notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details
gcta Genome-wide Complex Trait Analysis
1.94.1_2 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 1.94.1_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-04-15 15:22:11
Last Update: 2024-06-21 17:49:24
Commit Hash: e2cd113
License: GPLv3
WWW:
https://cnsgenomics.com/software/gcta/index.html
Description:
GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.
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 (5 items)
Collapse this list.
  1. bin/gcta64
  2. bin/gcta
  3. /usr/local/share/licenses/gcta-1.94.1_2/catalog.mk
  4. /usr/local/share/licenses/gcta-1.94.1_2/LICENSE
  5. /usr/local/share/licenses/gcta-1.94.1_2/GPLv3
Collapse this list.
Dependency lines:
  • gcta>0:biology/gcta
To install the port:
cd /usr/ports/biology/gcta/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/gcta
  • pkg install gcta
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: gcta
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1716931486 SHA256 (jianyangqt-gcta-v1.94.1_GH0.tar.gz) = 88400bf4ead6598587dfc7b99159cf008e616c7433512adbc8a0fdeab1f747ce SIZE (jianyangqt-gcta-v1.94.1_GH0.tar.gz) = 49152

Expand this list (2 items)

Collapse this list.

SHA256 (zhilizheng-plink-ng-3744540_GH0.tar.gz) = dfa4879bc6bcbe24411451748c7c5dc803e42cafa55b008134f0d123cd933222 SIZE (zhilizheng-plink-ng-3744540_GH0.tar.gz) = 3222588

Collapse this list.


Packages (timestamps in pop-ups are UTC):
gcta
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--------
FreeBSD:13:quarterly-1.94.1_1--1.94.1_1-1.94.1_1-
FreeBSD:14:latest--------
FreeBSD:14:quarterly-1.94.1_1--1.94.1_1-1.94.1_1-
FreeBSD:15:latest--n/a-n/a-1.94.1_11.94.1_1
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. boost-libs>0 : devel/boost-libs
  2. spectra>0 : math/spectra
  3. cmake : devel/cmake-core
  4. ninja : devel/ninja
  5. eigen3.pc : math/eigen3
Library dependencies:
  1. libgsl.so : math/gsl
  2. libopenblas.so : math/openblas
  3. libsqlite3.so : databases/sqlite3
  4. libzstd.so : archivers/zstd
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_gcta
USES:
cmake eigen:3 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/jianyangqt/gcta/tar.gz/v1.94.1?dummy=/
Collapse this list.

Number of commits found: 16

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.94.1_2
21 Jun 2024 17:49:24
commit hash: e2cd1133e68c54606b2b5e0c7b4dee0532a926fecommit hash: e2cd1133e68c54606b2b5e0c7b4dee0532a926fecommit hash: e2cd1133e68c54606b2b5e0c7b4dee0532a926fecommit hash: e2cd1133e68c54606b2b5e0c7b4dee0532a926fe files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
*/*: bump PORTREVISION after the upgrade to OpenBLAS
1.94.1_1
28 May 2024 21:26:06
commit hash: 3bf602d2a7d0bc83686fe197fa71ae7d089b63d0commit hash: 3bf602d2a7d0bc83686fe197fa71ae7d089b63d0commit hash: 3bf602d2a7d0bc83686fe197fa71ae7d089b63d0commit hash: 3bf602d2a7d0bc83686fe197fa71ae7d089b63d0 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/gcta: Unbreak build on 14.x aarch64

Missing #include <cstdint> in a few files

Reported by:    pkg-fallout
1.94.1_1
12 Dec 2023 19:03:50
commit hash: 22df0dbcfa877e85bf5c29d7ff6808f7116cafb7commit hash: 22df0dbcfa877e85bf5c29d7ff6808f7116cafb7commit hash: 22df0dbcfa877e85bf5c29d7ff6808f7116cafb7commit hash: 22df0dbcfa877e85bf5c29d7ff6808f7116cafb7 files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
Author: Eijiro Shibusawa
biology/gcta: chase the upgrade of OpenBLAS

GCTA should modify the LAPACK functios calls, this is a temporary fix.

