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/mbdyn: fix build on powerpc64*

In file included from bulk.cc:35:
In file included from ./dataman.h:47:
In file included from ./mbpar.h:107:
In file included from ./../../libraries/libmbutil/parsinc.h:108:
./../../libraries/libmbutil/parser.h:275:3: error: expected identifier
                FIRSTARG,
                ^
/usr/include/machine/frame.h:112:18: note: expanded from macro 'FIRSTARG'
                        ^
1 error generated.

math/suitesparse: adapt dependency lines after modularization

Do not bump PORTREVISION, because this should not change the resulting
packages.

Note for maintainers: try to not depend on the whole suitesparse package,
especially if your port do not require GraphBLAS (the biggest one).

science/mbdyn: Unbreak build by properly implementing get_nprocs() for FreeBSD.

It looks like it was only built for one CPU before and didn't fail.
Some change in the underlying libraries triggered the build to become
multi-CPU and it began failing because get_nprocs() wasn't available
for FreeBSD and also was't properly linked to the surrounding code.
Reported by:	fallout

Remove # $FreeBSD$ from Makefiles.

Add workaround for new failure with Fortran GCC 10 frontend:

  Type mismatch in argument 't' at (1); passed REAL(4) to INTEGER(4)

PR:		246700
Approved by:	maintainer

Mark as BROKEN on powerpc64:

  libraries/libmbutil/parser.h:275:3: error: expected identifier

Approved by:	portmgr (tier-2 blanket)

science/mbdyn: use math/metis instead of expired math/metis4 for METIS option

science/mbdyn: fix build on powerpc*

result is undefined:
wraptest.cc:325:9: error: 'result' was not declared in this scope
  325 |  time = result << 32;
      |         ^~~~~~

PR:		244202
Approved by:	yuri (maintainer)

Fix math/openblas and bump dependent ports

* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]

This is correcting issues from r523749 [1][2][4] and r515970 [3]

PR:		231371
Reported by:	build cluster [1]
Reported by:	Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by:	many [5]
Reviewed by:	mat, bapt
Approved by:	implicit, since this is a build fix

science/mbdyn: Update 1.7.2 -> 1.7.3

Reported by:	portscout

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

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

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

science/dftbplus science/mbdyn science/octopus: Change from math/arpack to
math/arpack-ng

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

science/mbdyn: Take maintainership.

Reset MAINTAINER on ports maintained by amutu@amutu.com

Based on the new policy of all maintained ports reset
when maintaner is absent for 3 months.

Bug#226400 for science/py-tensorflow is ignored since 2018-03-06 (3+ months).
portscout database indicates that 48.94% of his ports aren't updated.

math/suitesparse: Update 4.0.2 -> 5.2.0

Port changes:
* Change to DISTVERSION
* Update MASTER_SITES
* Change to LICENSE_COMB=dual
* Add LIB_DEPENDS
* Unbundle metis, made it a dependency
* Update do-build and do-install
* Update WWW

Bump 11 ports.
games/naev is marked broken because it depends on the no longer installed
library.

PR:		210579
Submitted by:	yuri
Submitted by:	pfg
Approved by:	maintainer timeout (maho@FreeBSD.org, 21 months)
Approved by:	maintainer timeout (fortran@FreeBSD.org, 45 days)

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

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

* Updated to 1.7.2
* New maintainer Jov <amutu@amutu.com>
* Sorted options

Changelog:	https://www.mbdyn.org/userfiles/downloads/CHANGELOG-1.7.txt

PR:		220157
Submitted by:	Jov <amutu@amutu.com> (maintainer), pfg
Reviewed by:	matthew (mentor), matt
Approved by:	matthew (mentor)
Differential Revision:	https://reviews.freebsd.org/D11481

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 version 1.7.1 [1]
- Enable multithreaded support with devel/libatomic_ops [1]
- Remove not supported TCL option [1]
- Add LICENSE_FILE
- Convert to options helpers

https://www.mbdyn.org/userfiles/downloads/CHANGELOG-1.5.txt
https://www.mbdyn.org/userfiles/downloads/CHANGELOG-1.6.txt
https://www.mbdyn.org/userfiles/downloads/CHANGELOG-1.7.txt

PR:		212464 [1]
Submitted by:	pfg [1]

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

With hat:	portmgr
Sponsored by:	Absolight

- Use blaslapack

- Fix configure with Gotoblas2

- Fix umfpack detection

- Pet portlint.

