math/R: Update to version 3.4.2

Also
 - Build Fortran code with flang by default on amd64.
 - Remove LTO option.  Upstream does not turn it on by default, it has
   caused problems with each GCC upgrade, and any benefit is unclear.
 - Do not specify USES=compiler:openmp since that just forces GCC.

devel/icu: update to 59.1

- Temporarily keep C++98 working in consumers for Clang's default -std=

Changes:	http://site.icu-project.org/download/59
PR:		218788
Submitted by:	takefu@airport.fm, dcarmich@dcarmichael.net (early version)
Exp-run by:	antoine

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

math/R: Do not specify minimum tk version

Specifying TCLTK_USES=tk:84+ was pulling in version 8.4 for package builds on
cluster, however the Tcl/Tk 8.4 ports are being deprecated.  Simply using
TCLTK_USES=tk pulls in the default version. [1]

While here, silence a portlint warning about the location of ONLY_FOR_ARCHS and
use DISTVESION instead of PORTVERSION.

Reported by:	gahr [1]

Remove USES=objc:compiler, R doesn't use any objective c code and this breaks
R-Cran-* on FreeBSD 10

Reported by:	pkg-fallout
With hat:	portmgr

math/R: Work around bug 221127.

PR:		221127
Reported by:	rs.os@t-online.de

math/R: Fix build issues when LIBR option is off and fix runtime issue by
permitting FLANG only with RBLAS

- Only apply SONAME patches when the relevant options are chosen. This
  prevents install errors when LIBR is off.
- Only permit the FLANG option when RBLAS is chosen, because FLANG causes
  some configure-time checks to fail and the shared RBLAS library is fallen
  back upon, but not properly packaged, which causes runtime issues.
- Bump PORTREVISION

Reported by:	rhurlin@gwdg.de
Differential Revision:	https://reviews.freebsd.org/D11726

math/R: set SONAME for libraries under lib/R/lib

PR:		219776
Submitted by:	pawel
Reviewed by:	pawel, mat
Differential Revision:	https://reviews.freebsd.org/D11615

math/R: Fix typos in option descriptions

PR:		220480
Submitted by:	Trond.Endrestol@ximalas.info

Setting OPTIONS_SINGLE_FORTRAN_armv6 was incorrect.  It should be
OPTIONS_SINGLE_FORTRAN_aarch64.

Submitted by:	jbeich

math/R: Update to version 3.4.1

Upstream changes:
https://cran.r-project.org/doc/manuals/r-release/NEWS.html

Port changes:
- Add aarch64 to ONLY_FOR_ARCHS [1]
- Add off-by-default option for experimental fortran support via flang [2]

Submitted by:	[1] andrew, [2] yuri@rawbw.com

math/R: Build with gmake and add devel/gmake to RUN_DEPENDS because some
internal packages use GNU make.  While here, sort ONLY_FOR_ARCHS value to
silence portlint warning.

PR:		220341
Reported by:	yuri@rawbw.com

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

math/R: Update to version 3.4.0

The configure script now detects the correct zlib version, so setting the
r_cv_header_zlib_h is no longer necessary.

Approved by:	swills (mentor, implicit)

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

math/R: Update to version 3.3.3.

Upstream changes: https://cran.r-project.org/doc/manuals/r-release/NEWS.html

Approved by:	swill (mentor, implicit)

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

Approved by:	portmgr blanket

Fix configure with zlib 1.2.10, configure script believes that version
1.2.10 is lower than 1.2.5

Reported by:	pkg-fallout
MFH:		2017Q1

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

Fix build issue when the LTO option is enabled, do not register
${PREFIX}/lib/R/lib with ldconfig, and fix typo.

GCC 4.9 now generates slim object files which only contain intermediate
language representation for LTO. This means, either -ffat-lto-objects must
be used to create files which also contain object code or gcc-ar/gcc-ranlib
must be used to create static libraries suitable for LTO processing. This
patch sets AR/RANLIB to gcc-ar/gcc-ranlib.

