math/polymake: update to 4.13

Changelog: https://polymake.org/doku.php/news/release_4_11
Changelog: https://polymake.org/doku.php/news/release_4_12
Changelog: https://polymake.org/doku.php/news/release_4_13

PR:		281853

math/singular: update 4-3-2 → 4-4-0

math/polymake: Remove NATIVE option and add GitHub to MASTER_SITES

* Add GitHub as primary download site and upstream website as backup
* Remove NATIVE option, users wanting to apply CPU specific optimization
should use CPUTYPE instead using ports framework
* Use OPTIMIZED_CFLAGS option to define O3 optimization

PR:		273316
Reviewed by:	Philipp Ost <bsd@philippost.de> (maintainer)
Sponsored by:	Blinkinblox

math/polymake: update to 4.10

ChangeLog: https://polymake.org/doku.php/news/release_4_10

interfaces

topcom:
 Extend interface to access other combinations of connected, fine, and regular
 support for topcom 1.x.

fulton

 weighted_projective_space: fix rays computation

group

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

math/polymake: Update to 4.9

PR:		270423
Reported by:	maintainer

math/polymake: Update to 4.7

 - Add patch to fix compilation on 32 bit architectures. The patch was
   provided by Benjamin Lorenz of the polymake team.
   https://forum.polymake.org/viewtopic.php?f=10&p=4000

ChangeLog:	https://polymake.org/doku.php/news/release_4_7
PR:		266792

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.

*/*: bump all consumers after recent boost upgrade

math: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Aaron Dalton <aaron@daltons.ca>
  *  Alessando Sagratini <ale_sagra@hotmail.com>
  *  Alex Dupre <ale@FreeBSD.org>
  *  Alexey Dokuchaev <danfe@FreeBSD.org>
  *  Amarendra Godbole <amarendra.godbole@gmail.com>
  *  Anders Nordby <anders@FreeBSD.org>
  *  Andreas Fehlner (fehlner@gmx.de)
  *  Andrew L. Neporada <andrew@chg.ru>
  *  Andrey <gugu@zoo.rambler.ru>
  *  Andrey Zakhvatov

math/flint2: Update 2.8.5 -> 2.9.0

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

*/*: Bump after math/singular update

PR:		262510
Reported by:	Philipp Ost <Philipp Ost>

math/polymake: update to version 4.6

Changelog at <https://polymake.org/doku.php/news/release_4_6>.

math/polymake: update to 4.5

Port changes:
- update DISTVERSION (obviously ;-))
- remove compiler:openmp after commit 07fb2d5e9d001934f1670d01aec1f536f14ebde2
- remove patches patch-libnauty and patch-support_install.pl since
  they have been incorporated upstream

Upstream changes: https://polymake.org/doku.php/news/release_4_5

PR:		260395
Reported by:	Philipp Ost <bsd@philippost.de> (maintainer)

*/*: Remove more compiler:openmp instances

Reported by: antoine@
Fixes:	07fb2d5e9d00

math/nauty: Update 27r1 -> 27r3

PR:		258237
Approved by:	moritz@schmi.tt (maintainer)

math/polymake: Update the backported patch to fix the testsuite regression

math/polymake: Backport patch allowing to use external Nauty library instead of
Nauty source tree

Also fix stripping of ideal.so

math/polymake: Minor Makefile improvement

PR:		256861

math/polymake: Re-add port: Software package for research in polyhedral geometry
@ version=4.4

PR:		256861
Submitted by:	Philipp Ost <bsd@philippost.de> (original version)

Remove expired ports:
2014-06-22 www/phpbb-devel: Use www/phpbb3 instead
2014-06-22 math/polymake: Does not build with any supported version of Perl
2014-06-22 www/phpsysinfo-dev: Use www/phpsysinfo instead

Remove all the bootstrap files (.bs) from the plists.

Starting with perl 5.20, they're not installed any more if empty,
and on FreeBSD, they're (always ?) empty.