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)

Update to 1.4.3
Stage
Strip binaries
Convert to USES=libtool

PR:		193074
Submitted by:	pfg

Reset maintainership for ports not staged with no pending PR

With hat:	portmgr

Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. A few Makefiles
where not included as they contain Latin-1 characters that break
the Phabricator workflow. Categories P-S.

CR:		D422
Approved by:	portmgr (bapt)

Modernize LIB_DEPENDS

With hat:	portmgr

- Chase revision r353611 to math/GiNaC.

Approved by:	portmgr (implicit)

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)

Convert science to new options framework

add math/metis4 to math/Makefile; update math/metis to 5.0.2; add appropriate
CONFLICTS, LATEST_LINK, and PORTSCOUT; adjust dependent ports; explicitly
note the restrictive license of the metis ports (while here, append the MPI port
to
*DEPENDS in math/parmetis, rather than using an assignment)

PR:             169578

adjust linking and comments in dependent ports after the math/atlas update;
math/atlas-devel will be updated to use the same constructs at a later date

PR:             162706
Approved by:    miwi (portmgr)
Feature safe:   yes

Mark as broken on powerpc: does not compile.

Hat:            portmgr
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

I forgot to remove unncessary patch..

Pointed out by: bf, erwin and pav

Update to 1.4.0 and unbreak for 8-exp gcc46 run.

Patch kindly sent by: bf
Discssed with: gerald

Fix for experimental gcc 4.6 build, and many small fixes
and improvements, and bump portrevision.

Submitted by:   bf

- Chase ginac shlib bump

Chase the upgrade of MPICH2.

Since I'm there, pet portlint where needed, e.g. by removing oblsolete
MD5 checksums.

PR:             ports/154715

Chase the upgrade of MPICH2.

PR:             ports/151868
Approved by:    maho (maintainer)

- Chase relocation of net/mpich2

- Bump PORTREVISION if needed

- Fix some portlint errors.

Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now
implies lang/gcc44 up from lang/gcc43.

Approved by:    portmgr

Update to 1.3.9 and unbreak.
Hoping sparc version is also builds as well.

Take over.

Mark BROKEN.

No longer pass FC, F77 and FFLAGS to CONFIGURE_ENV; this is now done via
Mk/bsd.gcc.mk.

Remove trailing whitespace to appease portlint.

Bump PORTREVISION due to change of USE_FORTRAN=yes to GCC 4.3.

- Add experimental option for Chaco.
- Remove BROKEN for Metis option: it builds fine
- Remove BROKENness for 4.x, we don't check that anymore.

PR:             126696
Submitted by:   Pedro Giffuni <pfgshield-freebsd at yahoo dot com>

Conversion from (now defunct) autoconf-2.61 to autoconf-2.62

Tested by:      exp build run (erwin)

Reset kay_lehmann@web.de by request due to lack to time to maintain ports.  We
appreciate all the help in the past.

- Remove patch files as per last PR

Reported by:    pointyhat
Pointy hat to:  araujo

- Update to 1.2.7.
- Now we use USE_FORTRAN=yes to use FORTRAN compiler.

PR:             ports/114805
Submitted by:   Kay Lehmann <kay_lehmann@web.de> (maintainer)
Approved by:    stas (mentor)

Remove always-false/true conditions based on OSVERSION 500000

Switch autoconf dependencies from 2.53 or 2.59 to 2.61.

PR:             ports/116639
Submitted by:   aDe

Fix build by renaming libcolamd.a to libcolamd_mbdyn.a.

Submitted by:   maho
Approved by:    maintainer

Fix build.

Approved by:    maintainer timeout (14 days)

Forgot to remove patch.

* remove unnecessary patch
* possible fix build on pointy hat
Approved by:    maintainer

* Migrate to gfortran.
* Bump port revision.
* Use gfortran compiled atlas/blas/lapack.
* Approved by:  portmgr(kris)

Conversion to a single libtool environment.

Approved by:    portmgr (kris)

Update to 1.2.6. [1]
Add a patch to unbreak compilation with mpich. [2]

PR:             ports/92909 [1], ports/93176 [2]
Submitted by:   Kay Lehmann <kay_lehmann@web.de> (maintainer)

SHA256ify

Approved by: krion@

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.

- Mark BROKEN on 4.X

- Does not compile on sparc64

Reported by:    krismail

New port for mbdyn, which is a MultiBody Dynamics simulation software. It comes
with lots of libraries etc.  There are two knobs which are in development at
the moment so I disabled them with an IGNORE message.  They need some work and
maybe some testing.

PR:             ports/81136
Submitted by:   Kay Lehmann <kay_lehmann@web.de>