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

3 files changed, 85 insertions, 16 deletions

diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile
index 5f2b0572cd7f..f8852192aa08 100644
--- a/biology/biococoa/Makefile
+++ b/biology/biococoa/Makefile
@@ -1,14 +1,15 @@
 # $FreeBSD$
 
 PORTNAME=	biococoa
-PORTVERSION=	1.6.0
-PORTREVISION=	2
+PORTVERSION=	2.2.1
+PORTREVISION=	0
 CATEGORIES=	biology gnustep
-MASTER_SITES=	${MASTER_SITE_DEBIAN}
+MASTER_SITES=	http://bioinformatics.org/biococoa/downloads/ ${MASTER_SITE_DEBIAN}
 MASTER_SITE_SUBDIR=	pool/main/b/biococoa.app
-DISTNAME=	biococoa.app_${PORTVERSION}.orig
+DISTNAME=	biococoa-${PORTVERSION}-src
+EXTRACT_SUFX=	.tgz
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	theraven@FreeBSD.org
 COMMENT=	Bioinformatics framework
 
 LICENSE=	LGPL21
@@ -18,6 +19,6 @@ USE_GNUSTEP_BACK=	yes
 USE_GNUSTEP_BUILD=	yes
 USE_GNUSTEP_INSTALL=	yes
 
-WRKSRC=		${WRKDIR}/biococoa
+WRKSRC=		${WRKDIR}/biococoa-${PORTVERSION}
 
 .include <bsd.port.mk>
diff --git a/biology/biococoa/distinfo b/biology/biococoa/distinfo
index 24ea23186a0d..4e46bf63bf24 100644
--- a/biology/biococoa/distinfo
+++ b/biology/biococoa/distinfo
@@ -1,2 +1,2 @@
-SHA256 (biococoa.app_1.6.0.orig.tar.gz) = dc9afef09686699532a5fa918de18778ae1bd3fea3a66d4bc9158b35f11d1931
-SIZE (biococoa.app_1.6.0.orig.tar.gz) = 22089
+SHA256 (biococoa-2.2.1-src.tgz) = f13855e83bd40fb6a16a6d0d04fb669a1b36fcbaea9484a5c894277467a9ae0d
+SIZE (biococoa-2.2.1-src.tgz) = 368512
diff --git a/biology/biococoa/pkg-plist b/biology/biococoa/pkg-plist
index 79f13f5f033f..af00d4f3f9fc 100644
--- a/biology/biococoa/pkg-plist
+++ b/biology/biococoa/pkg-plist
@@ -1,8 +1,76 @@
-GNUstep/Local/Applications/BioCocoa.app/BioCocoa
-GNUstep/Local/Applications/BioCocoa.app/Resources/BioCocoa.desktop
-GNUstep/Local/Applications/BioCocoa.app/Resources/Info-gnustep.plist
-GNUstep/Local/Applications/BioCocoa.app/Resources/biococoa.tiff
-GNUstep/Local/Applications/BioCocoa.app/stamp.make
-GNUstep/Local/Tools/BioCocoa
-@dirrm GNUstep/Local/Applications/BioCocoa.app/Resources
-@dirrm GNUstep/Local/Applications/BioCocoa.app
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/BioCocoa
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/BioCocoa
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCAminoAcid.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCAnnotation.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCAtom.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCachedFastaFile.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCachedSequenceFile.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCChain.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCodon.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCodonDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCodonRNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCDataMatrix.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCFoundation.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCFoundationDefines.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCGeneticCode.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCMCP.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCNucleotide.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCNucleotideDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCNucleotideRNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCPairwiseAlignment.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCParseSOFT.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCPlatform.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCPreferences.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCProteinStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCResidue.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSample.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCScoreMatrix.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSecondaryStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequence.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceAlignment.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceArray.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceCodon.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceReader.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceTool.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceWriter.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSeries.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCStringDefinitions.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSuffixArray.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSymbol.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSymbolSet.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolComplement.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolDigest.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolHydropathyCalculator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolMassCalculator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolSequenceFinder.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolSymbolCounter.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolTranslator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolTranslatorDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCUtilData.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCUtilStrings.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Resources/Info-gnustep.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Resources/aminoacids.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Resources/nucleotides.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/libBioCocoa.so
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/libBioCocoa.so.%%MAJORVERSION%%
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/libBioCocoa.so.%%VERSION%%
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/libBioCocoa.so
+GNUstep/Local/Library/Libraries/libBioCocoa.so
+GNUstep/Local/Library/Libraries/libBioCocoa.so.%%MAJORVERSION%%
+GNUstep/Local/Library/Libraries/libBioCocoa.so.%%VERSION%%
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Headers
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Resources
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/Current
+GNUstep/Local/Library/Headers/BioCocoa
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework
+@dirrm GNUstep/Local/Library/Headers/BioCocoa
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/Current
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Resources
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Resources
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Headers
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework