science/R-cran-cmprsk2.2.12

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

science/R-cran-cmprsk: Update to 2.2-12

Reported by:	portscout

*: 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)

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
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Frederic Culot <frederic@culot.org>
  *  Gea-Suan Lin <gslin@gslin.org>
  *  Glenn Johnson
  *  Greg Lewis <glewis@FreeBSD.org>
  *  Igor Serikov <iserikov@acm.org>
  *  Johannes Dieterich <dieterich@ogolem.org>
  *  Johannes Dieterich <jmd@FreeBSD.org>
  *  Johannes M Dieterich <jmd@FreeBSD.org>
  *  Johannes Meixner <johannes@perceivon.net>
  *  Ju Pengfei <jupengfei@gmail.com>
  *  Kay Lehmann <kay_lehmann@web.de>
  *  Klaus Aehlig <aehlig@linta.de>
  *  Kurt Kanzenbach <kurt@kmk-computers.de>
  *  Leland Wang <llwang@infor.org>
  *  Li-Lun Wang <llwang@infor.org>
  *  Markus Brueffer <markus@FreeBSD.org>
  *  NAKATA Maho <maho@FreeBSD.org>
  *  NAKATA, Maho <maho@FreeBSD.org>
  *  Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
  *  Nakata Maho <maho@FreeBSD.org>
  *  Pav Lucistnik <pav@FreeBSD.org>
  *  Pav Lucistnik <pav@oook.cz>
  *  Pedro F. Giffuni
  *  Pedro F. Giffuni <giffunip@tutopia.com>
  *  Pedro Giffuni
  *  Pedro Giffuni <giffunip@asme.org>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Rong-En Fan <rafan@FreeBSD.org>
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Seamus Venasse <svenasse@polaris.ca>
  *  Shin'ya Murakami <murakami@ahs.scitec.kobe-u.ac.jp>
  *  Shin-ya MURAKAMI <murashin@gfd-dennou.org>
  *  Shin-ya Murakami <murashin@gfd-dennou.org>
  *  Stas Timokhin <devel@stasyan.com>
  *  Stephen Montgomery-Smith <stephen@math.missouri.edu>
  *  Steve Wills <steve@mouf.net
  *  Steve Wills <steve@mouf.net>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@sunpoet.net>
  *  TAKATSU Tomonari <tota@FreeBSD.org>
  *  TAOKA Fumiyoshi
  *  Thierry Thomas <thierry@pompo.net>
  *  Tim Cas <ports@stdrand.com>
  *  Uffe Jakobsen <uffe@uffe.org>
  *  Veniamin Gvozdikov <vg@FreeBSD.org>
  *  Vsevolod Stakhov <vsevolod@highsecure.ru>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Wen heping <wenheping@gmail.com>
  *  Ying-Chieh Liao <ijliao@FreeBSD.org>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  anholt@FreeBSD.org
  *  bacon@smithers.neuro.mcw.edu
  *  batman <batman@udel.edu>
  *  db
  *  gurkan@phys.ethz.ch
  *  ijliao
  *  jbacon
  *  maintainer.freebsd@xpoundit.com
  *  mi
  *  rafan@infor.org
  *  shurd@FreeBSD.org
  *  thierry@pompo.net
  *  will

With hat:	portmgr

science/R-cran-cmprsk: Update to 2.2-11

Remove # $FreeBSD$ from Makefiles.

- Update to 2.2-10

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

- Update to 2.2-9

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

- Update to 2.2-8 - Fix LICENSE section

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

- Add new port: science/R-cran-cmprsk

Estimation, testing and regression modeling of subdistribution
  functions in competing risks, as described in Gray (1988), A class
  of K-sample tests for comparing the cumulative incidence of a
  competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ
  (1999), A proportional hazards model for the subdistribution of a
  competing risk, JASA, 94:496-509.

  WWW: https://cran.r-project.org/web/packages/cmprsk/