Update BioCocoa to the latest release.

Approved by:	bapt (mentor)

3 files changed, 68 insertions, 75 deletions

diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile
index fa8e9f98e374..01c8dc882ebf 100644
--- a/biology/biococoa/Makefile
+++ b/biology/biococoa/Makefile
@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	biococoa
-PORTVERSION=	2.2.1
+PORTVERSION=	2.2.2
 PORTREVISION=	0
 CATEGORIES=	biology gnustep
 MASTER_SITES=	http://bioinformatics.org/biococoa/downloads/ ${MASTER_SITE_DEBIAN}
@@ -21,5 +21,4 @@ USE_GNUSTEP_INSTALL=	yes
 
 WRKSRC=		${WRKDIR}/biococoa-${PORTVERSION}
 
-NO_STAGE=	yes
 .include <bsd.port.mk>
diff --git a/biology/biococoa/distinfo b/biology/biococoa/distinfo
index 4e46bf63bf24..4ae6601a5597 100644
--- a/biology/biococoa/distinfo
+++ b/biology/biococoa/distinfo
@@ -1,2 +1,2 @@
-SHA256 (biococoa-2.2.1-src.tgz) = f13855e83bd40fb6a16a6d0d04fb669a1b36fcbaea9484a5c894277467a9ae0d
-SIZE (biococoa-2.2.1-src.tgz) = 368512
+SHA256 (biococoa-2.2.2-src.tgz) = 383eea4e04ca584ecf5bc06507996acf193d3b1df9afecaca6fb58cbe41df384
+SIZE (biococoa-2.2.2-src.tgz) = 358850
diff --git a/biology/biococoa/pkg-plist b/biology/biococoa/pkg-plist
index af00d4f3f9fc..6d2080af1110 100644
--- a/biology/biococoa/pkg-plist
+++ b/biology/biococoa/pkg-plist
@@ -1,76 +1,70 @@
 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/2/BioCocoa
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCAnnotation.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCAtom.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCChain.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCodon.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCodonDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCodonRNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCFoundation.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCGeneticCode.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCMCP.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCNucleotide.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCPairwiseAlignment.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCParseSOFT.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCPlatform.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCPreferences.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCProteinStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCResidue.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSample.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCScoreMatrix.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSecondaryStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequence.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceAlignment.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSeries.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSuffixArray.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSymbol.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolComplement.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolDigest.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCUtilData.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Resources/aminoacids.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Resources/nucleotides.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2
 GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/Current
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/libBioCocoa.so
 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
+GNUstep/Local/Library/Libraries/libBioCocoa.so
+GNUstep/Local/Library/Libraries/libBioCocoa.so.2
+GNUstep/Local/Library/Libraries/libBioCocoa.so.2.2.2
+@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Resources
+@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers
+@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2
+@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions
+@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework