biology/plink1.90.b6.17_6

*/*: bump PORTREVISION after the upgrade of OpenBLAS

all: drop support for FreeBSD 13, mips and risc64sf

Reviewed by:            many (*)
Differential Revision:  https://reviews.freebsd.org/D55624
Differential Revision:  https://reviews.freebsd.org/D55642 (merged in from bofh)

many (*)
  acm arrowd brooks cmt dch decke dinoex eduardo fluffy fuz gahr garga
  jbeich joerg jrm kai kenrap martymac matthew mfechner michaelo mizhka
  nobutaka pkubaj se tagattie thj

  Anton Saietskii
  GenericRikka
  Gert Doering
  Jan Bramkamp
  Oleh Hushchenkov
  Oleksandr Kryvulia
  Ralf van der Enden
  Yamagi

  desktop kde python tcltk office

biology/plink: enable on powerpc64le by using SSE translation

*/*: bump PORTREVISION after OpenBLAS upgrade

Remark: this souldn’t be necessary, because the version of the library is the
same, but due to many changes between these releases, it is safer this way.

PR:		284314

*/*: bump PORTREVISION after the upgrade to OpenBLAS

*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree

- Remove all references to defunct ARCH arm
- Remove all references to defunct ARCH sparc64
- Remove x11-drivers/xf86-video-sunffb which requires defunct sparc64
  ARCH
- Remove sysutils/afbinit requires defunct sparc64 ARCH
- Remove all references to bktr driver
- Remove all references to defunct FreeBSD_12
- Remove all references to OSVERSION/OSREL corresponding to 12
- Remove conditionals in Mk/Uses/cabal.mk
- Remove sparc reference from Mk/Uses/qt-dist.mk
- Remove BROKEN_sparc64/NOT_FOR_ARCH=sparc64
- Remove BROKEN_FreeBSD_12* from:
- Remove OpenSSL patches from:
- Remove conditional flags for OSVERSION >= 1300000 to fixed flags.
  Also move conditional flags for non sparc64/arm ARCH to fixed flags.

Reviewed by:	brooks, jbeich, rene, salvadore
Differential Revision: https://reviews.freebsd.org/D42068

*/*: bump PORTREVISION after the upgrade of OpenBLAS

PR:		273219

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

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)

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)

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)

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

Remove # $FreeBSD$ from Makefiles.

Allow building on powerpc64le.

Approved by:	portmgr (tier-2 blanket)

Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas

biology/plink: Whole genome association analysis toolset

Reversed removal, commit r471892 2018/06/07
Upgraded to 1.90 beta 6.17

PR:             ports/243733
Submitted by:   mzaki@e-mail.ne.jp

Remove expired ports: 2018-06-06 biology/ssaha: Broken for more than 6 months 2018-06-06 biology/crux: Broken for more than 6 months 2018-06-06 biology/ariadne: Broken for more than 6 months 2018-06-06 cad/sceptre: Broken for more than 6 months 2018-06-06 cad/cider: Broken for more than 6 months 2018-06-06 chinese/scim-array: Broken for more than 6 months 2018-06-06 chinese/xpdf: Broken for more t

Deprecate ports broken for more than 6 months

Bump PORTREVISIONs of all users of math/mpc that we just updated to version 1.1.0 (via revision 464079).

Multiple ports: Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128

Mark as broken ports with no public distfiles

Bump PORTREVISION for ports depending on the canonical version of GCC (via Mk/bsd.default-versions.mk and lang/gcc) which has moved from GCC 5.4 to GCC 6.4 under most circumstances.

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, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275

Bump PORTREVISIONs for ports depending on the canonical version of GCC and lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707

Bump PORTREVISIONS for ports depending on the canonical version of GCC and lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some circumstances such as versions of FreeBSD or platforms), part II.

The first part covered  ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.

This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.

PR:		214965
Reported by:	thierry

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

- Update maintainer mail address - Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493

Update the default version of GCC in the Ports Collection from GCC 4.7.4 to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

Update the default version of GCC used in the Ports Collection from GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)

Convert b* to USES=zip

Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes".  In most cases USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)

Fix the build with more standards-compliant compilers such as GCC 4.7. [1]

On the way replace USE_GMAKE by USES=gmake.

PR:		184566 [1], 182136
Submitted by:	Christoph Moench-Tegeder <cmt@burggraben.net> [1]
Approved by:	maintainer (Jason Bacon <jwbacon@tds.net>) [1]

In preparation for making libtool generate libraries with a sane name, fix all LIB_DEPENDS in biology

Update to libmpc version 1.0.1 which brings the following fixes:

- Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
 - 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
 - Removed compatibility with K&R compilers, which was untestable due
   to lack of such compilers.
 - New functions
   . mpc_log10
   . mpc_mul_2si, mpc_div_2si
 - Speed-ups
   . mpc_fma
 - Bug fixes
   . mpc_div and mpc_norm now return a value indicating the effective
     rounding direction, as the other functions.
   . mpc_mul, mpc_sqr and mpc_norm now return correct results even if
     there are over- or underflows during the computation.
   . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
     infinite part and equals output variable is corrected.
   . mpc_fr_sub: Wrong return value for imaginary part is corrected.

Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.

Bump PORTREVISIONS of all dependent ports.

PR:		183141
Approved by:	portmgr (bdrewery)

Add NO_STAGE all over the place in preparation for the staging support (cat: biology)

Add new ports biology/plink [1] and biology/plinkseq [2]:

PLINK is a free, open-source whole genome association analysis toolset.
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data.

PR:		ports/171918 [1]
PR:		ports/171922 [2]
Submitted by:	Jason Bacon <jwbacon at tds.net>