science/minc2: Fix build with netcdf 4.9.3+

Reference:	https://github.com/Unidata/netcdf-c/commit/73b9f1828ebdf2e08f328eb24200f881fd4a5214
Approved by:	portmgr (blanket)

science/minc2: Moved man to share/man

Approved by:    portmgr (blanket)

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

science/minc2: fix build with -fno-common

Move the definition of two symbols from header to source file.
This fixes the build on FreeBSD 13+.

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/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>

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

*/*: Remove redundant '-[0-9]*' from CONFLICTS

The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").

Many CONFLICTS definitions used patterns like "bash-[0-9]*" to filter
for the bash package in any version. But that pattern is functionally
identical with just "bash".

Approved by:	portmgr (blanket)

Remove # $FreeBSD$ from Makefiles.

Mark BROKEN in 13/14 (via latest llvm update).

Bump PORTREVISION for science/netcdf shlib change

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

Update science/hdf5 to 1.10.4

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes
PR:		233070
Submitted by:	wen

Update science/hdf5 to 1.10.2

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.2#releasenotes
		https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt
PR:		231009
Exp-run by:	antoine

Update to 4.5.0

- Pet portlint: reorder LICENSE knobs

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

Update science/hdf5 to 1.10.1

- Bump PORTREVISION for shlib change

Changes:	https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1-RELEASE.txt

${RM} already has -f.

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

- Fix build
- Add LICENSE_FILE

- Fix trailing whitespace in pkg-descrs, categories [p-x]*

Approved by:	portmgr blanket

- Update to 1.10.0
- Add LICENSE_FILE
- Remove outdated PORTSCOUT
- Re-enable SZIP option by default: it was changed unintentionally in r398300

Changes:	https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.0/src/hdf5-1.10.0-RELEASE.txt
		https://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

science/minc2 is not jobs safe

lex needs gram.h before that header gets created.
I've seen this twice now.

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

With hat:	portmgr
Sponsored by:	Absolight

- Update to 1.8.15
- Bump PORTREVISION for science/hdf5 shlib change

Changes:	http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-RELEASE.txt
		http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

Update ports in the s* categores to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight

Convert to USES=autoreconf

Update USE_GITHUB so it does not require GH_COMMIT.

Using this new scheme allows only setting the _tag_ or _commit hash_ in
GH_TAGNAME and not having to know the hash for a tag.  This scheme will
download a tarball that has a different checksum than before due to a changed
directory name for extraction.

The following MASTER_SITES are provided to retain the old checksum and
directory structure (that require GH_COMMIT):
  GH -> GHL
  GITHUB -> GITHUB_LEGACY

Differential Revision:	https://reviews.freebsd.org/D748
Submitted by:	amdmi3
Reviewed by:	mat, swills, antoine, bdrewery
With hat:	portmgr

- Update to 1.8.14
- Update MASTER_SITES
- Use INSTALL_TARGET=install-strip instead of
MAKE_ENV=INSTALL_STRIP_FLAG=${STRIP}
- Bump PORTREVISION for science/hdf5 shlib change

Changes:	http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.14-RELEASE.txt
		http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

Update "BSD" license in science category

Fix build with Perl 5.18+.  While there, add a runtime dependency on Perl, a
few installed scripts need it.

Sponsored by:	Absolight

Cleanup plist

Use default LIBTOOLIZE_ARGS

science/minc2: Unbreak, Upgrade version 2.0.18 => 2.2.00 and stage

PR:		187764
Submitted by:	Ports Fury

Convert to USES=libtool

Mark BROKEN: Fails to build

libtool: compile:  cc -DHAVE_CONFIG_H -I. -I./libsrc -I./volume_io/Include
-I./volume_io/Include -I./progs/Proglib -I./conversion/Acr_nema -I./libsrc2
-I/usr/local/include -DH5_USE_16_API -O2 -pipe -fno-strict-aliasing -MT
libsrc/image_conversion.lo -MD -MP -MF libsrc/.deps/image_conversion.Tpo -c
libsrc/image_conversion.c  -fPIC -DPIC -o libsrc/.libs/image_conversion.o
libsrc/image_conversion.c: In function 'miicv_create':
libsrc/image_conversion.c:219: error: 'MAX_NC_OPEN' undeclared (first use in
this function)
libsrc/image_conversion.c:219: error: (Each undeclared identifier is reported
only once
libsrc/image_conversion.c:219: error: for each function it appears in.)
*** [libsrc/image_conversion.lo] Error code 1

Reported by:	pkg-fallout

- 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]

- Update to 1.8.12 (from science/hdf5-18)
- Add LICENSE
- Convert to new LIB_DEPENDS format
- Convert to new options helper
- Use NOT_FOR_ARCHS
- Strip shared library
- Remove deprecated PTHREAD_*
- Use MAKE_CMD
- Bump PORTREVISION for science/hdf5 shlib change [1]

Changes:	http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.12-RELEASE.txt
		http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
Approved by:	portmgr (bapt) [1]

- Downgrade to the latest stable release;

- Release maintainership.

