devel/R-cran-glmnet5.0

Update R-cran-* WWW to modern URL

Old R-cran-* ports have https://cran.r-project.org/web/packages/${PORTNAME}

New R-cran-* ports have https://cran.r-project.org/package=${PORTNAME}

Replace all the old WWW URLs with new WWW URLs

Reviewed by:	fuz
Differential Revision:	https://reviews.freebsd.org/D59714

devel/R-cran-shape: Remove duplicate port

Remove the port added in 1f4ad726a01d as it duplicates
graphics/R-cran-shape, which already provides the same package.

Update devel/R-cran-glmnet to depend on graphics/R-cran-shape instead.

Reported by:	Antoine Brodin <antoine@freebsd.org>

devel/R-cran-glmnet: Update to 5.0

Add the CRAN_DEPENDS (foreach, shape, Rcpp, RcppEigen) that the 2.x
and later releases require.

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

One more small cleanup, forgotten yesterday. Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

math/R: Update to version 4.0.0

Upstream changes:
https://stat.ethz.ch/pipermail/r-announce/2020/000653.html

Also bump PORTREVISION of ports that depend on math/R.

Submitted by:	wen (in part)
Reviewed by:	jwb, Rainer Hurling <rhurlin@gwdg.de>, thierry
Differential Revision:	https://reviews.freebsd.org/D24572

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

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

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

qa: add check for NO_ARCH

If NO_ARCH is set then check that no FreeBSD elf(5) files are in $STAGEDIR.
If an elf(5) file is bundles as part of the package, but is not meant to be
run directly (i.e. the elf(5) file is a payload, and not compiled) then
those files can be added to NO_ARCH_IGNORE to avoid the check from failing,

Changes to ports:
 - Ports that have NO_ARCH set, but actually compile files have had NO_ARCH
   removed.
 - Ports that have elf(5) payloads have had those files added to
   NO_ARCH_IGNORE.
 - R-cran ports that do not set USES=cran:compiles have NO_ARCH set,

PR:		218976
Reviewed by:	antoine, mat
Approved by:	portmgr

Convert tab after WWW: in pkg-descrs to single space as per PHB

Approved by:	portmgr blanket

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 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 Mk/bsd.cran.mk to the Uses framework.

PR:		ports/184699
Reviewed by:	bapt
Approved by:	portmgr (bdrewery), wen (maintainer, timeout > 2 weeks)

Add stage support to Mk/bsd.cran.mk and all USE_R_MOD ports (aka R-cran-*).

Since this patch converts all affected ports, bsd.cran.mk no longer supports
NO_STAGE and errors out if NO_STAGE is set.

Exp-run:	ports/184216
Reviewed by:	bdrewery
Approved by:	portsmgr, wen

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
 - 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
 - Removed compatibility with K&R compilers, which was untestable due
   to lack of such compilers.
 - New functions
   . mpc_log10
   . mpc_mul_2si, mpc_div_2si
 - Speed-ups
   . mpc_fma
 - Bug fixes
   . mpc_div and mpc_norm now return a value indicating the effective
     rounding direction, as the other functions.
   . mpc_mul, mpc_sqr and mpc_norm now return correct results even if
     there are over- or underflows during the computation.
   . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
     infinite part and equals output variable is corrected.
   . mpc_fr_sub: Wrong return value for imaginary part is corrected.

Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.

Bump PORTREVISIONS of all dependent ports.

PR:		183141
Approved by:	portmgr (bdrewery)

Add NO_STAGE all over the place in preparation for the staging support (cat: devel part 4)

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 to 1.8-5

update the R base ports to 2.15.2 and adjust dependent ports

Reviewed by:	thierry, tota, wen

Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, poisson regression and the Cox model. Two recent additions are the multiresponse gaussian, and the grouped multinomial.

WWW:	http://cran.r-project.org/web/packages/glmnet/