19:03 Thierry Thomas (thierry)  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@

    22df0db

11:49 Jason W. Bacon (jwb) 

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);

    f958801

12:52 Jason W. Bacon (jwb) 

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

    9d8c5cb

09:09 Gerald Pfeifer (gerald) 

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

    8d3e020

21:10 Stefan Eßer (se) 

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)

    b7f0544

20:40 Yuri Victorovich (yuri) 

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)

    5fa5065

08:09 Mathieu Arnold (mat) 

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

    cf118cc

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

17:09 jwb 

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

 

17:04 thierry 

- 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

 

14:31 jwb 

biology/gcta: Switch eigen3 dep to USES framework

PR:             ports/250949
Reported by:    lbartoletti

 

16:11 yuri 

Bump 46 ports depending on math/openblas because the after the recent
math/openblas update the library name changed in openblas.

 

15:22 jwb 

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.