biology/psi881.0_17

biology/psi88: Fix building with Flang

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

Remove WWW lines that have been moved into Makefiles

Approved by:	portmgr (implicit)

Move more WWW entries from pkg-descr files into Makefiles

The WWW: lines in the pkg-descr files of these ports where not at the
end of those files and have been missed in prior conversion runs.

Approved by:	portmgr (implicit)

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

Remove # $FreeBSD$ from Makefiles.

biology/psi88: Unbreak build with GCC 10

ctplot.f:69:29:

   69 |       CALL SYMBOL (XA,YA,.15,STRING,ANGLE,K)
      |                             1
Error: Rank mismatch in argument 'string' at (1) (scalar and rank-1)

http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2020-06-10_18h04m44s/logs/errors/psi88-1.0_16.log

PR:		246700

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

Related to revision 499061 bump ports with USES=fortran to have them benefit from the improved situation where libgcc_s is only used when absolutely necessary.

Suggested by:	tijl

Bump PORTREVISION for ports depending on the canonical version of GCC defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 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, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

Bump PORTREVISION for ports depending on the canonical version of GCC in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542

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

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

- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket

- Switch to options helpers

- Strip binaries

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)

Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)

Rename biology/ patch-xy patches to reflect the files they modify.

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)

USES=fortran, staging, miscellaneous cleanups.

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)

. NOPORTDOCS -> PORT_OPTIONS:MDOCS; . mute mdir commands and unmute install commands; . do not use mkdir for parent directories (mkdir implies "-p"); . introduce EXAMPLE option (do not install examples to DOCSDIR); . bump PORTREVISION; . make use of PLIST_FILES, PORTDOCS and PORTEXAMPLES at Makefile; . get rid of pkg-plist; . use standard DOCSDIR and EXAMPLESDIR (instead of a PREFIX/foo/bar path);

- Get Rid MD5 support

Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now implies lang/gcc44 up from lang/gcc43.

Approved by:	portmgr

Bump PORTREVISION due to change of USE_FORTRAN=yes to GCC 4.3.

Now we use USE_FORTRAN=yes to use FORTRAN compiler.

Build fix.

Submitted by:	kris via pointyhat and pav.

Forgot to commit a patch. Fixes build.

Submitted by:	kris via pointyhat.

* Migrate to gfortran. * Bump port revision. * fix build [1].

Submitted by:	kris [1]

* Add dummy knob WANT_FORTRAN for future gfortran   migration. currently it is not buildable with gfrotran42. * Honor FC and FFLAGS.

Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking about maintainer timeouts.

Hat:	portmgr

SHA256ify

Approved by:    krion@

- Fix MASTER_SITES

PR:		ports/67045
Submitted by:	Stefan Walter <sw@gegenunendlich.de>

SIZEify (maintainer timeout)

BROKEN: Does not fetch

Cosmetic fix: use %%DOCSDIR%% macro. No functionally changes.

Submitted by:	Oleg Karachevtsev <ok@etrust.ru>
A part of PR:	57992

De-pkg-comment.

update WWW and master site

PR:		31011
Submitted by:	maintainer

Add NOPORTDOCS support to pkg-plist

fix WWW:

PR:		25625
Submitted by:	maintainer

update with the new PORTNAME/PORTVERSION variables

ln -> ${LN}

Change Id->FreeBSD.

Make the psi88 port install into PREFIX instead of a hardcoded /usr/local.

PR:	12215
Submitted by:	Nick Hibma <nick.hibma@jrc.it>

Changed MASTER_SITES

PR:		11572
Submitted by:	maintainer

Fixed ${CATEGORIES} (removed misc from it)