science/harminv: update 1.3.1 → 1.4.2; add shared libraries

PR:	281283
Approved by:	devel@stasyan.com (maintainer's timeout; 36 days)

science/meep: Add missing Python dependencies

https://github.com/NanoComp/meep/issues/2912

science/meep: Add harminv run-time dependency

science/meep: update 1.28.0 → 1.29.0

*/*: bump PORTREVISION after the upgrade to OpenBLAS

science/meep: update 1.27.0 → 1.28.0

Reported by:	portscout

*/*: chase the upgrade of BLAS / LAPACK to 3.12.0

PR:		275860

*/*: bump PORTREVISION after the upgrade of OpenBLAS

PR:		273219

science/meep: Update 1.26.0 → 1.27.0

Reported by:	portscout

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

science/meep: Update 1.25.0 → 1.26.0

Reported by:	portscout

science/meep: Update 1.24.0 -> 1.25.0

Reported by:	portscout

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/meep: Fix build on i386

Reported by:	fallout

science/meep: Re-add port: Finite-difference time-domain software for
electromagnetic simulations

Remove expired ports:

2020-01-10 astro/viking: Depends on broken and expiring graphics/mapnik
2020-01-10 audio/slv2: Broken for more than 5 months
2020-01-10 audio/triceratops-lv2: Broken for more than 5 months
2020-01-10 cad/brickutils: Broken for more than 3 months, unmaintained
2020-01-10 deskutils/zanshin: Broken for more than 5 months
2020-01-10 devel/elixir-gen_state_machine: Broken for more than 6 months
2020-01-10 devel/elixir-swarm: Depends on broken and expiring
devel/elixir-gen_state_machine
2020-01-10 devel/erlang-clique: Depends on broken and expiring
devel/erlang-cuttlefish
2020-01-10 devel/erlang-gen_rpc: Broken for more than 6 months
2020-01-10 devel/erlang-msgpack: Broken for more than 6 months
2020-01-10 devel/ocaml-deriving-ocsigen: Broken for more than 6 months
2020-01-10 devel/p5-rpm-build-perl: Broken for more than 7 months
2020-01-10 devel/shedskin: Broken for more than 3 months, unmaintained

Deprecate ports broken for too long

math/gsl: update to 2.6

- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine

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 it should be fixed by updating.

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

devel/boehm-gc: update to 7.6.8

ChangeLog: https://github.com/ivmai/bdwgc/releases/tag/v7.6.8

* Giving maintainership to yasu@utahime.org
* Bumping PORTREVISION for dependent ports

PR:	230577
Submitted by:	yasu@utahime.org
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16704

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

Update math/gsl to 2.5

PR:		229067

science/meep: Add license; Add missing dependencies; Order USExx section

Approved by:	Approved by:    portmgr blanket

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

Fix options usage.

You cannot set a variable after any include and use it in options, as
options is one of the few things that are done very very early.

PR:		223071
Reported by:	antoine
Sponsored by:	Absolight

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

- Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL

Approved by:	portmgr blanket

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

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.

- 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

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

With hat:	portmgr
Sponsored by:	Absolight

Fix build. Options helpers cannot be used here.

Reported by:	amdmi3

Add an option for mpich2, and set de default according the OS version.

Submitted by:	Stas Timokhin (maintainer)

- 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

- Switch to guile2

- Upgrade meep to 1.2.1 and unbreak.

Submitted by:	Stas Timokhin <devel (at) stasyan.com>

- 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

Mark BROKEN: Depends on conflicting guile and guile2 (via libctl)

Reported by:	pkg-fallout

- Update net/openmpi to 1.8.4

Cleanup plist

- Update net/openmpi from 1.8.2 to 1.8.3

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)

- Update net/openmpi from 1.8.1 to 1.8.2

- Convert net/openmpi to USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Use BROKEN_sparc64

Approved by:	portmgr (implicit, bump unstaged port)

- Avoid dependency on bash
- Remove dependency on libltdl
- Add USES=libtool

Quote ${CC} and similar variables in MAKE_ARGS.

Reported by:	Dominic Fandrey <kamikaze@bsdforen.de>

- 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]

- Fix build [1]
- Mute REINPLACE_CMD

Reported by:	swills [1]

- Update openmpi from 1.6.5 to 1.8 (new stable version)
- Convert USE_BZIP2 to USES

- Support staging
- Convert LIB_DEPENDS to new syntax

Approved by:	portmgr (blanket)

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)

Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes".  In most cases
USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)

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

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

Update to 1.2

PR:		ports/178240
Submitted by:	Stas Timokhin <devel@stasyan.com>

- Fix build after USES=pathfix update obsoleted the need for a patch in
  r315827

Replace USE_GCC=4.6+ and USE_GCC=4.4+ by USE_GCC=yes.

Right now this is a noop in the former case and a noop in the latter
case unless lang/gcc44 has been installed explicitly.

This puts a bit more emphasis on standardizing on a canonical version
"current" GCC and makes it easier to update that canonical version
by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port.

That is, USE_GCC=yes means "use a decent/modern version of GCC" without
having to worry about details.

Approved by:	portmgr (bdrewery)

- Fix double usage of USES

- Fix pkgconfig

Reported by:	pkg (DEVELOPER_MODE)

- Convert USE_ICONV=yes to USES=iconv
- Change USE_GNOME=pkgconfig|gnomehack to USES=pathfix|pkgconfig and
  USE_GETTEXT=yes to USES=gettext while here

- Convert USE_GETTEXT to USES (part 3)

Approved by:	portmgr (bapt)

- Convert to Optionsng
- While here trim header

Replace USE_GCC=4.5+ by USE_GCC=4.6+ which has been transparently
done by the ports infrastructure for a while.

Approved by:    maintainer timeout
Feature safe:   yes

- 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

- Chase guile shared lib bump
- Add an entry to UPDATING

- Add optional dependency net/openmpi
- Add lib_depends textproc/gsed
- Make datadir safe
- Move pkgconfig from lib to libdata
- Make patches to configure prefix friendly

PR:             ports/155655
Submitted by:   Klaus Aehlig <aehlig@linta.de>
Approved by:    maho (mentor) and
                        Stas Timokhin <devel@stasyan.com> (maintainer)

Clean up "current" versions of autotools components to further reduce
tree-churn on updates.

- Fix build

PR:             146745
Submitted by:   Stas Timokhin <devel@stasyan.com> (maintainer)

Bounce PORTREVISION for gettext-related ports.  Have fun, ya'll.

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation
software package developed at MIT to model electromagnetic systems,
along with our MPB eigenmode package.

WWW: http://ab-initio.mit.edu/wiki/index.php/Meep

PR:             ports/142158
Submitted by:   Stas Timokhin <devel@stasyan.com>