math/rpy2: Update 2.7.8 -> 2.9.4; Move to math/py-rpy2

Port changes:
* Add LICENSE_FILE
* Update dependencies
* Support for python-2 is dropped
* Update WWW to https

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).

Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the

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

After r446199 libR.so has SONAME and was made visible for
consumer ports. Register correct dependency by using LIB_DEPENDS
instead of BUILD|RUN_DEPENDS dance.

math/rkward-kde4:
- Add 2 missing files to pkg-plist also

PR:		219776
Submitted by:	myself
Approved by:	maintainers timeouts

Update devel/readline to 7.0 patch 3

- Bump PORTREVISION for shlib change

Changes:	https://cnswww.cns.cwru.edu/php/chet/readline/CHANGES
		https://lists.gnu.org/archive/html/bug-bash/2016-09/msg00107.html
		https://lists.gnu.org/archive/html/bug-readline/2017-01/msg00002.html
Differential Revision:	https://reviews.freebsd.org/D11172
PR:		219947
Exp-run by:	antoine

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

math/rpy2: stop linking against math/R depends

While here, switch back to Clang build but keep RPATH which is a quirk
to avoid loading /usr/lib/libgcc_s.so during dlopen() race.

PR:		214384

- Update devel/icu to 57.1.
- Clean up the Makefile.
- Follow some upstream recommendations (--with-data-packaging=archive,
  --disable-renaming, -DICU_NO_USER_DATA_OVERRIDE).
- Patch makefiles to install static libraries with INSTALL_DATA so they
  aren't stripped.
- Patch config/mh-bsd-gcc to sync with config/mh-linux-gcc.
- Fix endianness detection in ICU.  The code wanted to use BYTE_ORDER
  defined in machine/endian.h, but this isn't visible because ICU is
  compiled with _XOPEN_SOURCE.  Patch the code to use _BYTE_ORDER instead.
- Compile ICU with C++11 compiler to enable move constructors.
- Patch ICU to fix a problem with atomics in the case of a C++11 compiler
  without C++11 header <atomic> (like Clang on FreeBSD 9).
- Bump all ports that depend on it due to library version change.
- Add USES=compiler:c++0x to some ports that pick up -std=c++0x from ICU
  pkgconfig files.
- Add USES=compiler:c++11-lib to graphics/libcdr01 because it also needs
  a C++11 runtime library now.  Add this to all ports that depend on it
  so their executables load the right libstdc++.so on FreeBSD 9.

PR:		205120
Exp-run by:	antoine
Approved by:	portmgr (antoine)

- Fix trailing whitespace in pkg-descrs, categories [g-n]*

Approved by:	portmgr blanket

Remove ${PORTSDIR}/ from dependencies, categories m, n, o, and p.

With hat:	portmgr
Sponsored by:	Absolight

Update to 2.7.8

PR:		207163
Submitted by:	tkato432 yahoo com
Sponsored by:	Absolight

- Strip libraries

Canonicalize some dependencies on numpy

- Convert ports of math/ to new USES=python

Approved by:	portmgr (implicit)

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)

Add USES=readline to fix build on -current.

- Stage support [1]
- Update to 2.4.0 [1]
- Reset maintainer to ports@

PR:		190365 [1]
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com> [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)

Update math/R to 3.0.2 patched r64207 and math/R-cran-SuppDists to 1.1-9.1;
adjust dependent ports

Reviewed by:	pfg, thierry, tota

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:
math)

- Update to 2.3.6

Update math/R to 3.0.1-patched, and adjust dependent ports;
synchronize math/rpy with upstream repository

Reviewed by:	wen
Approved by:	wen, tota

update math/R to 2.15.3, and adjust dependent ports

update the R base ports to 2.15.2 and adjust dependent ports

Reviewed by:	thierry, tota, wen

update math/R to 2.15.1, switch to the new options format, and
adjust dependent ports

- update png to 1.5.10

- update math/R-cran-psych to 1.2.1 [1]
- update math/R to 2.15.0, and adjust dependent ports
- minor changes to bsd.cran.mk [2]: rename MASTER_CRAN_SITES to
  MASTER_SITE_CRAN, as in bsd.sites.mk; make the install target more
  flexible and allow CRAN ports to override it; add a regression-test
  target; set USE_FORTRAN to match math/R; remove some of the
  redundant checks of USE_R_MOD; honor NOPORTDATA and NOPORTDOCS

Reviewed by:    thierry, tota, wen
Approved by:    D. Rue (maintainer) [1], wen [2]

- Update to 2.2.6

update math/R to 2.14.2, and adjust dependent ports

update math/R to 2.14.1, and adjust dependent ports

- update to 2.2.5

update math/R to 2.14.0, math/R-cran-sp to 0.9-91, and adjust
dependent ports

Approved by:    linimon (portmgr), thierry, tota, wen
Feature safe:   yes

- Update to 2.2.4

update math/R to 2.13.2, and adjust dependent ports

- Update to 2.2.3

update R to 2.13.1 [1], and adjust dependent ports (this
includes workarounds intended to fix the broken sparc64
build, and fixes to the static libR, which is now in a
separate slave port, math/libR)

PR:             158947 [1]
Submitted by:   wen ([1], independently)

- update to 2.13.0
- switch to the bundled Rblas and Rlapack by default (this
  can be changed by setting BLAS and LAPACK) which favors
  correctness in some corner cases over a slight performance
  penalty; this will be revisited after the blas and lapack
  updates
- replace the STATIC_LIBR option with a LIBR option (on
  by default): if on, libR.a and libR.so are installed,
  and R is linked to libR.so. Otherwise, R is static, and
  no libRs are installed.
- remove the superfluous copy of libR.so in ${LOCALBASE}/lib [1]
- enable the cairo and pango elements in the X11() graphics
  device by default, controlled by new PANGOCAIRO option
- add a few small patches to dependent ports, bumping
  PORTREVISION where necessary

PR:             153309 [1]
Approved by:    thierry (rkward*), wen (rpy*, R-cran-*)

- Get Rid MD5 support

- Update R to 2.12.2, a bugfix release
- Bump PORTREVISION of dependent ports,
  where necessary

Approved by:    makc, miwi (mentors, implicit)

- Update R to 2.12.1
- Bump PORTREVISION of
  dependent ports

Approved by:    makc, miwi (mentors, implicit)
                pav (portmgr)
Feature safe:   yes

- Update to 2.1.3

Feature safe:   yes

- Force repocopy rpy --> rpy2

Feature safe:   yes