See <https://github.com/jianyangqt/gcta/issues/59>.

PR:		273219
Approved by:	jwb@
1.94.1
15 Oct 2023 11:49:05
commit hash: f95880107ae1f12e660b08f24dacb3b88bf176bdcommit hash: f95880107ae1f12e660b08f24dacb3b88bf176bdcommit hash: f95880107ae1f12e660b08f24dacb3b88bf176bdcommit hash: f95880107ae1f12e660b08f24dacb3b88bf176bd files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/gcta: Add temporary hack for building on aarch64

Add USE_GCC to work around this issue with clang:

/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/ \
    plink2_base.h:1008:23: error: argument to '__builtin_neon_vshrq_n_v' \
    must be a constant integer
return R_CAST(VecW, _mm_srli_epi64(R_CAST(__m128i, vv), ct));
/usr/lib/clang/14.0.5/include/arm_neon.h:25260:24: note: expanded from \
    macro 'vshrq_n_u64'
__ret = (uint64x2_t) __builtin_neon_vshrq_n_v((int8x16_t)__s0, __p1, 51);
1.94.1
14 Oct 2023 12:52:46
commit hash: 9d8c5cb3ebf27b3f044cc0755dcc71727e1261becommit hash: 9d8c5cb3ebf27b3f044cc0755dcc71727e1261becommit hash: 9d8c5cb3ebf27b3f044cc0755dcc71727e1261becommit hash: 9d8c5cb3ebf27b3f044cc0755dcc71727e1261be files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/gcta: Update to 1.94.1

Too many changes since v1.26 to list here
Changes: https://yanglab.westlake.edu.cn/software/gcta/#Download

Reported by:    pkg-fallout
1.26.0_4
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)
1.26.0_3
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)
1.26.0_3
06 Jul 2022 20:40:04
commit hash: 5fa506511af383c8b1a2f49f861df31966d32493commit hash: 5fa506511af383c8b1a2f49f861df31966d32493commit hash: 5fa506511af383c8b1a2f49f861df31966d32493commit hash: 5fa506511af383c8b1a2f49f861df31966d32493 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/gcta: Use bundled version of eigen3

... in preparation to upgrading math/eigen to 3.4.0.

This version of gcta (1.26.0) doesn't support eigen-3.4.0, and
it can't be upgraded because latest versions of gcta use
Intel's closed source MKL library.

PR:		265032
Suggested by:	tcberner@
Approved by:	portmgr (interoperability)
1.26.0_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
1.26.0_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.
1.26.0_3
11 Jan 2021 17:09:38
Revision:561231Original commit files touched by this commit
jwb search for other commits by this committer
biology/gcta: Drop dependency on gcc

Replace compiler:openmp with compiler:c++11-lang
Clang build also requires localbase:ldflags
Build tested on amd64, i386 and powerpc64 12.x-RELEASE

PR:             port/247753, ports/252379
1.26.0_2
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
1.26.0_1
08 Nov 2020 14:31:00
Revision:554467Original commit files touched by this commit
jwb search for other commits by this committer
biology/gcta: Switch eigen3 dep to USES framework

PR:             ports/250949
Reported by:    lbartoletti
1.26.0_1
06 May 2020 16:11:15
Revision:534185Original commit files touched by this commit
yuri search for other commits by this committer
Bump 46 ports depending on math/openblas because the after the recent
math/openblas update the library name changed in openblas.
1.26.0
15 Apr 2020 15:22:04
Revision:531770Original commit files touched by this commit
jwb search for other commits by this committer
biology/gcta: Genome-wide Complex Trait Analysis

GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate
the proportion of phenotypic variance explained by genome- or chromosome-wide
SNPs for complex traits (the GREML method), and has subsequently extended for
many other analyses to better understand the genetic architecture of complex
traits.

Number of commits found: 16