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Port details
gemma Genome-wide Efficient Mixed Model Association
0.98.3_1 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 0.98.3_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-17 14:45:38
Last Update: 2021-06-16 19:31:27
Commit Hash: 63e653a
License: GPLv3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (26 items)
Collapse this list.
  1. /usr/local/share/licenses/gemma-0.98.3_1/catalog.mk
  2. /usr/local/share/licenses/gemma-0.98.3_1/LICENSE
  3. /usr/local/share/licenses/gemma-0.98.3_1/GPLv3
  4. bin/gemma
  5. share/examples/gemma/BXD_covariates.txt
  6. share/examples/gemma/BXD_covariates2.txt
  7. share/examples/gemma/BXD_geno.txt.gz
  8. share/examples/gemma/BXD_pheno.txt
  9. share/examples/gemma/BXD_snps.txt
  10. share/examples/gemma/HLC.bed
  11. share/examples/gemma/HLC.bim
  12. share/examples/gemma/HLC.fam
  13. share/examples/gemma/HLC.simu.pheno.txt
  14. share/examples/gemma/HLC_covariates.txt
  15. share/examples/gemma/demo.txt
  16. share/examples/gemma/mouse_hs1940.anno.txt
  17. share/examples/gemma/mouse_hs1940.bed
  18. share/examples/gemma/mouse_hs1940.bim
  19. share/examples/gemma/mouse_hs1940.fam
  20. share/examples/gemma/mouse_hs1940.geno.txt.gz
  21. share/examples/gemma/mouse_hs1940.pheno.txt
  22. share/examples/gemma/mouse_hs1940_snps.txt
  23. share/examples/gemma/mouse_hs1940_snps_anno.txt
  24. @owner
  25. @group
  26. @mode
Collapse this list.
Dependency lines:
  • gemma>0:biology/gemma
To install the port: cd /usr/ports/biology/gemma/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/gemma
  • pkg install gemma
PKGNAME: gemma
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
gemma
ABIlatestquarterly
FreeBSD:11:aarch64-0.98.1_5
FreeBSD:11:amd640.98.3_10.98.3_1
FreeBSD:11:armv6--
FreeBSD:11:i3860.98.3_10.98.3_1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-0.98.3_1
FreeBSD:12:amd640.98.3_10.98.3_1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.98.3_10.98.3_1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-0.98.3
FreeBSD:13:aarch640.98.30.98.3_1
FreeBSD:13:amd640.98.3_10.98.3_1
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3860.98.3_10.98.3_1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch640.98.3_1-
FreeBSD:14:amd640.98.3_1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3860.98.3_1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc640.98.3-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. eigen3.pc : math/eigen3
  2. gmake>=4.3 : devel/gmake
Library dependencies:
  1. libgsl.so : math/gsl
  2. libopenblas.so : math/openblas
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/genetics-statistics/GEMMA/tar.gz/0.98.3?dummy=/
Collapse this list.

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Jun 2021 19:31:27
 files touched by this commit commit hash:63e653adaa7493aa98f17f9fbc834c0aed7e096e  0.98.3_1
tcberner search for other commits by this committer
math/gsl: update to 2.7

From [1]

* What is new in gsl-2.7:
	* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
	* fixed bug #60335 (spmatrix test failure, J. Lamb)
	* fixed bug #36577
	* clarified documentation on interpolation accelerators (V. Krishnan)
	* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M.
Sitte)
	* fixed doc bug #59758
	* fixed bug #58202 (rstat median for n=5)
	* added support for native C complex number types in gsl_complex
	   when using a C11 compiler
	* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6
(Only the first 15 lines of the commit message are shown above View all of this commit message)
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  0.98.3
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  0.98.3
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
02 Jan 2021 22:05:58
Original commit files touched by this commit Revision:559975  0.98.3
jwb search for other commits by this committer
biology/gemma: Upgrade to 0.98.3

Minor bug fixes and enhancements

Reported by:    portscout
12 Dec 2020 17:04:37
Original commit files touched by this commit Revision:557839  0.98.1_6
thierry search for other commits by this committer
- Upgrade math/eigen3 to 3.3.8;

- Add some dependencies which might be detected by Find_Package but not
registered;

- Bump PORTREVISION of consumers.

PR:		250833
Submitted by:	/me
Approved by:	tcberner@ (KDE / maintainer) + exp-run
06 May 2020 16:39:12
Original commit files touched by this commit Revision:534190  0.98.1_5
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
30 Jan 2020 14:17:44
Original commit files touched by this commit Revision:524642  0.98.1_4
swills search for other commits by this committer
Fix math/openblas and bump dependent ports

* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]

This is correcting issues from r523749 [1][2][4] and r515970 [3]

PR:		231371
Reported by:	build cluster [1]
Reported by:	Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by:	many [5]
Reviewed by:	mat, bapt
Approved by:	implicit, since this is a build fix
21 Jan 2020 22:03:19
Original commit files touched by this commit Revision:523749  0.98.1_3
swills search for other commits by this committer
math/openblas: Update to 0.3.7

While here, improve formatting and fix build of dependant ports.

PR:		231371
Submitted by:	yuri (initial version), pkubaj (ppc fixes)
Approved by:	Eijiro Shibusawa <phd_kimberlite@yahoo.co.jp> (maintainer)
14 Jan 2020 22:35:36
Original commit files touched by this commit Revision:523074  0.98.1_3
jwb search for other commits by this committer
biology/gemma: Unbreak build

Conflict between cblas.h and gsl_cblas.h
25 Oct 2019 23:41:34
Original commit files touched by this commit Revision:515671  0.98.1_2
tcberner search for other commits by this committer
math/gsl: update to 2.6

- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  0.98.1_1
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

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, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
18 May 2019 22:41:16
Original commit files touched by this commit Revision:501990  0.98.1
jwb search for other commits by this committer
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC

Reported by:    danfe, Gerald Pfeifer
17 May 2019 14:45:20
Original commit files touched by this commit Revision:501873  0.98.1
jwb search for other commits by this committer
biology/gemma: Genome-wide Efficient Mixed Model Association

GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
and related models to genome-wide association studies (GWAS) and other
large-scale data sets.

Number of commits found: 13