The libraries under ${PREFIX}/lib/R/lib are not intended (by upstream) to
be registered with ldconfig, but are opened by dlopen(3). This means pkg
will not register shared library dependencies, so we will have to adjust
and bump ports as necessary. When necessary, unfortunately, is unclear
based on how things work upstream.

Fix typo: OPENMP_USE=compiler:openmp should have been
OPENMP_USES=compiler:openmp.

Bump PORTREVISION.

PR:	214785
        214666
Reported by:	taozhenext@gmail.com (214785), dbn (214666)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8650

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.

devel/icu: update to 58.1

Changes:	http://site.icu-project.org/download/58
PR:		214384
Exp-run by:	antoine
Approved by:	office (bapt)

math/R: More docuementation changes.

The feedback has been clear. Installing the TeX-dependent documentation
files by default is bad for users, even if that means one documentation
knob does not control the installation of all documentation files.

Reported by:	mat marino
Reviewed by:	mat
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8440

math/R: Revert documentation changes and bump PORTREVISION

In an attempt to simplify the handling of documentation for users, changes
were made in the last commit. When the documentation knob was off, (almost)
no HTML, PDF, etc. files or their sources were installed, and when the knob
was on, all these files were installed. Because some of these documentation
files depended on some very large TeX ports, despite the usual convention,
the knob was turned off by default. Unfortunately, this caused problems for
a few R-dependent ports, because they copy documentation files from math/R
when they are installed.

Reported by:	antoine
Reviewed by:	mat
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8429

math/R: Fix typo and bump PORTREVISION

Reported by:	rhurlin@gwdg.de
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8420

math/R: Update to version 3.3.2 and other changes

- Changes in version 3.3.2:
  https://cran.r-project.org/doc/manuals/r-release/NEWS.html

- Port Changes
    - Definitively set PORTNAME after removal of slave ports
    - Set MASTERS_SITES to CRAN
    - Make documentation installation simpler for users
        - make the DOCS option the only option for extra documentation
          (remove PDF option)
        - turn this option off by default since it pulls in over 1 GB of
          build dependencies (TeX and friends)
    - Do not make INFO option imply DOCS option
    - Cosmetic changes

Reviewed by:	mat
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8330

Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093

- 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)

Update email address to jrm@FreeBSD.org for ports that I maintain

Reviewed by:	mat, swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D7995

math/R: maintainer rework

See PR for signficant changes to math/R port including options,
build defaults, and patch updates.

PR:		211393
Submitted by:	Joseph Mingrone (maintainer)

math/R: Tweak previous ${OSVERSION} without ${OPSYS} commit

I made a mistake; some of the post-patch target does apply to DragonFly
as well as the pre-configure target.  Tighten up which code is designated
as FreeBSD only.  (again, a No-Op for FreeBSD)

Approved by:	OSVERSION/OPSYS blanket

math/R: Fix usage of ${OSVERSION} without ${OPSYS}

There are several OSVERSION checks but everything is specific to FreeBSD
so the entire block is wrapped with a single OPSYS check to minimize
changes to the makefile.

Approved by:	OSVERSION/OPSYS blanket

Fix dependencies, Makefile cleanups

Detailed maintainer log:
- Explicitly rely on required perl for the build
- math/R cannot be built in poudriere when math/atlas is chosen for the
  BLAS implementation.  It's not the default, so handle gracefully with
  an IGNORE (could also have set MANUAL_PACKAGE_BUILD with
  ATLAS_VARS= MANUAL_PACKAGE_BUILD=...)
- fix a type: DOC_BUILD_DEPEND -> DOCS_BUILD_DEPEND

PR:		210983
Submitted by:	jrm@ftfl.ca (maintainer)

Prevent PKGNAME collision with math/libR

Modernize and simplify port

PR:		210866
Submitted by:	jrm@ftfl.ca (maintainer)
Reviewed by:	rhurlin@gwdg.de, bapt, riggs

Bump PORTREVISION for the icu revert.

This time not bumping lang/php70, but devel/php70-intl which is the one
really depending on icu.

