*: Bump PORTREVISIONs for math/mpc update to 1.3.1

science/vmd: Add another alternate MASTER_SITE for tachyon

jedi.ks.uiuc.edu is timing out

science/vmd: Update to 1.9.4a57

Unbreak build: 1.9.3 incompatible with latest python tools
Clean up portlint and stage qa issues

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.

science: remove 'Created by' lines

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

  *  Andreas Fehlner <fehlner@gmx.de>
  *  Brad Huntting <huntting@glarp.com>
  *  Chao Shin <quakelee@cn.FreeBSD.org>
  *  Cheng-Lung Sung <clsung@FreeBSD.org>
  *  Chia-Hsing Yu <me@davidyu.org>
  *  Chris Rees <utisoft@gmail.com>
  *  David Naylor <dbn@FreeBSD.org>
  *  Dmitry Sivachenko <demon@FreeBSD.org>
  *  Ed Schouten <ed@FreeBSD.org>
  *  Eric Freeman <freebsdports@chillibear.com>
  *  Erik B Knudsen

science/netcdf: Update to 4.8.1

- Update MASTER_SITES
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/Unidata/netcdf-c/releases

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

Remove # $FreeBSD$ from Makefiles.

Bump PORTREVISION for science/netcdf shlib change

Return dbn's ports to the pool after safekeeping his commit bit.

Add USES=xorg USES=gl, ports categories s

Add USES=xorg and USES=gl to ports in categories starting with 's'
While here, try to sprinkle other USES (mostly gnome and sdl) as needed.

science/vmd: Add USES=gl

Pet portlint, group USExx lines.

PR:		237066
Approved by:	dbn (maintainer's timeout 4+ months)

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

Update science/netcdf to 4.6.3

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/Unidata/netcdf-c/releases
		https://github.com/Unidata/netcdf-c/blob/master/RELEASE_NOTES.md

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

science/vmd: Remove RESTRICTED: not required

Reported by:	mat
Approved by:	portmgr

science/vmd: License auto-accept -> no-auto-accept

VMD license requires specific acknowledgement if VMD is used for published
results, therefore no auto-accept.

science/vmd: Add RESTRICTED clause.

This software comes from the University of Illinois, same as science/namd,
and is for non-commercial use only.

Also add it to ports/LEGAL.

Approved by:	portmgr blanket

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

Update to 4.5.0

- Pet portlint: reorder LICENSE knobs

Changes:	https://github.com/Unidata/netcdf-c/releases

science/vmd: various fixes

 - fix spelling of VMD license [1]
 - use USES=tcl,tk instead of direct dependency
 - patch vmd to support (tcl|tk)86
 - fix shebang for tcl [1]
 - fix detection of netcdf
 - add sqlite as a dependency (for dmsplugin) [1]
 - add expact as a dependency (for hoomdplugin)
 - rework configuration:
   - explicitly list required components (CONFIGURE_ARGS)
   - call configure directly (instead of via gmake(1))
   - patch configure to accept TCLLDFLAGS and TKLDFLAGS
   - pass PREFIX as an environment variable instead of using sed(1)
   - patch Make-arch to accept environment TCLLDFLAGS and NETCDFLDFLAGS
 - add support for parallel building (except for building plugins)
 - bump PORTREVISION

PR:		219642
Reported by:	Yuri Victorovich <yuri@rawbw.com>

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

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

science/vmd: unbreak build

 - Remove patches that are not required with the new sources for stride
 - Add stride license test

science/vmd: correct the wording of numpy keyword

science/vmd: fix port to depend on numpy.

Reported by:	Ruslan Makhmatkhanov <cvs-src@yandex.ru>

science/vmd: update to 1.9.3

 - update MASTER_SITES to use upstream stride (the old - repackages - sources
   were no longer working).
 - take maintainership: although I don't use the software I am happy to respond
   to PR's and check for updates periodically,
 - add license information for each source:
   - vmd: custom license that requires the user to explicitly download (and
          accept the license before downloading).  Mark the license as
          auto-accept here as the present of the DISTFILE will indicate that
          the license has been accepted
   - tachyon: standard 3-clause BSD license :-)
   - stride: almost BSD license, except only for academic use (i.e.
             non-commersial) and a requirement to report bugs to the author.
             Add a plain text copy of the license file to the port.
   - add missing dependencies: gl, x11
   - fix detection of python.
   - simplify configure patch.
   - update pkg-plist for changes in plugin versions.

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).

In particular that is 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.

Remove ${PORTSDIR}/ from dependencies, categories r, s, t, and u.

With hat:	portmgr
Sponsored by:	Absolight

3 ports categories: Remove $PTHREAD_LIBS

Categories: print, science, emulators

approved by:	PTHREAD blanket

science/vmd: Improve cc/gcc replacement patterns for Makefiles

PR:		197103
Submitted by:	Sakaue Mamoru

science/vmd: Unbreak on F10+

This patch removes the hardcoded "gcc" so that it works with USE_GCC
variable.  There is a slightly newer version of vmd available, so a
version upgrade may soon follow.