PR:		190681
Submitted by:	mat
Exp-Run by:	antoine
Sponsored by:	Absolight

Deprecate and set expiration date: Does not build with any supported
version of Perl

With hat:	portmgr

Reset a few maintainers

<adam.freebsd@fastmail.fm>: host in1-smtp.messagingengine.com[66.111.4.72]
    said: 550 5.1.1 <adam.freebsd@fastmail.fm>: Recipient address rejected:
    User unknown in local recipient table (in reply to RCPT TO command)

<dnscheckengine-port@academ.com>: host ASPMX.L.GOOGLE.com[74.125.131.26] said:
    550-5.1.1 The email account that you tried to reach does not exist. Please

<kawahara@nlp.kuee.kyoto-u.ac.jp>:
Sorry, no mailbox here by that name. (#5.1.1)

<hnsmaster@h14m.org>: Host or domain name not found. Name service error for
    name=h14m.org type=AAAA: Host found but no data record of requested type

Replace USE_GCC=4.2+ by USE_GCC=any. [1]
And USE_GMAKE by USES=gmake where touching a port because of the above.

Approved by:	portmgr (bapt) [1]

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

- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)

- When DISABLE_MAKE_JOBS or MAKE_JOBS_UNSAFE is set, also set
  MAKE_JOBS_NUMBER to 1. This makes it safe to do -j${MAKE_JOBS_NUMBER}
  without any extra logic.
- Cleanup ports working around the empty MAKE_JOBS_NUMBER
- This also fixes several ports that were expecting MAKE_JOBS_NUMBER
  to always have a number

Reviewed by:	bapt
Spotted by:	John Marino <draco@marino.st>
With hat:	portmgr

- Set default perl version for ports which currently using
  (5.x+ and x < 12) scheme.

Approved by: bapt@ (portmgr@)

- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@ (bapt@)

Fix spacing.

Mark as ignored with Perl 5.14+
(port must be upgraded at least to 2.10 to unbreak build)

- Update to 2.9.9
- Add warning that make_jobs_safe may overwhelm some computers
- Portlint

PR:             ports/152152
Submitted by:   Ewgenij Gawrilow <ewgenij.gawrilow@o2online.de>
Approved by:    maho (mentor)

- Get Rid MD5 support

Get rid of USE_GCC=3.4

PR:             ports/144669
Submitted by:   Andrius Morkunas <hinokind@gmail.com>
Approved by:    maintainer timeout (6 weeks)

Switch to use newer GMP version.

PR:             ports/144487
Submitted by:   ale
Approved by:    portmgr (-exp run by erwin)

Chase libgmp and bump PORTREVISION.

Introduce Perl 5.10.0

- Update to 2.3

PR:             108549
Submitted by:   Ewgenij Gawrilow<gawrilow@math.tu-berlin.de> (maintainer)

Chase gmp library and bump PORTREVISION.

- Apply vendor patch 1:
  Description: Fixed errors in handling derived object types (like TightSpan).

Submitted by:   Ewgenij Gawrilow <gawrilow@math.TU-Berlin.DE> (maintainer)

- Another stab on doing pkg-plist right

- Fix plist creation

Reported by:    krismail
Pointy hat to:  pav

- Update to 2.2

PR:             ports/94476
Submitted by:   Ewgenij Gawrilow <gawrilow@math.tu-berlin.de> (maintainer)

SHA256ify

Approved by: krion@

- Unbreak checksums
- Simplify a little

PR:             ports/76959
Submitted by:   Ewgenij Gawrilow <gawrilow@math.TU-Berlin.DE> (maintainer)

BROKEN: Size mismatch

- Update to patchlevel 2
- Don't install perl modules in configure phase

PR:             ports/75856, ports/75965
Submitted by:   Ewgenij Gawrilow <gawrilow@math.TU-Berlin.DE> (maintainer)

Polymake is a versatile framework for experimental discrete mathematics.  The
standard distribution contains tool collections for the algorithmic treatment
of polytopes and polyhedra, and finite simplicial complexes.  It offers an
unified interface to a wide variety of algorithms and free software packages
from the computational geometry field, such as convex hull computation or
visualization tools.

PR:             ports/75405
Submitted by:   Ewgenij Gawrilow <gawrilow@math.TU-Berlin.DE>