Remove non staged ports without pending PR from s*

Convert a bunch of USE_BZIP2 to USES=tar:bzip2

Approved by:	portmgr (not really, but touches unstaged ports)

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)

Fix some non default LIB_DEPENDS

With hat:	portmgr

Modernize LIB_DEPENDS

With hat:	portmgr

Convert GMAKE to MAKE_CMD
Please note that lots of invocation of MAKE_CMD here are wrong as they do not
properly respect MAKE_ENV and friends

With hat:	portmgr

Mark broken: Fails to build

c++  -O2 -pipe -Wno-error=return-type -fno-strict-aliasing -DHAVE_CMATH=1
-DHAVE_CSTDIO=1 -DHAVE_CSTDLIB=1 -DHAVE_CSTRING=1 -DHAVE_CSTDDEF=1
-DHAVE_DECL_PUTENV=1 -DHAVE_PUTENV=1 -DHAVE_DECL_SETENV=1 -DHAVE_SETENV=1
-DHAVE_FUNC_ISINF=1   -I. -I../../../include
-I/wrkdirs/usr/ports/science/psi3/work/psi3/include
-I/wrkdirs/usr/ports/science/psi3/work/psi3/src/lib -I../../../src/lib  -c
ip_read.cc -o ip_read.o
ip_read.cc:63:3: error: use of undeclared identifier 'yyparse'
  yyparse();
  ^
ip_read.cc:105:3: error: use of undeclared identifier 'yyparse'
  yyparse();
  ^
2 errors generated.

Reported by:	pkg-fallout since february 2014
With hat:	portmgr

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)

- Fix all cases of 'No newline at end of file' in ports tree

Approved by: portmgr (bapt)

Host some documens in local-distfiles. Somehow documents are dissapeared.
The reason seems that developers are now interested in psi4.

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

 - remove MD5

Build fix with gotoblas.

Feature safe:   yes.

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

Approved by:    portmgr

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

Silent update of distfiles, update is only for pdf documents.
pdf files are also updated to 3.4.0.

Build fix with gcc44 (upcoming)

Spotted by: gerald

Update to 3.4.0.

Fix build with gcc43.

Spotted by:     pav

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

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

Tested by:      exp build run (erwin)

A build fix.

* Update to 3.3.0.
* Build fix with
NOPORTDOCS=yes,  NOPORTEXAMPLES=yes, NOPORTDATA=yes, FORCE_PACKAGE=yes [1].

Spotted by: itetcu [1]

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

* Only use gfrotran42. not using gcc42.
* Bump portrevision.

*bump port revision
*use gfortran compiled atlas/blas/lapack

Migrate to gfortran.
BLAS is now user settable (math/blas or math/atlas).

Remove USE_REINPLACE from all categories starting with S

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.

update to 3.2.3

Fix build
pdf files are updated without changing the version number.
Recently psi3 3.2.2 has been released, and users manual,
programmers manual and installation doc pdfs are updated accordingly.

This is tempral fix and we must update to 3.2.2 soon.

Submitted by:   kris via pointyhat
Approved by:    portmgr (marcus)

BROKEN: Size mismatch

Approved by:    portmgr (kris)

remove extra dir

Submitted by:   kris via pointyhat

fix pkg-plist

Submitted by:   kris via pointyhat

BROKEN on 4.x: Does not compile

Fix build with WITH_OPTIMIZED_FLAGS defined

PR:             74013
Submitted by:   Jie Gao <gaoj at cpsc.ucalgary.ca>

Fix build on 5-STABLE

Submitted by:   pointyhat

Autotools cleanup.  Remove autoconf257 (259), automake17 (18), and
libtool14 (13/15).

PR:             67768
Submitted by:   ade
Approved by:    4-exp bento runs (thanks, kris!)

update to 3.2.1

Make portlint happy by replacing space to tab

PR:             65409
Submitted by:   trevor

1) add documents
2) add note for citation in pkg-message

The PSI3 suite of quantum chemical programs is designed for efficient,
high-accuracy calculations of properties of small to medium-sized molecules.
The package's current capabilities include a variety of Hartree-Fock,
coupled cluster, complete-active-space self-consistent-field,
and multi-reference configuration interaction models.
Molecular point-group symmetry is utilized throughout to maximize efficiency.