Since I'm there, support staging.

PR:		ports/182077
Submitted by:	Jason Bacon <jwbacon (at) tds.net> (maintainer)

Mark as broken: does not build with newer hdf5 version:

wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c: In
function 'hdf_put_dimorder':
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:621:
error: too many arguments to function 'H5Acreate'
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c: In
function 'hdf_set_length':
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:928:
error: too many arguments to function 'H5Acreate'
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c: In
function 'hdf_attput':
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:1110:
warning: cast to pointer from integer of different size
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:1189:
error: too many arguments to function 'H5Acreate'
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c: In
function 'hdf_copy_attr':
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:2054:
warning: cast from pointer to integer of different size
/wrkdirs/usr/ports/science/minc2/work/minc-2.2.00/libsrc/hdf_convenience.c:2071:
error: too many arguments to function 'H5Acreate'

Fix package name collision

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

science/minc2: Switch license to BSD

The license was defined as "AS-IS" but this license has no definition in
bsd.license*.mk.  As a result, this port would not build in bulk because
there was no implied acceptance of the "AS-IS" license.  Upon
re-examination, the maintainer believes it is close enough in spirit to
BSD license to be classified as BSD.

   Copyright 1993-2000 Peter Neelin and David MacDonald, McConnell Brain
   Imaging Centre, Montreal Neurological Institute, McGill University.
   Permission to use, copy, modify, and distribute this software and its
   documentation for any purpose and without fee is hereby granted,
   provided that the above copyright notice appear in all copies. The
   author and McGill University make no representations about the
   suitability of this software for any purpose. It is provided "as is"
   without express or implied warranty.

The PORTREVISION was bumped because when a license is specified, it
modifies the pkg-plist.

PR:		181350
Approved by:	bapt/culot (mentors, implicit), jwbacon (maintainer)

Upgrade to 2.2.00.

PR:		ports/180411
Approved by:	jwbacon (at) tds.net (maintainer)

Update to version 2.0.18 [1]
Fix build with clang [2]
Change WWW in pkg-descr and pkg-message to point to current web side [3]

PR:		ports/169925 [1]
Submitted by:	Jason Bacon <jwbacon@tds.net> (maintainer) [1], kwm [2], [3]
Approved by:	maintainer, kwm (mentor)

- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead

PR:             157936
Submitted by:   myself
Exp-runs by:    pav
Approved by:    pav

 - remove MD5

Sync to new bsd.autotools.mk

-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.

It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.

With help:      marcus and kwm
Pointyhat-exp:  a few times by pav
Tested by:      pgollucci, "Romain Tartière" <romain@blogreen.org>, and
                a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by:    marcus
Approved by:    portmgr

Update maintainer's email address.  Had already been done for his
other ports.

Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.

To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.

To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.

Changes to Mk/*:
 - Add runtime detection magic in bsd.port.mk

- Remove USE_GCC where it can be satisfied with base compiler on following
  FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT

science/netcdf
- Update to 3.6.2

graphics/gmt
math/grace
math/gri
math/p5-NetCDF
math/py-scientific
math/ruby-netcdf
science/gnudatalanguage
science/minc
science/minc2
science/v_sim
science/vis5d+
- Bump PORTREVISION for the changing of science/netcdf's major library version
number

PR:             111347
Submitted by:   Sunpoet Po-Chuan Hsieh <sunpoet AT sunpoet.net> (maintainer)
Approved by:    clsung (mentor)

- Fix after objformat removal

Reported by:    pointyhat

Add science/minc2.

MINC (Medical Imaging NetCDF) is a medical imaging data format and an
associated set of tools and libraries. MINC was created in 1993 by Peter
Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological
Institute. Many others have contributed to the design and implementation
MINC over the years.

PR:             ports/93495
Submitted by:   Jason Bacon <bacon (at) smithers.neuro.mcw.edu>
Repocopied by:  marcus