science/InsightToolkit: Fix build with CMake 3.29

Support for the Comeau compiler was removed. Upstream has since updated
it's copy of VNL, which doesn't require this patch.

PR:		278693
Approved by:	portmgr (blanket)

graphics/dcmtk: update 3.6.7 → 3.6.8

Reported by:	portscout

graphics/tiff: Update to 4.6.0

PR:		278577
Exp-run by:	antoine

science/InsightToolkit: Eliminate conflict with lp_solve by renaming the shared
library

liblp_solve55.so is renamed into liblp_solve55_itk.so

References:
* https://github.com/InsightSoftwareConsortium/ITK/issues/4031
* https://github.com/RTKConsortium/RTK/issues/548

*/*: Bump jpeg-turbo users treewide

New major version 3.0.0

math/vtk9: Update 9.2.2 → 9.2.6

Reported by:	portscout

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

science/InsightToolkit: Update 5.3rc04 -> 5.3.0

science/InsightToolkit: Use more external libraries

Added external library dependencies for eigen, vxl, double-conversion.

science/InsightToolkit: Update 5.2.1 -> 5.3rc04

Also include most remote modules.

graphics/elastix: New port: Image registration toolbox

science/InsightToolkit: Update 5.0.1 -> 5.2.1

Also fork InsightToolkit to InsightToolkit501 for graphics/vv.

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

*/*: Replace science/szip with science/libaec

- Bump PORTREVISION of dependent ports for dependency change

szip does not allow redistribution in binary form without proper commercial
license. Its LICENSE_PERMS should be set to no-auto-accept which blocks building
this port, therefore building dependent ports are also blocked. Switch all
dependent ports to science/libaec to avoid conflicts and license issue.

PR:		228743, 246097, 250165

*/*: Fix ENOTIME: return my ports to the pool

Reset maintainership of my ports to ports@FreeBSD.org so others can
step in to help where I haven't been able to find the time.

Remove # $FreeBSD$ from Makefiles.

- Upgrade math/eigen3 to 3.3.8;

- Add some dependencies which might be detected by Find_Package but not
registered;

- Bump PORTREVISION of consumers.

PR:		250833
Submitted by:	/me
Approved by:	tcberner@ (KDE / maintainer) + exp-run

- Update devel/gdcm to 3.0.7.
- Bump portrevision of dependent ports.

- Update devel/gdcm to 3.0.6.
- Bump portrevision of dependent ports.

- Update devel/gdcm to 3.0.5.
- Bump portrevision of dependent ports.

- Update devel/gdcm to 3.0.4.
- Bump portrevision of dependent ports.

- Update devel/gdcm to 3.0.3.
- Bump portrevision of dependent ports.

science/InsightToolkit: fix build with GCC-based architectures

Compiling with GCC requires changes in pkg-plist.

Approved by:    tcberner (mentor)
Differential Revision:  https://reviews.freebsd.org/D21428

- Update devel/gdcm to 3.0.2.
- Bump portrevision of dependent ports.

Remove patch that does not apply

Reported by:	pkg-fallout

Temporarily mark this as broken on powerpc64 until I can investigate
further.

The full error message is:

  pkg-static: Unable to access file
/wrkdirs/usr/ports/science/InsightToolkit/work/stage/usr/local/include/ITK-5.0/compilers/ITK_COMPILER_INFO_Clang_CXX.h:No
such file or directory

I am taking this unusual step because this port takes 21 hours on the
build cluster just to get to this point.

Approved by:	portmgr (tier-2 blanket)

science/InsightToolkit: Update to 5.0.1

Changes this release:
  https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.0.0
  https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.0.1

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 devel/gdcm to 3.0.0.
- Bump portrevision of dependent ports.

- Update devel/gdcm to 2.8.9.
- Bump portrevision for dependent ports.

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

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

This port currently doesn't build on GCC-based architectures, due to
not supporting GCC8.  Make GCC8 use the same macros as the newest
supported version, GCC 7.3.

PR:		234056
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)

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

- Take maintainership of devel/gdcm.
- Update devel/gdcm to 2.8.8.
- Bump portrevision of dependent ports.

Fix typo in previous commit.

PR:		232776
Submitted by:	Piotr Kubaj
Pointy hat to:	linimon

Fix build with GCC-based architectures.

PR:		232079
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)

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

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

science/InsightToolkit: Modify patch to use ${CMAKE_DL_LIBS}

${CMAKE_DL_LIBS} expands to "" on FreeBSD where the dl functions are
included in the Standard C library (libc), but to "dl" on operating
systems where the dl functions are part of libdl.