PR:		205120
With hat:	portmgr
Sponsored by:	Absolight

devel/icu: bump PORTREVISION on dependent ports

Joseph Mingrone <jrm@ftfl.ca> has volunteered to maintain R in bf@'s absence

PR:		210754
Submitted by:	jrm@ftfl.ca

- Update to 3.3.1
- Remove PCRE_PORT option
- Really strip the .so file
- Minor cleanup

PR:		210513
Submitted by:	wen@(myself)

Reset ports maintained by bf@ until he has time again to work on them.

PR:		210474
Submitted by:	jbeich
With hat:	portmgr-secretary

math/R: add LIBR to OPTIONS_DEFAULT to allow math/rkward-kde4 to build

PR:		207425
Reported by:	thierry

math/R: Add optimization related options to Makefile

There are a couple of enhancements that can be made to math/R
regarding optimization: one would be to enable LTO and OpenMP
whenever the compiler supports it, another one would be to allow
linking to OpenBLAS besides ATLAS or R's internal BLAS implementation.
The patch was inspired by math/octave's handling of BLAS.

PR:		207425
Submitted by:	elferdo@gmail.com
Approved by:	bf (maintainer timeout)

math/R: unbreak index.

Reported by:	cperciva@ (Portsnap buildbox)

Mk/Uses/cran: add "compiles" argument.

[1] Add "compiles" argument to cran to allow R-cran ports need to compile
code to bring in the correct compiler dependencies.  Also, ensure
consistency between the compiler selected by the R port and the R-cran ports.

[2] Migrate R-cran ports that manually specify the compiler to
USES=cran,compiles.

PR:		210343
Approved by:	wen (1), portmgr (2, blanket)

math/R: 3.2.2 -> 3.3.0

Changes: https://stat.ethz.ch/pipermail/r-announce/2016/000602.html

PR:		209315
Submitted by:	wen
Approved by:	bf (maintainer, by mail)

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

With hat:	portmgr
Sponsored by:	Absolight

Make print/ghostscript9-agpl-base the default Ghostscript port.  Upstream
changed the license to the AGPL 3 in version 9.07 so print/ghostscript9-base
is stuck at 9.06 which is almost 4 years old now.

Fix the logic in Uses/ghostscript.mk so "agpl" is treated as a real version
on its own instead of as a variant of other versions.

Fix print/ghostscript9-agpl-base to install eps2write.

Update math/asymptote to 2.37 to support newer Ghostscript.

PR:		208159
Exp-run by:	antoine
Approved by:	portmgr (antoine)

- Update to 3.2.2

PR:		203418
Submitted by:	wen@(myself)
Reviewed by:	tota@
Approved by:	maintainer(timeout, > 25 days)
Thanks to:	freebsd-bugs@mackler.org harrison.grundy@astrodoggroup.com

Use trick from arm/powerpc to fix build on sparc64.

Approved by:	portmgr (sparc64 blanket)

- Split ghostscript into X11-independent and -dependent parts:

 * print/ghostscript{7,8,9,9-agpl}-base

   Installs Ghostscript binary, libgs, and related files.
   These ports do not depend on X11 libraries (i.e. x11* devices
   are not available).  USES=ghostscript will set dependency on
   one of them depending on GHOSTSCRIPT_DEFAULT.

   The default device is set to "display" or "bbox".

 * print/ghostscript{7,8,9,9-agpl}-x11

   Installs a shared library which provides X11 support to
   the installed Ghostscript binaries.  x11* devices will be

Convert code in bsd.port.mk for USE_GHOSTSCRIPT* to USES=ghostscript.

Add GHOSTSCRIPT_DEFAULT to bsd.default-versions.mk for easy version selection.
Arguments supported: <empty>, build, run, nox11 and agpl

PR:		201201 (exp-run)
Approved by:	portmgr (mat@)
Exp run by:	antione@ (previous patch)
Differential Revision:	https://reviews.freebsd.org/D2938

Fix build with texinfo 6.0

Reported by:	pkg-fallout

Convert to USES=jpeg

MASTER_SITES cleanup.

- Replace ${MASTER_SITE_FOO} with FOO.
- Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9%
  of the time.)
- Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and
  no hint of what it should be was present.
- Fix some logic.
- And generally, make things more simple and easy to understand.

While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and
SAMBA macros.

