*/*: bump consumers after devel/boost* update

With hat:	office
Sponsored by:	Future Crew, LLC

science/openbabel: Add perl build dependency

PR:		272978

science/openbabel: Fix build with llvm16

This was a bit ambiguous as it uses USE_CXXSTD for GCC while gnu++98 for
clang. However this patch was tested on 12.4-RELEASE i386/amd64,
13.1-RELEASE amd64 and MAIN amd64.

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation

science/openbabel: Update 3.1.1 → 3-1-1-178; Add tests

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

science/openbabel: Remove PYTHON option

Python bindings will be spun out into a separate port.

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.

*/*: bump all consumers after recent boost upgrade

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

devel/boost-all: bump all library consumers after boost upgrade

PR:	246106

devel/cmake: Update to 3.23.0

Update to 3.23.0.
Fix pkg-plist: using the default share/man location

Release Notes:
  https://cmake.org/cmake/help/v3.23/release/3.23.html

PR:		262886
Exp-run by:	antoine

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

*/*: Remove redundant '-*' from CONFLICTS definitions

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").

Approved by: portmgr (blanket)

science/coordgenlibs: Update 2.0.3 -> 3.0.0

science/coordgenlibs: Update 1.4.2 -> 2.0.3

Remove # $FreeBSD$ from Makefiles.

science/openbabel: Fix pkg-plist issues with non-default Python versions

PR:		253815
Approved by:	portmgr (build fix)

science/openbabel: Update 2.4.1 -> 3.1.1

- 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

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

Prepare for powerpc-on-clang by deleting hard-coded tests for libstdc++.so
as a stand-in for "are we running on gcc".

For people already testing powerpc on clang, it is possible that they
already have both compilers in base.  Thus, the assumption that "gcc is
in base" (e.g.  libstdc++.so exists) always means "force use of GCC" is
already broken.  It will be for everyone on -CURRENT once the switch is
made.

While here, standardize on compiler:c++11-lang instead of -lib (they are
equivalent these days), pet portlint, and do some other cleanup.

Approved by:	portmgr (tier-2 blanket)

Bump a few PORTREVISIONs after r498529

With hat:	portmgr

Update math/eigen3 to 3.3.7

- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7

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

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

Unbreak

science/openbabel: fix build with GCC-based architectures

While here, also add USES=gnome.

PR:		233912
Submitted by:	Piotr Kubaj <pkubaj@anongoth.pl>

science/openbabel: Take maintainership; Add the GUI option using wxWidgets-3.0

GUI is "on" by default because that's what CMakeLists.txt suggests as default.
Also improve helpers use.

New USES=eigen

  Usage:
    USES=eigen:<version>[,<type>]

    version: 2 or 3 (required)
    type:    build (default), run

  For example:
    USES=eigen:2,build,run
  will add a BUILD- and RUN_DEPENDS on math/eigen2, and
    USES=eigen:3
  will add a BUILD_DEPENDS on math/eigen3.

* Convert the existing ports to use it
  - biology/iqtree: remove run time dependency (seemed not to be needed)
  - graphics/movit: remove run time dependency (seemed not to be needed)
  - science/avogadro: add run time dependeny (installed cmake file requires it
to be present)

Reviewed by:	rakuco, mat
Differential Revision:	https://reviews.freebsd.org/D13702

science/openbabel: Update to 2.4.1

Patches removed:
  patch-git_c3abbdda, patch-gcc5-support (Integrated upstream)
  patch-scripts__CMakeLists.txt (Builds without it)

While here, set LICENSE and simplify BUILD_DEPENDS.

Changes: https://github.com/openbabel/openbabel/releases

PR:	219382
Submitted by:	Yuri Victorovich <yuri@rawbw.com>
Approved by:	garga (mentor)
Differential Revision:	https://reviews.freebsd.org/D10837

Provide more descriptive error messages for ports failing on powerpc64.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

science/openbabel: unbreak with GCC >= 6

GCC defaults to C++14 since 6.0 which no longer converts istream to
bool by default. Instead of fixing just downgrade to C++98.

PR:		216036

Reassign makc's ports back to the pool.

See "Maintainer Reset" in
https://www.freebsd.org/portmgr/policies_contributors.html. makc's last commit
was in March 31st (r412218), and his ports have been timing out since at least
July (r418155).

I also emailed him 2 weeks ago and have received no response so far.

many ports: mark broken on powerpc64

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

With hat:	portmgr
Sponsored by:	Absolight

Convert my ports to new options helpers

science/openbabel: Support gcc5 (taken from upstream)

This was really painful.   I consolidated numerous shared_ptr (TR1)
patches to a single big patch (including moving part of an existing
patch to it because the target needed yet another change).

Tested on FreeBSD 8/i386 and FreeBSD 10/amd64.  This was previously
built on DragonFly with gcc 4.7, but libstdc++ incompatibilities caused
avogadro to break which eventually broken kde4 metapackage.

