biology/molden: Update 6.7 -> 7.1

PR:		265245
Approved by:	jmd@ (maintainer)

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>

biology/molden: Unbreak build; Correct WWW

For unbreak:
- pass FFLAGS to the build
- fix several errors in C
- remove the failing 'ex' command from makefile

Reported by:	fallout
Approved by:	portmgr (unbreak)

*: Clean up some things

- Fix typos
- Fix overwritten variables

Reported by:	portscan

biology/molden: update to 6.7

PR:		238858
Reported by:	yuri@

graphics/mesa-libs: Bump reverse deps for libglvnd

Per discussion with bapt on helping pkg handle the changing of these
deps and avoiding impossible upgrade senarios.

PR:		246767
Reviewed by:	manu, bapt
Approved by:	x11
Differential Revision:	https://reviews.freebsd.org/D30824

Deorbit RESTRICTED && NO_CDROM, part one.

For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.

Approved by:	rene
Differential Revision:	https://reviews.freebsd.org/D30010

Remove # $FreeBSD$ from Makefiles.

biology/molden: Fix build with gfortran10

Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.

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

biology/molden: update to 5.8.2

Also add do-install-{option}-on targets and shadow ${MKDIR} commands.

PR:		233060
Submitted by:	yuri

biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gcc

Add $(LDFLAGS) to makefile.
While here, add USES=gl.

Approved by:	portmgr

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

biology/molden: Unbreak by updating the MASTER_SITES URL

The upstream keeps changing the URL.

Mark BROKEN: unfetchaable

Reported by:	pkg-fallout

biology/molden: Unbreak by updating the MASTER_SITES URL

Mark BROKEN: unfetchable

Reported by:	pkg-fallout
MFH:		2018Q3

biolog/molden: unbreak after at least two intransparent distfile updates

Reviewed by:	zeising (mentor)
Approved by:	zeising (mentor)
Differential Revision:	https://reviews.freebsd.org/D15333

Mark BROKEN: checksum and size mismatch

Reported by:	pkg-fallout
MFH:		2018Q2

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

biology/molden: chase another intransparent upstream distfile upgrade.

Reviewed by:	swills (mentor), mat
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D12829

biology/molden: unbreak by chasing latest intransparent distfile update.

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D12521

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

Chase next distfile update. Upstream contacted whether we would be allowed to
host a distfile copy.

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D11586

biology/molden: Unbreak by chasing their latest opaque update to the
distribution.

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D11338

Mark BROKEN.

=> Attempting to fetch ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz
fetch: ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz: size mismatch:
expected 5339411, actual 5339467
=> Couldn't fetch it - please try to retrieve this

Sponsored by:	Absolight

Previous commit unbroke the port.

Reported by:	xmj

biology/molden: Chase recent upstream change of molden distfile.

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10864

Revision bump of all ports with USE_GL after consolidation of mesa-libs

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10845

Mark BROKEN: checksum and size mismatch

Reported by:	pkg-fallout

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

biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION.

Reviewed by:	swills (mentor), pi (former maintainer)
Approved by:	swills (mentor), pi (former maintainer)
Differential Revision:	https://reviews.freebsd.org/D9501

- Mark BROKEN: does not fetch, size/checksum mismatch

Approved by:	portmgr blanket

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

biology/molden: distfile was updated in xwin.c

biology/molden: add missing LICENSE_NAME

Reported by:	pkg-fallout

biology/molden: fix distinfo, set LICENSE

Submitted by:	marino
Reported by:	Eduardo Lemos de Sa <eduardo.lemosdesa@gmail.com>
MFH:		2016Q4

Mark BROKEN: unfetchable, size mismatch

Reported by:	pkg-fallout

biology/molden: 5.4 -> 5.7

- Adds editable text fields that are longer than the visible string
  and introduces a new way of selecting a range of amino acids.
- introduces interfaces to the open source packages openbabel and pharmer.
  Openbabel is used to create 2D images of the molecules in a .sdf
  file. It is also used to do 2D fingerprint searching.
  Pharmer is used to pharmacophore (3D) searching against indexed
  databases of .sdf files.

- Mark BROKEN: does not fetch (distfile was removed from ftp)

Approved by:	portmgr blanket

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

Approved by:	portmgr blanket

biology/molden: updated distfile, take maintainer

- upstream distfile is moving target with same version number

Submitted by:	antoine

Mark BROKEN: checksum and size mismatch

Reported by:	pkg-fallout

biology/molden: 5.0.7 -> 5.4

Changes:
- Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally.
- Pdb files can now be clipped.
- Fixes missing residues. Introduces an alternative way of generating rotamers,
  without using z-matrices. This potentially a faster algorithm.
- Supports Movie making through avconv/ffmpeg.
- calculates the Electron Localization Function (ELF).
- Updated code of ambfor/ambmd to speed up optimisations/MD of proteins
  solvated in water (Jan, 2014).

PR:		204341

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)

Catch a couple of missing convertsion to :tu/:tl

Submitted by:	ak
With hat:	portmgr

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)

- Update to 5.0.7

PR:		185942
Submitted by:	ports fury

- USES=fortran gmake.
- Add dependency on xproto.
- Fix build with new CFLAGS.
- Staging.
- New WWW.

