science/mpb 1.12.0_1

*/*: bump PORTREVISION after the upgrade of OpenBLAS

science/mpb: Update to 1.12.0

- Add support for anisotropic subpixel smoothing
- Add support for computing mode-overlap integral under symmetry operation
- Disable subpixel smoothing for mesh size of one
- Various minor fixes and additional documentation

All tests passed.

Changelog:	https://github.com/NanoComp/mpb/compare/v1.11.1...v1.12.0

Reported by:	Repology

*/*: Bump PORTREVISION after math/nlopt update

*/*: bump PORTREVISION after OpenBLAS upgrade

Remark: this souldn’t be necessary, because the version of the library is the
same, but due to many changes between these releases, it is safer this way.

PR:		284314

science/mpb: Fix build with GCC 14

error: implicit declaration of function 'SCM_NEWCELL'
[-Wimplicit-function-declaration]

Thanks for the patch to salvadore@

PR:		281245

*/*: Bump PORTVERSION of math/nlopt consumers

..due to shlib change

*/*: bump PORTREVISION after the upgrade to OpenBLAS

science/mpb: Move man pages to share/man

Approved by:	portmgr (blanket)

*/*: bump PORTREVISION after the upgrade of OpenBLAS

PR:		273219

*/*: adapt to new guile framework

- change all ports using guile to USES=guile
 - flavorize guile-lib, guile-cairo, slib-guile

PR:		260960
Reported by:	Martin Neubauer <m.ne@gmx.net>
Approved by:	bofh
Differential Revision:	https://reviews.freebsd.org/D40194

science/mpb: Additions and improvements

- Add shared library
- Remove NLOPT option
- Add test target
- Pet portlint

Contrary to the patch from the PR, USE_GCC=yes is kept, otherwise errors under CURRENT (with LLVM15).

Co-authored-by:	Rainer Hurling <rhurlin@FreeBSD.org>
PR:		270105

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

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
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Frederic Culot <frederic@culot.org>
  *  Gea-Suan Lin <gslin@gslin.org>
  *  Glenn Johnson
  *  Greg Lewis <glewis@FreeBSD.org>
  *  Igor Serikov <iserikov@acm.org>
  *  Johannes Dieterich <dieterich@ogolem.org>
  *  Johannes Dieterich <jmd@FreeBSD.org>
  *  Johannes M Dieterich <jmd@FreeBSD.org>
  *  Johannes Meixner <johannes@perceivon.net>
  *  Ju Pengfei <jupengfei@gmail.com>
  *  Kay Lehmann <kay_lehmann@web.de>
  *  Klaus Aehlig <aehlig@linta.de>
  *  Kurt Kanzenbach <kurt@kmk-computers.de>
  *  Leland Wang <llwang@infor.org>
  *  Li-Lun Wang <llwang@infor.org>
  *  Markus Brueffer <markus@FreeBSD.org>
  *  NAKATA Maho <maho@FreeBSD.org>
  *  NAKATA, Maho <maho@FreeBSD.org>
  *  Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
  *  Nakata Maho <maho@FreeBSD.org>
  *  Pav Lucistnik <pav@FreeBSD.org>
  *  Pav Lucistnik <pav@oook.cz>
  *  Pedro F. Giffuni
  *  Pedro F. Giffuni <giffunip@tutopia.com>
  *  Pedro Giffuni
  *  Pedro Giffuni <giffunip@asme.org>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Rong-En Fan <rafan@FreeBSD.org>
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Seamus Venasse <svenasse@polaris.ca>
  *  Shin'ya Murakami <murakami@ahs.scitec.kobe-u.ac.jp>
  *  Shin-ya MURAKAMI <murashin@gfd-dennou.org>
  *  Shin-ya Murakami <murashin@gfd-dennou.org>
  *  Stas Timokhin <devel@stasyan.com>
  *  Stephen Montgomery-Smith <stephen@math.missouri.edu>
  *  Steve Wills <steve@mouf.net
  *  Steve Wills <steve@mouf.net>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@sunpoet.net>
  *  TAKATSU Tomonari <tota@FreeBSD.org>
  *  TAOKA Fumiyoshi
  *  Thierry Thomas <thierry@pompo.net>
  *  Tim Cas <ports@stdrand.com>
  *  Uffe Jakobsen <uffe@uffe.org>
  *  Veniamin Gvozdikov <vg@FreeBSD.org>
  *  Vsevolod Stakhov <vsevolod@highsecure.ru>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Wen heping <wenheping@gmail.com>
  *  Ying-Chieh Liao <ijliao@FreeBSD.org>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  anholt@FreeBSD.org
  *  bacon@smithers.neuro.mcw.edu
  *  batman <batman@udel.edu>
  *  db
  *  gurkan@phys.ethz.ch
  *  ijliao
  *  jbacon
  *  maintainer.freebsd@xpoundit.com
  *  mi
  *  rafan@infor.org
  *  shurd@FreeBSD.org
  *  thierry@pompo.net
  *  will

With hat:	portmgr

Remove # $FreeBSD$ from Makefiles.

science/mpb: Update to 1.11.1

Changelog: https://github.com/NanoComp/mpb/blob/master/NEWS.md

- Update from version 1.5 to 1.11.1
- Change MASTER_SITES to Github releases
- Remove MAKE_JOBS_UNSAFE
- Change dependency math/fftw to math/fftw3
- Change dependency math/blas to math/openblas
- Add devel/boehm-gc-threaded to LIB_DEPENDS
- Add USES=readline
- Use GCC compiler because of Fortran code
- Reorder Makefile
- Add option for OpenMP
- Remove post-patch target
- Add post-install target to install examples
- Change URL in pkg-descr
- Update pkg-plist

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D27031

Change the maintainer entry in rhurlin's ports

After I got a commit bit for ports, it is time now to change the maintainers entry in all 'owned' ports.

