07_7
10 Sep 2017 20:55:39
Revision:449591Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
1.07_6
01 Apr 2017 15:23:32
Revision:437439Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
1.07_5
07 Dec 2016 13:24:57
Revision:428057Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.

The first part covered  ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.

This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.

PR:		214965
Reported by:	thierry
1.07_4
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
1.07_4
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
1.07_4
10 Sep 2014 20:50:37
Revision:367888Original commit files touched by this commit
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
1.07_3
10 Mar 2014 20:55:22
Revision:347809Original commit files touched by this commit
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
1.07_2
07 Mar 2014 15:52:40
Revision:347402Original commit files touched by this commit
bapt search for other commits by this committer
Convert b* to USES=zip
1.07_2
16 Feb 2014 17:15:32
Revision:344614Original commit files touched by this commit
tijl search for other commits by this committer
Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes".  In most cases
USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)
1.07_1
13 Dec 2013 09:34:40
Revision:336328Original commit files touched by this commit
gerald search for other commits by this committer
Fix the build with more standards-compliant compilers such as GCC 4.7. [1]

On the way replace USE_GMAKE by USES=gmake.

PR:		184566 [1], 182136
Submitted by:	Christoph Moench-Tegeder <cmt@burggraben.net> [1]
Approved by:	maintainer (Jason Bacon <jwbacon@tds.net>) [1]
1.07_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
1.07_1
26 Oct 2013 00:52:36
Revision:331644Original commit files touched by this commit
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.07
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)
1.07
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: 30