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Port details
gemma Genome-wide Efficient Mixed Model Association
0.98.3_4 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_4Version 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: 2023-12-12 19:03:50
Commit Hash: ab17137
License: GPLv3
WWW:
https://github.com/genetics-statistics/GEMMA
Description:
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.
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 (26 items)
Collapse this list.
  1. /usr/local/share/licenses/gemma-0.98.3_4/catalog.mk
  2. /usr/local/share/licenses/gemma-0.98.3_4/LICENSE
  3. /usr/local/share/licenses/gemma-0.98.3_4/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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: gemma
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1609514940 SHA256 (genetics-statistics-GEMMA-0.98.3_GH0.tar.gz) = 8c27874634269f52a194a41048e70c17e2128563f56bb8ef59338a93147c61ba SIZE (genetics-statistics-GEMMA-0.98.3_GH0.tar.gz) = 49572695

Packages (timestamps in pop-ups are UTC):
gemma
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.98.3_40.98.3_4-0.98.3_40.98.3_4---
FreeBSD:13:quarterly0.98.3_40.98.3_4-0.98.3_40.98.3_4-0.98.3_4-
FreeBSD:14:latest0.98.3_40.98.3_4-0.98.3_40.98.3_4---
FreeBSD:14:quarterly0.98.3_40.98.3_4-0.98.3_40.98.3_4-0.98.3_4-
FreeBSD:15:latest0.98.3_40.98.3_4n/a0.98.3_4n/a-0.98.3_40.98.3_4
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. 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:
===> The following configuration options are available for gemma-0.98.3_4: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
biology_gemma
USES:
blaslapack:openblas compiler:c++11-lang eigen:3 gmake localbase:ldflags
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: 18

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.98.3_4
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
0.98.3_3
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)
0.98.3_2
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)
0.98.3_2
12 Jan 2022 19:41:22
commit hash: 654acd81409d31495f8b1b11db61e1afbf640981commit hash: 654acd81409d31495f8b1b11db61e1afbf640981commit hash: 654acd81409d31495f8b1b11db61e1afbf640981commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
math/gsl: bump portrevision of consumers after update to 2.7.1

PR:		260201
0.98.3_1
16 Jun 2021 19:31:27
commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e files touched by this commit
Tobias C. Berner (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)
0.98.3
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
0.98.3
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.
0.98.3
02 Jan 2021 22:05:58
Revision:559975Original commit files touched by this commit
jwb search for other commits by this committer
biology/gemma: Upgrade to 0.98.3

Minor bug fixes and enhancements

Reported by:    portscout
0.98.1_6
12 Dec 2020 17:04:37
Revision:557839Original commit files touched by this commit
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
0.98.1_5
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
0.98.1_4
30 Jan 2020 14:17:44
Revision:524642Original commit files touched by this commit
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
0.98.1_3
21 Jan 2020 22:03:19
Revision:523749Original commit files touched by this commit
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)
0.98.1_3
14 Jan 2020 22:35:36
Revision:523074Original commit files touched by this commit
jwb search for other commits by this committer
biology/gemma: Unbreak build

Conflict between cblas.h and gsl_cblas.h
0.98.1_2
25 Oct 2019 23:41:34
Revision:515671Original commit files touched by this commit
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
0.98.1_1
26 Jul 2019 20:46:57
Revision:507372Original 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
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
0.98.1
18 May 2019 22:41:16
Revision:501990Original commit files touched by this commit
jwb search for other commits by this committer
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC

Reported by:    danfe, Gerald Pfeifer
0.98.1
17 May 2019 14:45:20
Revision:501873Original commit files touched by this commit
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: 18