Also, replace some EXTRACT_SUFX occurences with USES=tar:*.

Checked by:	make fetch-urlall-list
With hat:	portmgr
Sponsored by:	Absolight

R does not create proper libraries (with SONAME) pkg 1.5.2 is know skipping this
kind of libraries to avoid messing the solver with wrong provides.

Bump the port to enforce users to rebuild the package with 1.5.2 and having not
satifisfiable problem for the solver

- Don't install static libraries with INSTALL_LIB (part 1/2)

Approved by:	portmgr blanket
MFH:		2015Q2

Update icu to 55.1

math category: Remove $PTHREAD_LIBS

Note that math/PDL did not pass stage-QA before, so it was fixed.

approved by:	PTHREAD blanket

Add powerpc/powerpc64 to the list of ARCH that get libmissing by default.

Reviewed by:	jhibbits

Repair overflow condition where WCHAR_MAX != INT_MAX
https://github.com/andreas-schwab/tre/commit/182e1060dc3bfc175490f6e0e961d9330971299c

Add MISSING option to the default build on armv6.

PR:		194183
Submitted by:	mikael.urankar@gmail.com, Adreas Schwab
Approved by:	maintainer timeout (3 months without PR comment)

Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgrade

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)

Change INSTALL_DATA to install with mode 644
Remove patches and hacks that were used to work around the previous
situation
This allows to stage more ports as a regular user

Differential Revision:	https://reviews.freebsd.org/D703
Reviewed by and discussed with:	bapt
With hat:	portmgr

Fix build on head by adding missing USES=readline
(uncovered by removal of readline dep from pcre)

Repair instances, almost all courtesy of bf ;-), of spaces
and/or tabs before the =. This made doing regular expressions
on the ports tree really difficult.

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

Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.

Allow to build with texinfo from ports

With hat:	portmgr

Convert all :U to :tu and :L to :tl

Since FreeBSD 8.4 and FreeBSD 9.1 make(1) do support :tu and :tl as a
replacement for :U and :L (which has been marked as deprecated)

bmake which is the default on FreeBSD 10+ only support by default
:tu/:tl a hack has been added at the time to support :U and :L to ease
migration. This hack is now not necessary anymore

Note that this makes the ports tree incompatible with make(1) from
FreeBSD 8.3 or earlier

With hat:	portmgr

Stage support

With hat:	portmgr

Readd pre-configure-script to avoid warning about duplicated pre-configure

Support stage
Strip libR.a

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)

Chase boost and icu bump
While here convert some LIB_DEPENDS

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)

Convert to new perl framework
Convert USE_GMAKE to USES

pkg-config is needed for cairo detection

Approved by:	portmgr (bapt)

Update math/libmissing to 20130815, and adjust a dependent port

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

Rectify USE_TEX to support both of teTeX and TeXLive.

TEX_DEFAULT:
	A knob to choose teTeX or TeXLive.  One can specify in /etc/make.conf.

USE_TEX:
	A knob for port developers.  Valid keywords are listed in
	bsd.tex.mk.

Remove *_DEPENDS from ports which depend on teTeX and add USE_TEX=tetex
instead to make migration to TeXLive easier.

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

Reviewed by:	zeising

- Convert USE_GETTEXT to USES (part 3)

Approved by:	portmgr (bapt)

remove a problematic mirror

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

Chase icu, graphite2 and libexttextcat bump

Update PCRE to 8.32
Introduces the UTF-32 library pcre32
Bump PORTREVISION in dependent ports

fix compiler runtime library path after recent changes to bsd.gcc.mk

Prodded by:	gerald
Feature safe:	yes

- Remove limitation on unthreaded version of Tk

PR:		171156
Submitted by:	gahr
Approved by:	maintainer (timeout 20 days)

tell portscout to ignore the irrelevant bugfix distfile

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

- update png to 1.5.10

prevent some of the older base system texinfo utilities from being
used with others from print/texinfo; mark the non-default option
WITH_PDF_MANUALS broken (reported by A. Shterenlikht)

- 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]

fix the build with a non-default LOCALBASE

Reported by:    tota
Feature safe:   yes

update math/R to 2.14.2, and adjust dependent ports