Those openbabel guys are long overdue for a new release, this was a bit
absurd although maybe some clever sed'ding could have reduced the patch
count.

Approved by:	blanket (gcc5 & DF breakage)

Cleanup plist

- Convert ports of science/ and security to new USES=python

Approved by:	portmgr (implicit)

The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well

Add upstream patch to fix the build with libc++.

The original commit has been slightly tuned so that it builds with the code
in the latest stable release.

Approved by:	makc (maintainer)

- Add dependency on pkgconfig when building with cairo support [1]
- Support staging
- Use option helpers

Reported by:	Andreas Nilsson via mail [1]

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

- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)

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

Approved by:	portmgr (miwi)

science/openbabel:
- Update openbabel to 2.3.2
- Switch to CMake build system
- Add PYTHON and CAIRO options
- Don't rename babel binary, mark conflict with ancient biology/babel

science/py-openbabel:
- Merge py-openbabel to openbabel

other:
- chase openbabel update

- Remove WITH_FBSD10_FIX, is no longer needed

- Fix build on FreeBSD 10

Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since
mid 2008.

PR:             ports/159624
Submitted by:   Ruslan Mahmatkhanov <cvs-src@yandex.ru>

 - remove MD5

Sync to new bsd.autotools.mk

Update to 2.2.3

Feature safe:   yes

Builds on ia64.

Approved by: makc

Respect LOCALBASE.

Reported by:    QATty

Update to 2.2.2
Mark MAKE_JOBS_SAFE

-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 boost to 1.39
- Split boost port to separate components, with boost-all metaport

PR:             ports/137054
Submitted by:   Alexander Churanov <churanov.port.maintainer@gmail.com>
(maintainer)

Update to 2.2.1

Use my @FreeBSD.org email for the rest of my ports

- s/PORTREVSION/PORTREVISION

- Fix build on 6.3

PR:             125728
Submitted by:   Max Brazhnikov <makc@issp.ac.ru>

- Fix build on 6.X

Reported by:    ionbot, pavbot
Approved by:    maintainer via im

- Update to 2.2.0
- Pass maintainership to submitter

PR:             ports/125335
Submitted by:   Max Brazhnikov <makc@issp.ac.ru>

- Update to 2.1.1

PR:             115397
Submitted by:   KATO Tsuguru <tkato432@yahoo.com>

- Set --mandir and --infodir in CONFIGURE_ARGS if the configure script
  supports them.  This is determined by running ``configure --help'' in
  do-configure target and set the shell variable _LATE_CONFIGURE_ARGS
  which is then passed to CONFIGURE_ARGS.
- Remove --mandir and --infodir in ports' Makefile where applicable
  Few ports use REINPLACE_CMD to achieve the same effect, remove them too.
- Correct some manual pages location from PREFIX/man to MANPREFIX/man
- Define INFO_PATH where necessary
- Document that .info files are installed in a subdirectory relative to
  PREFIX/INFO_PATH and slightly change add-plist-info to use INFO_PATH and
  subdirectory detection.

PR:             ports/111470
Approved by:    portmgr
Discussed with: stas (Mk/*), gerald (info related stuffs)
Tested by:      pointyhat exp run

- Update to 2.1.0

- s,INSTALLS_SHLIB,USE_LDCONFIG,g
- these include misc/ multimedia/ net/ net-mgmt/ net-im/
  net-p2p/ palm/ print/ science/ maintained by ports@

PR:             ports/101916
Submitted by:   Gea-Suan Lin <gslin_AT_gslin dot org>

- Upgrade to 2.0.2 [1]
- portlint(1) tweak

PR:             ports/101196
Submitted by:   KATO Tsuguru <tkato432@yahoo.com>

- Update to version 2.0.1

PR:             ports/96010
Submitted by:   Ports Fury

Conversion to a single libtool environment.

Approved by:    portmgr (kris)

BROKEN on ia64: gcc internal error during build

Update to 2.0.0.

PR:             ports/90558
Submitted by:   Ports Fury

- Add SHA256

Mass-conversion to the USE_AUTOTOOLS New World Order.  The code present
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.

Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.

Preliminary documentation can be found at:
        http://people.FreeBSD.org/~ade/autotools.txt

which is in the process of being SGMLized before introduction into the
Porters Handbook.

Light blue touch-paper.  Run.

USE_LIBTOOL instead of local patch

- Update to 1.100.2

PR:             ports/63756
Submitted by:   Ports Fury

Add a dependency on gnometarget to quiet a configure warning.

* Update to 1.100.1
* Remove patches in favor of --program-prefix=open
* Install the .pc file in the correct location

PR:     53845
Submitted by:   Pav Lucistnik <pav@oook.cz>

forgot to add the patches.

science/openbabel and biology/babel binary names conflict

        renamed the binaries and manpages of science/openbabel to
        openbabel instead of babel.

PR:             ports/47109
Submitted by:   Glenn Johnson <gjohnson@srrc.ars.usda.gov>

De-pkg-comment.

add openbabel 1.100.0
Chemistry file translation program