Current status

plink Whole genome association analysis toolset

1.90.b6.17_1 biology =0 1.90.b6.17_1Version of this port present on the latest quarterly branch.

Maintainer: mzaki@e-mail.ne.jp

Port Added: 2012-09-27 10:00:09

Last Update: 2020-09-27 08:44:15

SVN Revision: 550249

License: GPLv3

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 WWW: https://www.cog-genomics.org/plink/

SVNWeb : Homepage

pkg-plist: as obtained via: make generate-plist

Expand this list (10 items)

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1. /usr/local/share/licenses/plink-1.90.b6.17_1/catalog.mk
2. /usr/local/share/licenses/plink-1.90.b6.17_1/LICENSE
3. /usr/local/share/licenses/plink-1.90.b6.17_1/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

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• plink>0:biology/plink

To install the port: cd /usr/ports/biology/plink/ && make install clean

To add the package: pkg install plink

PKGNAME: plink

Flavors: there is no flavor information for this port.

NOT_FOR_ARCHS: aarch64 mips64 powerpc64 powerpc64le sparc64

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

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. gfortran9 : lang/gcc9
3. as : devel/binutils

Runtime dependencies:

1. gfortran9 : lang/gcc9

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_1: 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

USES:

gmake fortran blaslapack:openblas

Master Sites:

Expand this list (1 items)

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1. https://codeload.github.com/chrchang/plink-ng/tar.gz/79b2df8c?dummy=/
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Allow building on powerpc64le.

Approved by:	portmgr (tier-2 blanket)

Bump 37 ports depending on math/openblas through USES=blaslapack:openblas
because after the recent math/openblas update the library name changed in
openblas

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

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

Deprecate ports broken for more than 6 months

Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).

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

Mark as broken ports with no public distfiles

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

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

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

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493

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)

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)

Convert b* to USES=zip

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)

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]

In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology

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

Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)

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>

16 vulnerabilities affecting 115 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2021-02-23 14:01:53