PR:		197103
Submitted by:	Sakaue Mamoru

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)

Stage science/vmd

I clobbered the Makefile diff (sorry danfe@).  The entire makefile was
tabbed over 3 times.  There was also no respect for 80 columns so a good
part of the clobber came from line wrapping.  I also made $TAR use
real switches (e.g. -xzf) rather than undocumented by supported (zxf)

This is another manual package / obtain restricted data files/ only port
so I can't test much of it.

PR:		193090
Submitted by:	turutani (Kyoto)

Reset maintainership for ports not staged with no pending PR

With hat:	portmgr

Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. A few Makefiles
where not included as they contain Latin-1 characters that break
the Phabricator workflow. Categories P-S.

CR:		D422
Approved by:	portmgr (bapt)

Convert GMAKE to MAKE_CMD
Please note that lots of invocation of MAKE_CMD here are wrong as they do not
properly respect MAKE_ENV and friends

With hat:	portmgr

Remove all space characters from Makefile assignments.

No functional changes included.

CR:		D193 (except math/sedumi)
Approved by:	portmgr (bapt)

- Update to 4.3.2 (from science/netcdf4)
- Bump PORTREVISION for science/netcdf shlib change and
  dependency change from science/netcdf4 to science/netcdf [1]

Changes:	http://www.unidata.ucar.edu/software/netcdf/docs/release_notes.html
Approved by:	portmgr (bapt) [1]

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

- convert to the new perl5 framework
- convert USE_GMAKE to Uses

Approved by:	portmgr (bapt@, blanket)

- Remove bogus conditional IGNORE for PACKAGE_BUILDING; these should
  be IGNOREd regardless of PACKAGE_BUILDING. Soem have no MASTER_SITES
  and require manual fetching, others are already marked RESTRICTED.
- Trim headers
- Convert some pre-fetch errors into IGNORE
- Remove needless quoting in java/jdk7-doc IGNORE

With hat:	portmgr

Fix minor nit: use the canconical FreeBSD.org form for email addresses.
This was causing me issues when attempting to gather certain statistics.

While here trim header

Approved by:	miwi, adrian, tj
No objection from:	db, bjk, cperciva, scheidell, osa

In categories starting with [n-s], remove empty lines (and also few cases of
trailing slashes) from pkg-plist.

Update to 1.9.1.

Submitted by:   bjk

re-assignment of echo_msg breaks 'make readme'
unbreak

PR: ports/163257
Submitted by: Jason Helfman <jhelfman@experts-exchange.com>
Approved by: maintainer, crees (mentor)

- Add files/patch-bin_vmd.csh, files/patch-bin_vmd.sh
  to fix a runtime error (the "ARCH" value is not set)
- Bump PORTREVISION
- Remove MD5 checksum from distinfo
- Set ONLY_FOR_ARCHS (i386 and amd64)

PR:             ports/152955
Submitted by:   Benjamin Kaduk <kaduk-fbsd at mit.edu> (maintainer)

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

- Chase x11-toolkits/fltk update

- Remove comments from IGNORE section. Left in by mistake with last commit.

Feature safe:   yes

- Update to 1.8.7
- Pass maintainer to submitter

PR:             ports/142513
Submitted by:   Ben Kaduk <kaduk@mit.edu>
Feature safe:   yes

- update to jpeg-8

- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin

Relinquish maintainership at maintainer's request.

Approved by:    portmgr (self)

- 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)

- Move from versioned tcl/tk CATEGORIES to simple tcl and tk categories

With hat:       portmgr

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

NO_PACKAGE and NO_CDROM are superfluous here

Remove USE_REINPLACE from all categories starting with S

- Group master sites with distfiles

PR:             ports/87078
Submitted by:   Sangwoo Shim <borishim@gmail.com> (maintainer)

Add B-Dep on imake
Update Maintainer email

PR:             86419
Submitted by:   Sangwoo Shim <sangwoos@gmail.com>

Upgrade to 1.8.3.

PR:             ports/80682
Submitted by:   maintainer.

- Fix build/run on amd64.

PR:             ports/76941
Submitted by:   Sangwoo Shim <ssw@neo.redjade.org> (maintainer)

Reassign maintainer to Sangwoo Shim <ssw@neo.redjade.org>

Requested by:   old maintainer

Add missing files.

PR:             ports/75342
Submitted by:   maintainer.

Fix build in presence of x11/nvidia-driver

PR:             ports/71052
Submitted by:   Stephen Montgomery-Smith (maintainer)

Add vmd, a molecular visualization program for displaying, animating, and
analyzing large biomolecular systems using 3-D graphics and built-in scripting.

PR:             ports/70509
Submitted by:   Stephen Montgomery-Smith <stephen@math.missouri.edu>