This change to the patch does not result in a change in contents of the
resulting package.

Reported by:	jbeich

science/InsightToolkit: Fix build (r457496 accidentally excluded patch)

science/InsightToolkit: Update to 4.13.0

Changes this release:
  https://discourse.itk.org/t/itk-4-13-has-been-released/549

science/InsightToolkit: Update to 4.12.2

Changes this release:
  https://public.kitware.com/pipermail/community/2017-September/013607.html

science/InsightToolkit: Update to 4.12.1

Changes this release:
  http://public.kitware.com/pipermail/community/2017-August/013534.html

science/InsightToolkit: Update to 4.12.0

Changes this release:
  http://public.kitware.com/pipermail/community/2017-June/013214.html

science/InsightToolkit: Update to 4.11.1

Changes this release:
  http://public.kitware.com/pipermail/insight-users/2017-May/054519.html

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

science/InsightToolkit: Fix build with clang 4.0

PR:		216617
Reported by:	jbeich
Obtained from:	http://review.source.kitware.com/#/c/22043/
MFH:		2017Q2

science/InsightToolkit: Fix pkg-plist post r433341

Reported by:	tcberner

science/InsightToolkit: Update to 4.11.0

Changes this release:
  http://public.kitware.com/pipermail/insight-users/2017-January/054193.html

Fix pkg-plist post r424008

Approved by:	adamw (mentor, implicit)

science/InsightToolkit: Update to 4.10.1

Changes this release:
  http://public.kitware.com/pipermail/insight-users/2016-October/053981.html

Approved by:	adamw (mentor, implicit)

science/InsightToolkit:
- Update to 4.10.0
- Add ITK_VER variable to Makefile to simplify future pkg-plist updates
- Convert to USES=jpeg
- Add dependency on science/szip (notified by new stage-qa warning)

Changes this release:
  http://public.kitware.com/pipermail/community/2016-June/011491.html

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D6737

Update the maintainer email address for the ports I
maintain to woodsb02@FreeBSD.org

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D6278

Update to 4.9.1

PR:		208982
Submitted by:	Ben Woods <woodsb02@gmail.com> (maintainer)
Sponsored by:	Essen Linuxhotel Hackathon 2016

- 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

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

With hat:	portmgr
Sponsored by:	Absolight

Update to 4.9.0.

This update to the port also adds a lot of dependencies on system libraries
instead of using the versions bundled with ITK.

PR:		206977
Submitted by:	Ben Woods <woodsb02@gmail.com> (maintainer)

science/InsightToolkit: update 4.8.1 -> 4.8.2

PR:		204727
Submitted by:	Ben Woods <woodsb02@gmail.com> (maintainer)

Update to 4.8.1.

PR:		203472
Submitted by:	maintainer
Sponsored by:	Absolight

science/InsightToolkit: update 4.7.2 -> 4.8.0

PR:		201945
Submitted by:	Ben Woods <woodsb02@gmail.com> (maintainer)

- Update to 4.7.2
- Pass maintainership to submitter

PR:		199812

Cleanup plist

Now when it builds on 10.x, drop maintainership

- Support staging
- Fix build on 10.x

- Take maintainership

PR:		183450
Submitted by:	Jason Bacon <jwbacon@tds.net> (maintainer)

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

Readd specific EXAMPLES description because of specific comment in it

Submitted by:	kvm

Add missing description

Convert science to new options framework

- convert USE_CMAKE to USES
- while here clean up some ports from CMAKE_VERBOSE, which is intended
  for users

Approved by:	portmgr (miwi)

 - remove MD5

- Switch SourceForge ports to the new File Release System: categories starting
with P,R,S

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

bump PORTREVISION after cmake update

- Add common code to support for cmake based ports.
- Update devel/cmake to 2.6.0 (also fix ports/123092)
- Use the new CMAKE build framework in all ports using cmake

Approved by:    portmgr (pav)

Retire NO_FILTER_SHLIBS now that it no longer serves a purpose

ITK is an open-source software toolkit for performing registration and
segmentation. Segmentation is the process of identifying and classifying
data found in a digitally sampled representation. Typically the sampled
representation is an image acquired from such medical instrumentation as
CT or MRI scanners. Registration is the task of aligning or developing
correspondences between data. For example, in the medical environment,
a CT scan may be aligned with a MRI scan in order to combine the
information contained in both.

WWW: http://www.itk.org

Port maintainer: Jason W. Bacon
                 bacon@smithers.neuro.mcw.edu

PR:             ports/95166
Submitted by:   bacon at smithers.neuro.mcw.edu