biology/biococoa2.2.2_9

GNUstep: Bump dependent PORTREVISION

*/*: Convert to USES=tar:tgz

Convert from EXTRACT_SUFX= .tgz to USES= tar:tgz

Approved by:	blanket

audio/opus: bump consumers after update to 1.4

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.

Update a few GNUstep ports:

* devel/gnustep-make: Update to 2.8.0
 * lang/gnustep-base: Update to 1.27.0
 * x11-toolkits/gnustep-back: update to 0.28.0
 * x11-toolkits/gnustep-gui: update to 0.28.0

Also bump PORTREVISION on dependent ports.

Return theraven's ports to the pool after safekeeping his commit bit.

Move Objective-C ports to the v2 GNUstep ABI.

* Bump the LLVM revision used for GNUstep to 7, the minimum to support
   the new ABI.
 * GNUstep-back does not work with lld, so mark it to use Gold (BFD LD
   doesn't seem able to link Objective-C things).
 * Turn off some annoying debug logs in GNUstep back, which generate
   several messages per second when you move the mouse.  These should
   never have been enabled in a release build anyway.
 * Downgrade Cenon to 4.0.2.  This was the last version to actually work
   with GNUstep (the later ones use XCode >= 5 .xib files, which GNUstep
   can't parse).
 * Update gorm to git head. The current release doesn't work with the
   new Objective-C ABI, but -head has the patches to fix it.
 * Update PikoPixel and add it to the gnustep-app meta-package.
 * Update the three core GNUstep packages to the latest release.
 * Update gnumail and pantomime to the latest release and fix a linking
   error with the new ABI.
 * Update GNUstep FTP to the latest version.

Reviewed by:	bapt (previous version)

Update Objective-C LLVM version to 6.0.

Fixes aarch64 build.  Reduces depends on obsolete LLVM 4.0.

PR:		230116
Submitted by:	mikael.urankar@gmail.com
Approved by:	theraven (prior version)
Sponsored by:	DARPA, AFRL

Fix configure options for gnustep-make

We were not setting the flag to select the GNUstep ABI, so were defaulting to
using the GCC-compatible version, which was likely to trigger a lot of subtle
bugs.  This was noticed when C++ exceptions thrown through Objective-C stack
frames caused segfaults.

Mark as broken ports with no public distfiles

Update GNUstep core libraries.

Update the default Objective-C compiler.

Fix various build failures in GNUstep ports from newer versions of the GNUstep
core libraries and from changes to GNUstep Make.

Update various ports that use GNUstep and bump the portrevision of the ones
that haven't had a new release.

Make all GNUstep ports install into the System domain so that the Local domain is available for stuff built from source.

Some ports were already installing in the System domain, for these just remove the Makefile lines explicitly specifying the install domain.

The rest are installed in the Local domain, remove any overrides, update their pkg-plists and any explicit paths in the Makefiles and then bump port revision.

Approved by:	bapt (mentor)
Differential Revision:	https://reviews.freebsd.org/D2977

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

Convert bsd.gnustep.mk to USES=gnustep

Simplify gnustep ports
Hook into the regular ports framework:
- LIB_DEPENDS for library dependencies
- Use regular USE_LDCONFIG

Reuse USES=objc (automatic)
USE_GNUSTEP is now a macro to set the dependencies and build feature needed.
Accepted arguments: back base build gui

Merge deskutils/preferencepanes into deskutils/systempreferences

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)

Update BioCocoa to the latest release.

Approved by:	bapt (mentor)

Add NO_STAGE all over the place in preparation for the staging support (cat: biology)

Update to latest GNUstep core libraries. Update dependent packages with more recent releases. Remove old and bit-rotted ones. Switch to using clang 3.3 and libobjc2 1.7 by default, so modern Objective-C features work out of the box and remove a lot of configurable options for sub-optimal (and, often, unsupported / deprecated upstream) configurations. Take maintainership of GNUstep-related ports.

Several of the ports left in have scary warnings which mean that they are likely broken in lots of cases.  Future commits will fix them.

Approved by:	bapt

- cleanup comments Feature safe: yes

- reset MAINTAINER

- Get Rid MD5 support

LICENSE LGPL21

- drop USE_GNUSTEP_PREFIX

- add LICENSE:

Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)

- update for gnustep-make-2.0.0

- Welcome X.org 7.2 \o/. - Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}. - Bump PORTREVISION for ports intalling files in ${X11BASE}.

- add category gnustep PR:		103931 Approved by:	pav

The BioCocoa framework provides developers with the opportunity to add support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT files by writing only three lines of code. The framework is written in Cocoa (Objective-C).

WWW: http://bioinformatics.org/biococoa/