Re: BioCocoa
Le Sun, Oct 12, 2008 at 03:57:33PM -0700, Scott Christley a écrit :
>
> So I got BioCocoa to produce a new source code release, and worked on
> modifying the package files. The patch is not very big so I've attached
> it. This is my first attempt, so I welcome any comments. The resultant
> deb installs fine, and I compiled some code against the installed
> BioCocoa, so it looks ok.
Dear Scott,
thanks a lot for the patch. Do you want write access to our Subversion
repository to ease your work ?
I have two comments about your patch.
There is a surprisingly high number of users (relative to our other
packages) who seem to use the current biococoa.app package for the
sequence converter demo application. I think that it would be good that
the updated biococoa source package would ship it in a binary package
that could be named sequenceconverter.app, and that could superseede
biococoa.app (in dpkg words: replace, provide and conflict).
I tried to build the new "biococoa" Debian package, with objective C
compilers from the GCC version 4.3.2. It produced the attached error
messages and did not complete. Which version of your tools are you
using?
Have a nice day,
--
Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan
dh_testdir
gs_make
This is gnustep-make 2.0.6. Type 'make print-gnustep-make-help' for help.
make[1]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0'
Making build-headers in subprojects of framework BioCocoa...
make[2]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation'
Making build-headers in subprojects of subproject BCFoundation...
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCAlignment'
Making build-headers for subproject BCAlignment...
Creating ../../BioCocoa.framework/Versions/0/Headers...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCPairwiseAlignment.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCScoreMatrix.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSequenceAlignment.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCAlignment'
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCAnalysis'
Making build-headers for subproject BCAnalysis...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCMCP.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSuffixArray.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCAnalysis'
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCGeneticCode'
Making build-headers for subproject BCGeneticCode...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCCodonDNA.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCCodon.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCCodonRNA.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCGeneticCode.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCGeneticCode'
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCProteinStructure'
Making build-headers for subproject BCProteinStructure...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCAtom.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCProteinStructure.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSecondaryStructure.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCChain.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCResidue.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSequenceStructure.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCProteinStructure'
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCSequence'
Making build-headers for subproject BCSequence...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCAnnotation.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSequence.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSequenceArray.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSequenceCodon.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCSequence'
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCSequenceIO'
Making build-headers for subproject BCSequenceIO...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSequenceReader.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSequenceWriter.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCCachedSequenceFile.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCCachedFastaFile.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCSequenceIO'
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCSymbol'
Making build-headers for subproject BCSymbol...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCAminoAcid.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCNucleotide.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSymbol.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCNucleotideDNA.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCNucleotideRNA.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSymbolSet.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCSymbol'
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCTools'
Making build-headers for subproject BCTools...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCSequenceTool.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCToolDigest.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCToolHydropathyCalculator.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCToolMassCalculator.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCToolComplement.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCToolSequenceFinder.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCToolSymbolCounter.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCToolTranslator.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCToolTranslatorDNA.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCTools'
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCUtils'
Making build-headers for subproject BCUtils...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCUtilData.h...
Creating ../../BioCocoa.framework/Versions/0/Headers/BCUtilStrings.h...
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCUtils'
Making build-headers for subproject BCFoundation...
Creating ../BioCocoa.framework/Versions/0/Headers/BCFoundation.h...
Creating ../BioCocoa.framework/Versions/0/Headers/BCFoundationDefines.h...
Creating ../BioCocoa.framework/Versions/0/Headers/BCStringDefinitions.h...
make[2]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation'
Making build-headers for framework BioCocoa...
Creating derived_src/.stamp...
Creating BioCocoa.framework/Versions/0/Resources...
Updating Version/Current symlink...
Making all in subprojects of framework BioCocoa...
make[2]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation'
Making all in subprojects of subproject BCFoundation...
make[3]: Entering directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCAlignment'
Making all for subproject BCAlignment...
Compiling file BCPairwiseAlignment.m ...
In file included from BCPairwiseAlignment.m:24:
BCSequenceAlignment.h:29:34: warning: Foundation/Foundation.h: No such file or directory
In file included from BCSequenceAlignment.h:30,
from BCPairwiseAlignment.m:24:
../BCSequence/BCSequence.h:45: error: cannot find interface declaration for 'NSObject', superclass of 'BCSequence'
../BCSequence/BCSequence.h:45: error: cannot find protocol declaration for 'NSCopying'
../BCSequence/BCSequence.h:47: error: expected specifier-qualifier-list before 'NSData'
../BCSequence/BCSequence.h:49: error: expected specifier-qualifier-list before 'NSArray'
../BCSequence/BCSequence.h:50: error: expected specifier-qualifier-list before 'NSMutableDictionary'
../BCSequence/BCSequence.h:71: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:84: error: expected ')' before 'NSData'
../BCSequence/BCSequence.h:95: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:106: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:120: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:128: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:128: error: expected ')' before 'NSRange'
../BCSequence/BCSequence.h:135: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:135: error: expected ')' before 'NSRange'
../BCSequence/BCSequence.h:141: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:148: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:155: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:162: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:169: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:176: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:185: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:191: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:191: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:203: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:209: error: expected ')' before 'NSData'
../BCSequence/BCSequence.h:215: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:228: error: expected ')' before 'NSData'
../BCSequence/BCSequence.h:279: error: expected ')' before 'BOOL'
../BCSequence/BCSequence.h:288: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:300: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:317: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:317: error: expected ')' before 'NSRange'
../BCSequence/BCSequence.h:323: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:323: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:331: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:331: error: expected ')' before 'NSRange'
../BCSequence/BCSequence.h:339: error: expected ')' before 'NSRange'
../BCSequence/BCSequence.h:349: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:358: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:371: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:371: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:378: error: expected ')' before 'NSString'
../BCSequence/BCSequence.h:384: error: expected ')' before 'NSMutableDictionary'
../BCSequence/BCSequence.h:404: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:412: error: expected ')' before 'NSRange'
../BCSequence/BCSequence.h:465: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:466: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:466: error: expected ')' before 'BOOL'
../BCSequence/BCSequence.h:467: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:467: error: expected ')' before 'BOOL'
../BCSequence/BCSequence.h:467: error: expected ')' before 'BOOL'
../BCSequence/BCSequence.h:468: error: expected ')' before 'NSArray'
../BCSequence/BCSequence.h:468: error: expected ')' before 'BOOL'
../BCSequence/BCSequence.h:468: error: expected ')' before 'BOOL'
../BCSequence/BCSequence.h:468: error: expected ')' before 'NSRange'
In file included from BCScoreMatrix.h:25,
from BCSequenceAlignment.h:31,
from BCPairwiseAlignment.m:24:
../BCSymbol/BCSymbol.h:40: error: cannot find interface declaration for 'NSObject', superclass of 'BCSymbol'
../BCSymbol/BCSymbol.h:40: error: cannot find protocol declaration for 'NSCopying'
../BCSymbol/BCSymbol.h:43: error: expected specifier-qualifier-list before 'NSString'
../BCSymbol/BCSymbol.h:44: error: expected specifier-qualifier-list before 'NSString'
../BCSymbol/BCSymbol.h:45: error: expected specifier-qualifier-list before 'NSDictionary'
../BCSymbol/BCSymbol.h:46: error: expected specifier-qualifier-list before 'NSSet'
../BCSymbol/BCSymbol.h:47: error: expected specifier-qualifier-list before 'NSSet'
../BCSymbol/BCSymbol.h:89: error: expected ')' before 'NSString'
../BCSymbol/BCSymbol.h:109: error: expected ')' before 'NSString'
../BCSymbol/BCSymbol.h:120: error: expected ')' before 'NSString'
../BCSymbol/BCSymbol.h:129: error: expected ')' before 'NSString'
../BCSymbol/BCSymbol.h:142: error: expected ')' before 'NSDictionary'
../BCSymbol/BCSymbol.h:161: error: expected ')' before 'NSString'
../BCSymbol/BCSymbol.h:170: error: expected ')' before 'NSString'
../BCSymbol/BCSymbol.h:245: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbol.h:247: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbol.h:255: error: expected ')' before 'NSSet'
../BCSymbol/BCSymbol.h:263: error: expected ')' before 'NSSet'
../BCSymbol/BCSymbol.h:272: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbol.h:280: error: expected ')' before 'BOOL'
In file included from BCScoreMatrix.h:26,
from BCSequenceAlignment.h:31,
from BCPairwiseAlignment.m:24:
../BCSymbol/BCSymbolSet.h:54: error: cannot find interface declaration for 'NSObject', superclass of 'BCSymbolSet'
../BCSymbol/BCSymbolSet.h:54: error: cannot find protocol declaration for 'NSCopying'
../BCSymbol/BCSymbolSet.h:56: error: expected specifier-qualifier-list before 'NSSet'
../BCSymbol/BCSymbolSet.h:69: error: expected ')' before 'NSArray'
../BCSymbol/BCSymbolSet.h:76: error: expected ')' before 'NSArray'
../BCSymbol/BCSymbolSet.h:85: error: expected ')' before 'NSString'
../BCSymbol/BCSymbolSet.h:88: error: expected ')' before 'NSArray'
../BCSymbol/BCSymbolSet.h:89: error: expected ')' before 'NSArray'
../BCSymbol/BCSymbolSet.h:90: error: expected ')' before 'NSString'
../BCSymbol/BCSymbolSet.h:114: error: expected ')' before 'NSSet'
../BCSymbol/BCSymbolSet.h:115: error: expected ')' before 'NSArray'
../BCSymbol/BCSymbolSet.h:116: error: expected ')' before 'NSCharacterSet'
../BCSymbol/BCSymbolSet.h:117: error: expected ')' before 'NSString'
../BCSymbol/BCSymbolSet.h:120: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbolSet.h:120: error: expected ')' before 'NSString'
../BCSymbol/BCSymbolSet.h:122: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbolSet.h:123: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbolSet.h:124: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbolSet.h:125: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbolSet.h:137: error: expected ')' before 'BOOL'
../BCSymbol/BCSymbolSet.h:141: error: expected ')' before 'NSArray'
../BCSymbol/BCSymbolSet.h:141: error: expected ')' before 'NSArray'
../BCSymbol/BCSymbolSet.h:142: error: expected ')' before 'NSString'
../BCSymbol/BCSymbolSet.h:142: error: expected ')' before 'NSString'
../BCSymbol/BCSymbolSet.h:143: error: expected ')' before 'NSData'
../BCSymbol/BCSymbolSet.h:143: error: expected ')' before 'NSData'
../BCSymbol/BCSymbolSet.h:149: error: expected ')' before 'NSZone'
In file included from BCSequenceAlignment.h:31,
from BCPairwiseAlignment.m:24:
BCScoreMatrix.h:29: error: cannot find interface declaration for 'NSObject', superclass of 'BCScoreMatrix'
BCScoreMatrix.h:30: error: expected specifier-qualifier-list before 'NSArray'
BCScoreMatrix.h:37: error: expected ')' before 'BOOL'
In file included from BCPairwiseAlignment.m:24:
BCSequenceAlignment.h:42: error: cannot find interface declaration for 'NSObject', superclass of 'BCSequenceAlignment'
BCSequenceAlignment.h:43: error: expected specifier-qualifier-list before 'NSArray'
BCSequenceAlignment.h:46: error: expected ')' before 'NSArray'
BCSequenceAlignment.h:69: error: expected ')' before 'NSRange'
BCSequenceAlignment.h:76: error: expected ')' before 'NSArray'
BCSequenceAlignment.h:107: error: expected ')' before 'NSString'
BCSequenceAlignment.h:123: error: expected ')' before 'NSArray'
BCSequenceAlignment.h:123: error: expected ')' before 'NSDictionary'
BCSequenceAlignment.h:130: error: expected ')' before 'NSArray'
BCSequenceAlignment.h:130: error: expected ')' before 'NSDictionary'
In file included from BCPairwiseAlignment.m:25:
../BCStringDefinitions.h:34: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:39: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:44: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:49: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:54: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:59: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:64: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:69: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:74: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:79: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:84: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:89: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:99: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:106: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:111: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:118: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:125: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:130: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:135: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:143: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
../BCStringDefinitions.h:148: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
BCPairwiseAlignment.m:48: error: expected ')' before 'NSArray'
BCPairwiseAlignment.m:48: error: expected ')' before 'NSDictionary'
BCPairwiseAlignment.m: In function '+[BCSequenceAlignment(PairwiseAlignment) needlemanWunschAlignmentWithSequences:properties:]':
BCPairwiseAlignment.m:52: error: 'BCSubstitutionMatrixProperty' undeclared (first use in this function)
BCPairwiseAlignment.m:52: error: (Each undeclared identifier is reported only once
BCPairwiseAlignment.m:52: error: for each function it appears in.)
BCPairwiseAlignment.m:52: warning: no '-objectForKey:' method found
BCPairwiseAlignment.m:52: warning: (Messages without a matching method signature
BCPairwiseAlignment.m:52: warning: will be assumed to return 'id' and accept
BCPairwiseAlignment.m:52: warning: '...' as arguments.)
BCPairwiseAlignment.m:55: warning: no '-objectAtIndex:' method found
BCPairwiseAlignment.m:56: warning: no '-objectAtIndex:' method found
BCPairwiseAlignment.m:59: warning: no '-UTF8String' method found
BCPairwiseAlignment.m:59: warning: initialization from incompatible pointer type
BCPairwiseAlignment.m:60: warning: no '-UTF8String' method found
BCPairwiseAlignment.m:60: warning: initialization from incompatible pointer type
BCPairwiseAlignment.m:63: error: 'NSNumber' undeclared (first use in this function)
BCPairwiseAlignment.m:63: error: expected expression before ')' token
BCPairwiseAlignment.m:70: warning: implicit declaration of function 'malloc'
BCPairwiseAlignment.m:70: warning: incompatible implicit declaration of built-in function 'malloc'
BCPairwiseAlignment.m:172: error: 'NSString' undeclared (first use in this function)
BCPairwiseAlignment.m:176: warning: 'BCSequenceAlignment' may not respond to '+alloc'
BCPairwiseAlignment.m:176: error: 'NSArray' undeclared (first use in this function)
BCPairwiseAlignment.m:176: error: 'nil' undeclared (first use in this function)
BCPairwiseAlignment.m:176: warning: no '-autorelease' method found
BCPairwiseAlignment.m: At top level:
BCPairwiseAlignment.m:180: error: expected ')' before 'NSArray'
BCPairwiseAlignment.m:180: error: expected ')' before 'NSDictionary'
BCPairwiseAlignment.m: In function '+[BCSequenceAlignment(PairwiseAlignment) smithWatermanAlignmentWithSequences:properties:]':
BCPairwiseAlignment.m:181: error: 'nil' undeclared (first use in this function)
BCPairwiseAlignment.m:182: warning: control reaches end of non-void function
make[4]: *** [obj/BCPairwiseAlignment.o] Error 1
make[3]: *** [BCAlignment.all.subproject.variables] Error 2
make[3]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation/BCAlignment'
make[2]: *** [BCFoundation.all.subproject.variables] Error 2
make[2]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0/BCFoundation'
make[1]: *** [BioCocoa.all.framework.variables] Error 2
make[1]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/biococoa/biococoa-2.1.0'
make: *** [build-stamp] Error 2
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