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D26398

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 Guile to version 2.2.5, modern stable version, and fix dependent ports to build against it.  Most changes are rather minor and mechanical except for the devel/gdb (obtained via their bugtracker [1], courtesy of Doug Evans).  One port (science/meep) I had to mark BROKEN after fixing it proved to be very tedious and actually unreliable.  It is very old, there are newer versions available so i

One port (devel/libruin) had revealed a bug in the new Guile code (an
auxiliary script, really) that had to be worked-round; reference to the
problematic upstream commit is provided in the patch.

PR:		229613
Exp-run by:	antoine

[1] https://sourceware.org/bugzilla/show_bug.cgi?id=21104#c8

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

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

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

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 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

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

science/mpb: back out r459622 after base r328286

For a short time LLD_BOOTSTRAP (on amd64) broke many USES=fortran
consumers but now that it's fixed the workaround can go away.
-CURRENT support in ports is primarily limited to the latest tip,
not an arbitrary old version.

PR:		225230
Tested by:	Rainer Hurling (maintainer)

Fix the build on FreeBSD 12+ by using a current version of GCC which is already used by some of the dependencies.

This avoids build errors of the following kind:

  /lib/libgcc_s.so.1: version GCC_4.6.0 required by
  /usr/local/lib/gcc6/libgfortran.so.3 not found

Submitted by:	maintainer (Rainer Hurling <rhurlin@gwdg.de>)
PR:		225230

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

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

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

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

- 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 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

3 ports categories: Remove $PTHREAD_LIBS

Categories: print, science, emulators

approved by:	PTHREAD blanket

- 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

science/mpb: put option helpers at the correct place

Submitted by:	antoine via #bsdports

Resurrect science/mpb, pass maintainership to PR submitter. - update to 1.5 - change to lang/guile2 - fix up USES and post-patch - add optional dependency on math/nlopt - install header files

PR:		196179
Submitted by:	Rainer Hurling

Remove expired ports: 2014-12-27 games/secretmaryochronicles-music: Depends on expiring games/secretmaryochronicles 2014-12-27 science/mpb: Broken for more than 6 months 2014-12-27 x11-fm/pbi-thumbnailer: Broken for more than 6 months

Deprecated ports broken for more than 6 months

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)

lang/guile: - Add USES=libtool and bump dependent ports - Replace Makefile.* patches with USES=pathfix - Replace config.h.in patch with USE_AUTOTOOLS=autoheader - Avoid automake by touching Makefile.in

Approved by:	portmgr (implicit, bump unstaged port)

Mark BROKEN: Fails to build

cc -DHAVE_CONFIG_H -I../util -I../matrices -I. -I/usr/local/include -I/usr/local/include -I/usr/local/include -D_THREAD_SAFE -pthread -c -O2 -pipe -fno-strict-aliasing -Wall -W -Wbad-function-cast -Wcast-qual -Wpointer-arith -Wcast-align -pedantic matrixio.c -o matrixio.o
In file included from /usr/local/include/hdf5.h:24,
                 from matrixio.h:24,
                 from matrixio.c:34:
/usr/local/include/H5public.h:151: warning: ISO C90 does not support 'long long'
/usr/local/include/H5public.h:152: warning: ISO C90 does not support 'long long'
In file included from /usr/local/include/hdf5.h:45,
                 from matrixio.h:24,
                 from matrixio.c:34:
/usr/local/include/H5FDlog.h:65: warning: ISO C90 does not support 'long long'
matrixio.c: In function 'write_attr':
matrixio.c:91: error: too few arguments to function 'H5Dcreate2'
matrixio.c:97: error: too few arguments to function 'H5Acreate2'

Reported by:	pkg-fallout

- 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]

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)

- New LIB_DEPENDS syntax. - USES=fortran. - Replace WITH_ATLAS with ATLAS option. - Staging.

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
 - 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
 - Removed compatibility with K&R compilers, which was untestable due
   to lack of such compilers.
 - New functions
   . mpc_log10
   . mpc_mul_2si, mpc_div_2si
 - Speed-ups
   . mpc_fma
 - Bug fixes
   . mpc_div and mpc_norm now return a value indicating the effective
     rounding direction, as the other functions.
   . mpc_mul, mpc_sqr and mpc_norm now return correct results even if
     there are over- or underflows during the computation.
   . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
     infinite part and equals output variable is corrected.
   . mpc_fr_sub: Wrong return value for imaginary part is corrected.

Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.

Bump PORTREVISIONS of all dependent ports.

PR:		183141
Approved by:	portmgr (bdrewery)