biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/

Port changes:
* Take maintainership
* Implement the 'benchmarks' target, and stop installing benchmarks
* Add USES=gmake
* Update license
* Change MASTER_SITES and WWW to https
* Silence some commands

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).

Fix the context of some patches so that they apply with stricter patch(1)

PR:		223545
With hat:	portmgr

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

Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight

${RM} already has -f.

PR:		213570
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight

Convert ports to use the options helpers in categories [abc]*, and minor fixes.

Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3412?

Remove $FreeBSD$ from patches files in categories a-j.

With hat:	portmgr
Sponsored by:	Absolight

- Update to 7.1.3

Update from 7.1.1 to 7.1.2.

Unbreak by updating from 7.0.1 to 7.1.1. Hopefully, the authors will
stop rerolling releases (and breaking downstream checksums) now.

While here, allow parallel builds (seems to work again now) and stop
extraction of unused subdirectories.

Mark BROKEN: Checksum and size mismatch

Reported by:	pkg-fallout

biology/tinker: 6.2.6 -> 7.0.1

PR:		196376
Submitted by:	Nikola Kolev <koue@chaosophia.net>

Cleanup plist

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)

- Un-break fetch stage: the name scheme of the source tarballs has changed
- Add LICENSE*
- Remove conflict with hunspell:
  - Rename the 'analyze' binary to 'analyze_t'
  - put a note in pkg-message.in
- Pet portlint

PR:		ports/187569
Submitted by:	Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
Approved by:	thierry (mentor)
MFH:	2014Q2

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)

- biology/tinker: USES=fortran, staging.
- Add CONFLICTS_INSTALL between hunspell and tinker.
  Both install bin/analyze.

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

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

biology/tinker: Regenerate distinfo to unbreak fetch

Apparently the distfile was rerolled.  The sizes of the file are only a few
bytes apart.  Since the master site never changed, it's reasonable just to
regenerate the distinfo and bump the PORTREVISION.

PR:		180664
Approved by:	bapt/culot (mentors, implicit)

- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)

- Update to 6.2.06

PR:		180518
Submitted by:	Ports Fury

- Update to 6.2.05

PR:		179061
Submitted by:	Ports Fury

- Update to 6.2.04

PR:		178590
Submitted by:	Ports Fury

- Update to 6.2.02

PR:		178031
Submitted by:	Ports Fury

- Update to 6.2.01

PR:		177261
Submitted by:	ports fury

- Update to version 6.1.01
- Add MAKE_JOBS_SAFE
- Convert to optionsng
- Trim Makefile header

PR:           ports/171971
Submitted by: KATO Tsuguru <tkato432 _at_ yahoo.com>
Approved by:  beat (mentor)
Feature safe: yes

- ${FFLAGS} might contain commas

Reported by:    pointyhat

- Update to 5.1.09

PR:             154359
Submitted by:   Ruslan Mahmatkhanov <cvs-src@yandex.ru>
Feature safe:   yes

- Unbreak by removing some old and adding some new master sites
- Bump PORTREVISION
PR:             ports/151733
Submitted by:   Chris Petrik [c.petrik.sosa gmail.com]

Mark BROKEN: does not fetch.

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.

- Remove unneeded dependency from gtk12/gtk20 [1]
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+

Thanks to all Helpers:
        Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
        ehaupt, nox, itetcu, flz, pav

PR:             116263
Tested on:      pointyhat
Approved by:    portmgr (pav)

Now we use USE_FORTRAN=yes to use FORTRAN compiler.

swap MASTER_SITES to improve fetchiness on pointyhat which is blocked from
dasher.wustl.edu

BROKEN: Unfetchable

- Unbreak
- Add backup MASTER_SITES

PR:             111963
Submitted by:   Jason Harris <jharris@widomaker.com>

BROKEN: Unfetchable

- MASTER_SITE is back, remove BROKEN

PR:             ports/109954
Submitted by:   Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>

BROKEN: Unfetchable

* Migrate to gfortran.
* Bump port revision.

Remove USE_REINPLACE from all categories starting with B

- Add SHA256

Upgrade to latest revision to make fetchable again.

Approved by:    portmgr (marcus)

- Unbreak by upgrading to 4.2;

- Use DIST_SUBDIR because tarball is not versioned;

- Add sysdate to PORTVERSION to handle minor revisions;

- Do some cleaning.

Use X_IMAKE_PORT instead of dist-specific imake dependencies.  While here,
make the BROKEN message a little more informative.

BROKEN: Checksum mismatch

Tidy up whitespace.

- Update checksum again, seems author removes .ps version of documentation
  from tarball
- Unmark broken, it builds for me just fine

Approved by:    adamw (mentor)

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

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

Forced commit to add rationale.  (Note: this port was previously
broken due to a bad checksum; the initial intent of the update
was to try to fix only that.  However, the new revision fails
as well, but this led to my being sloppy with the checkin.
As Maxwell Smart said, "Sorry about that, Chief.")

New distfile 9/13.  "Changes from TINKER 4.0 include some new force
field parameter sets, improvements to rigid body dynamics, a
Nose-Hoover thermostat, and numerous minor additions and bug fixes."

However, the compilation fails in sockets.c with an undefined
ref to <jni.h>.  This is part of: "an interface between TINKER Fortran
code and FFE Java objects used for socket based communication."

Some interested party is going to have to take up this one, I'm
afraid, as I have no idea what is involved.

Reminded by: kris

Fixes the checksum problem, but doesn't fix the port; adds a BROKEN
line about how it fails.  Some other interested person will have
to take it from here.

PR:             56882

Some clean-up.
a) ECHO-> ECHO_CMD
b) place of WITH_OPTIMIZED_FLAGS seems to be wrong.
c) fix errors reported from freshports.org

Duplicated the `pre-extract:' and `post-build:'

Submitted by:   Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Pointy hat to:  myself

a) Some corrupts with Makefile and pkg-plist.
b) forgot to notice that drop maintainership to ports@

Submitted by:   Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Pointy hat to:  myself

a) Forgot to update distinfo 52498
b) added LEGAL. author requests no distribution
   except from his FTP site
c) clean-ups for compiler optimization

Submitted by:   Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Pointy hat to:  maho; partially :)

Maintainer update of biology/tinker port to version 4.0.

PR:             52498
Submitted by:   Glenn Johnson <gjohnson@srrc.ars.usda.gov>

Update the biology/tinker Makefile so it builds on -current

PR:             ports/50371
Submitted by:   Glenn Johnson <gjohnson@srrc.ars.usda.gov>

De-pkg-comment.

Upgrade tinker to the latest revision    

style fix: un"echo" commands    

Update to 3.9    

Add NOPORTDOCS support to pkg-plist    

Update distfile checksum (PORTREVISION bumped)    

update from 3.7 to 3.8    

Convert category biology to new layout.  

Clean up this port so that it installs stuff in a more proper location   as per
hier(7) and Porter's Handbook.