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Port details
bolt-lmm Mixed model association testing and variance component analysis
2.3.6_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 Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-26 03:37:05
Last Update: 2023-01-16 19:32:07
Commit Hash: e1287d0
License: GPLv3
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (12 items)
Collapse this list.
  1. /usr/local/share/licenses/bolt-lmm-2.3.6_3/catalog.mk
  2. /usr/local/share/licenses/bolt-lmm-2.3.6_3/LICENSE
  3. /usr/local/share/licenses/bolt-lmm-2.3.6_3/GPLv3
  4. bin/bolt
  5. share/bolt-lmm/tables/LDSCORE.1000G_EUR.tab.gz
  6. share/bolt-lmm/tables/genetic_map_hg17_withX.txt.gz
  7. share/bolt-lmm/tables/genetic_map_hg18_withX.txt.gz
  8. share/bolt-lmm/tables/genetic_map_hg19_withX.txt.gz
  9. share/bolt-lmm/tables/genetic_map_hg38_withX.txt.gz
  10. @owner
  11. @group
  12. @mode
Collapse this list.
Dependency lines:
  • bolt-lmm>0:biology/bolt-lmm
Conflicts:
CONFLICTS_INSTALL:
  • rubygem-bolt
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/bolt-lmm/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bolt-lmm
  • pkg install bolt-lmm
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bolt-lmm
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
bolt-lmm
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd642.3.4_42.3.4_4
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3862.3.4_42.3.4_4
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout2.3.6_2
FreeBSD:12:amd642.3.6_32.3.6_2
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i3862.3.6_32.3.6_2
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-fallout2.3.4_4
FreeBSD:13:aarch642.3.6_32.3.6_2
FreeBSD:13:amd642.3.6_32.3.6_2
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i3862.3.6_32.3.6_2
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch642.3.6_2pkg-fallout
FreeBSD:14:amd642.3.6_3pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i3862.3.6_3pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc642.3.6_2pkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
Library dependencies:
  1. libnlopt.so : math/nlopt
  2. libopenblas.so : math/openblas
  3. libboost_program_options.so : devel/boost-libs
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://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/
Collapse this list.

Number of commits found: 20

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.3.6_3
16 Jan 2023 19:32:07
commit hash:e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash:e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash:e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash:e1287d0d1228d93e469256fa6c4c824b9d20426b files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*:	bump libboost*.so libraries consumert after Boost upgrade
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)
2.3.6_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)
2.3.6_2
12 Aug 2022 14:46:53
commit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
2.3.6_1
22 May 2022 20:17:16
commit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cd files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
2.3.6
21 Apr 2022 17:11:13
commit hash:6812895caa6624a5bcc41c918feb3aca08aa72c6commit hash:6812895caa6624a5bcc41c918feb3aca08aa72c6commit hash:6812895caa6624a5bcc41c918feb3aca08aa72c6commit hash:6812895caa6624a5bcc41c918feb3aca08aa72c6 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/bolt-lmm: remove unnecessary CFLAGS_powerpc64
2.3.6
17 Apr 2022 11:05:53
commit hash:b48c8810a83a46f32cad5fa95ebcc9c72cfa1452commit hash:b48c8810a83a46f32cad5fa95ebcc9c72cfa1452commit hash:b48c8810a83a46f32cad5fa95ebcc9c72cfa1452commit hash:b48c8810a83a46f32cad5fa95ebcc9c72cfa1452 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/bolt-lmm: remove unnecessary flags for powerpc64le
2.3.6
20 Mar 2022 15:29:01
commit hash:0297052e221a1c1e754fa6d10380a527985f4cf5commit hash:0297052e221a1c1e754fa6d10380a527985f4cf5commit hash:0297052e221a1c1e754fa6d10380a527985f4cf5commit hash:0297052e221a1c1e754fa6d10380a527985f4cf5 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bolt-lmm: Update to 2.3.6

Changes: https://alkesgroup.broadinstitute.org/BOLT-LMM/\
	 BOLT-LMM_manual.html#x1-60002.1

Also fixed build on aarch64: Replaced non-portable _mm_malloc() with
aligned_alloc()

Reported by:    pkg-fallout
2.3.4_4
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)
2.3.4_4
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
2.3.4_4
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.
2.3.4_4
27 Sep 2020 07:41:33
Revision:550247Original commit files touched by this commit
linimon search for other commits by this committer
Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.

Approved by:	portmgr (tier-2 blanket)
2.3.4_4
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.
2.3.4_3
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
2.3.4_2
11 Dec 2019 17:53:49
Revision:519824Original commit files touched by this commit
jbeich search for other commits by this committer
devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
2.3.4_1
19 Aug 2019 15:35:28
Revision:509290Original commit files touched by this commit
jbeich search for other commits by this committer
devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
2.3.4
13 Aug 2019 15:30:22
Revision:508832Original commit files touched by this commit
jwb search for other commits by this committer
biology/bolt-lmm: Upgrade to 2.3.4

Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream
2.3.2_2
04 Aug 2019 23:48:22
Revision:508135Original commit files touched by this commit
jwb search for other commits by this committer
PR:             239613
Submitted by:   pkubaj
2.3.2_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
2.3.2
26 May 2019 03:36:49
Revision:502673Original commit files touched by this commit
jwb search for other commits by this committer
biology/bolt-lmm: Mixed model association testing and variance component
analysis

The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).

Number of commits found: 20