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non port: biology/gemma/Makefile

Number of commits found: 17

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
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
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (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
Wednesday, 12 Jan 2022
19:41 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
commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 654acd8
Wednesday, 16 Jun 2021
19:31 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
	* updated exponential fitting example for nonlinear least squares
	* added banded LU decomposition and solver (gsl_linalg_LU_band)
	* New functions added to the library:
	      - gsl_matrix_norm1
	      - gsl_spmatrix_norm1
	      - gsl_matrix_complex_conjtrans_memcpy
	      - gsl_linalg_QL: decomp, unpack
	      - gsl_linalg_complex_QR_* (thanks to Christian Krueger)
	      - gsl_vector_sum
	      - gsl_matrix_scale_rows
	      - gsl_matrix_scale_columns
	      - gsl_multilarge_linear_matrix_ptr
	      - gsl_multilarge_linear_rhs_ptr
	      - gsl_spmatrix_dense_add (renamed from gsl_spmatrix_add_to_dense)
	      - gsl_spmatrix_dense_sub
	      - gsl_linalg_cholesky_band: solvem, svxm, scale, scale_apply
	      - gsl_linalg_QR_UD: decomp, lssolve
	      - gsl_linalg_QR_UU: decomp, lssolve, QTvec
	      - gsl_linalg_QR_UZ: decomp
	      - gsl_multifit_linear_lcurvature
	      - gsl_spline2d_eval_extrap
	* bug fix in checking vector lengths in gsl_vector_memcpy (dieggsy@pm.me)
	* made gsl_sf_legendre_array_index() inline and documented
	      - gsl_sf_legendre_nlm()

[1] http://git.savannah.gnu.org/cgit/gsl.git/tree/NEWS

PR:		256423
Exp-run by:	antoine
commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e 63e653a
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
Saturday, 2 Jan 2021
22:05 jwb search for other commits by this committer
biology/gemma: Upgrade to 0.98.3

Minor bug fixes and enhancements

Reported by:    portscout
Original commitRevision:559975 
Saturday, 12 Dec 2020
17:04 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
Original commitRevision:557839 
Wednesday, 6 May 2020
16:39 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
Original commitRevision:534190 
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 
Tuesday, 21 Jan 2020
22:03 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)
Original commitRevision:523749 
Tuesday, 14 Jan 2020
22:35 jwb search for other commits by this committer
biology/gemma: Unbreak build

Conflict between cblas.h and gsl_cblas.h
Original commitRevision:523074 
Friday, 25 Oct 2019
23:41 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
Original commitRevision:515671 
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 
Saturday, 18 May 2019
22:41 jwb search for other commits by this committer
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC

Reported by:    danfe, Gerald Pfeifer
Original commitRevision:501990 
Friday, 17 May 2019
14:45 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.
Original commitRevision:501873 

Number of commits found: 17