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)

- Update to 5.0.6

PR:		178032
Submitted by:	Ports Fury

Update to 5.0.4

- Update to version 5.0.2
- Add MAKE_JOBS_UNSAFE
- Convert to optionsng

PR:           ports/171970
Submitted by: KATO Tsuguru <tkato432 _at_ yahoo.com>
Approved by:  beat (mentor)
Feature safe: yes

Mea culpa, s/Whom/Created by/

- Adjust "Created by" tag to include more complete submitter's information
- Mute MKDIRs, remove trailing dot from RESTRICTED, drop leading indefinite
  article from COMMENT where appropriate

- Reassign to the heap at maintainer's request

Switch from libglut to freeglut and retire libglut. Libglut hasn't been
developed in years and has been dropped from the MESA 8.0 distribution.
Freeglut is a rewrite of glut and is actively developed and is used by
many linux distributions instead of libglut.

Bump all ports that directly depend on libglut because of the shlib version
change.

There are some extra items in this patch.

*) Because freeglut doesn't have the same dependancies as libglut, some ports
	need extra dependencies added to USE_XORG to make them build.
*) Mark graphics/f90gl broken, f90gl depends on a header that is only shipped
	with libglut.
*) Remove option for libglut/freeglut selection in games/cake, only freeglut
	remains now.
*) While here fix a png related build issue games/vegastrike.

Thanks to miwi for running the exp-run.

Approved by:	portmgr (miwi)

Collaboration with:	zeising@
Obtained from:	xorg-dev staging area.

The vast majority of pkg-descr files had the following format when they
had both lines:

Author: ...
WWW: ....

So standardize on that, and move them to the end of the file when necessary.

Also fix some more whitespace, and remove more "signature tags" of varying
forms, like -- name, etc.

s/AUTHOR/Author/

A few other various formatting issues

- 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

- Unbreak fetch

Submitted by:   maintainer

- Unbreak distinfo after portrevision bump

Reported by:    pointyhat

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

- Remove conditional checks relevant only on FreeBSD 5.x and older

- Roll back to 4.6 as 4.7 is the development version and is constantly being
  re-rolled.
- Move post-patch target into files/patch-xwin.c to remove sed invocation.
- Respect NOPORTDATA and DATADIR.
- Bring files/patch-aa back (to preserve history) and retire patch-makefile.
- Fixup files/patch-xwin.c so it applies cleanly to this version.

Mark as broken since it has been re-rolled for the 4th(?) time.

Distfile was re-rolled.  The changes were to fix some bugs in the code.
While I'm here, make it respect NOPORTDOCS.

Update to 4.7

PR:             ports/128476
Submitted by:   fulvio ciriaco <oivulf@gmail.com>

Unbreak building for 8-x.

Submitted by:   Steve Kargl <sgk at troutmask.apl.washington.edu> at ports@ ML

- Mark BROKEN on -CURRENT: error: 'linkat' redeclared as different kind of
symbol

Reported by:    pointyhat

- 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.

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

- Update to 4.5

- Fix typo

Using only gfortran42. not gcc42.
Bump portrevision.

Migrated to gfortran.

Unbreak: molden has been updated on Aug 17, with the same DISTNAME.

Changelog at <http://www.cmbi.ru.nl/molden/HISTORY>.

BROKEN: Size mismatch.  Since this is unmaintained, deprecate and schedule
for termination on 2006-12-01

NO_CDROM and NO_PACKAGE are not appropriate here

Remove USE_REINPLACE from all categories starting with B

- Update graphics/libglut to 6.4.1.
- Shared lib version and PORTREVISION bumb for all affected ports.

While I'm here:
- Remove USE_MESA knob where it was (35 ports).
  It marked as depricated for 2 years.

PR:             ports/90247
Submitted by:   Ermal Lu?i <eri--@albabsd.org>

- Unbreak by updating to 4.4
- Add dependecy to MESA

PR:             ports/89795
Submitted by:   Johan van Selst <johans@stack.nl>

- BROKEN: Size mismatch

o update to 4.3
o unbreak
o due to no fix for long period, drop maintainership to ports.

This port is scheduled to be removed on 2005-02-18 if it is still
broken at that time, and a fix has not been submitted to GNATS.

BROKEN: Checksum mismatch

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

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

enhancement, build and install the opengl viewer, moldenogl.
update to 3.9, not 3.8, which is newer :)

Committed by maintainer timeout:
> Sat Apr  5 17:46:57 EST 2003 - edwin - informed maintainer

PR:             47177
Submitted by:   Glenn Johnson <gjohnson@srrc.ars.usda.gov>

De-pkg-comment.

Update to 3.8

Approved by:    rmiya@cc.hirosaki-u.ac.jp (maintainer)

Note distribution term.
Requested by:   maintainer

Back my last commit out.
We couldn't update distinfo without inspecting distfile's changes.
PR:     ports/37476
Suggested by:   kris

distfile has silently changed,
so md5 has to be rewritten.
PR:     ports/37476
Submitted by:   maintainer

o update to 3.7.   differences from the PR:    - this port requires Xlib so add
USE_XLIB.    - remove unnecessary PORTREVISION.    

chase checksum for repacked distfile almost an year ago.   Maintainer does not
have previous distfile.   As the distfile for this port is not distributable, it
is OK to me to change   distinfo now.