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non port: biology/bolt-lmm/Makefile

Number of commits found: 24

Tuesday, 13 Feb 2024
14:44 Dima Panov (fluffy) search for other commits by this committer
devel/boost: bump consumers after library update
commit hash: db616534ff99d6268997e2f30858891e20641a1e commit hash: db616534ff99d6268997e2f30858891e20641a1e commit hash: db616534ff99d6268997e2f30858891e20641a1e commit hash: db616534ff99d6268997e2f30858891e20641a1e db61653
Tuesday, 12 Dec 2023
19:03 Thierry Thomas (thierry) search for other commits by this committer
*/*: bump PORTREVISION after the upgrade of OpenBLAS

PR:		273219
commit hash: ab1713728d621e7b57d276ef27de37a8754e6ee0 commit hash: ab1713728d621e7b57d276ef27de37a8754e6ee0 commit hash: ab1713728d621e7b57d276ef27de37a8754e6ee0 commit hash: ab1713728d621e7b57d276ef27de37a8754e6ee0 ab17137
Wednesday, 27 Sep 2023
14:36 Dima Panov (fluffy) search for other commits by this committer
devel/boost*: bump all consumers after 1.83.0
commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 21d8008
Thursday, 27 Apr 2023
18:25 Dima Panov (fluffy) search for other commits by this committer
*/*: bump all direct Boost cunsumers
commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 3e45e8e
Sunday, 23 Apr 2023
09:09 Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b 8d3e020
Monday, 16 Jan 2023
19:32 Dima Panov (fluffy) search for other commits by this committer
*/*:	bump libboost*.so libraries consumert after Boost upgrade
commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b e1287d0
Wednesday, 7 Sep 2022
21:10 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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Friday, 12 Aug 2022
14:46 Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed 4cf39de
Sunday, 22 May 2022
20:17 Dima Panov (fluffy) search for other commits by this committer
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd b082b3d
Thursday, 21 Apr 2022
17:11 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/bolt-lmm: remove unnecessary CFLAGS_powerpc64
commit hash: 6812895caa6624a5bcc41c918feb3aca08aa72c6 commit hash: 6812895caa6624a5bcc41c918feb3aca08aa72c6 commit hash: 6812895caa6624a5bcc41c918feb3aca08aa72c6 commit hash: 6812895caa6624a5bcc41c918feb3aca08aa72c6 6812895
Sunday, 17 Apr 2022
11:05 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/bolt-lmm: remove unnecessary flags for powerpc64le
commit hash: b48c8810a83a46f32cad5fa95ebcc9c72cfa1452 commit hash: b48c8810a83a46f32cad5fa95ebcc9c72cfa1452 commit hash: b48c8810a83a46f32cad5fa95ebcc9c72cfa1452 commit hash: b48c8810a83a46f32cad5fa95ebcc9c72cfa1452 b48c881
Sunday, 20 Mar 2022
15:29 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
commit hash: 0297052e221a1c1e754fa6d10380a527985f4cf5 commit hash: 0297052e221a1c1e754fa6d10380a527985f4cf5 commit hash: 0297052e221a1c1e754fa6d10380a527985f4cf5 commit hash: 0297052e221a1c1e754fa6d10380a527985f4cf5 0297052
Sunday, 6 Feb 2022
18:36 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)
commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e bdd2d4a
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Sunday, 27 Sep 2020
07:41 linimon search for other commits by this committer
Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:550247 
Wednesday, 6 May 2020
16:11 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.
Original commitRevision:534185 
Thursday, 30 Jan 2020
14:17 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
Original commitRevision:524642 
Wednesday, 11 Dec 2019
17:53 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
Original commitRevision:519824 
Monday, 19 Aug 2019
15:35 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
Original commitRevision:509290 
Tuesday, 13 Aug 2019
15:30 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
Original commitRevision:508832 
Sunday, 4 Aug 2019
23:48 jwb search for other commits by this committer
PR:             239613
Submitted by:   pkubaj
Original commitRevision:508135 
Friday, 26 Jul 2019
20:46 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
Original commitRevision:507372 
Sunday, 26 May 2019
03:36 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).
Original commitRevision:502673 

Number of commits found: 24