Package: biococoa Version: 2.2.2-2 Severity: important User: [email protected] Usertags: ftbfs-gcc-6 gcc-6-unknown-type-name
This package fails to build with GCC 6. GCC 6 has not been released yet, but it's expected that GCC 6 will become the default compiler for stretch. Note that only the first error is reported; there might be more. You can find a snapshot of GCC 6 in experimental. To build with GCC 6, you can set CC=gcc-6 CXX=g++-6 explicitly. You may be able to find out more about this issue at https://gcc.gnu.org/gcc-6/changes.html > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux ... > gcc BCPairwiseAlignment.m -c \ > -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-import > -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_RUNTIME=1 > -DGNUSTEP_BASE_LIBRARY=1 -fno-strict-aliasing -fexceptions -fobjc-exceptions > -D_NATIVE_OBJC_EXCEPTIONS -pthread -fPIC -Wall -DGSWARN -DGSDIAGNOSE > -Wno-import -O2 -fgnu-runtime -fconstant-string-class=NSConstantString -I.. > -I../BCAnalysis -I../BCGeneticCode -I../BCProteinStructure -I../BCSequence > -I../BCSequenceIO -I../BCSymbol -I../BCTools -I../BCTools/BCDigest > -I../BCTools/BCSequenceProperty -I../BCTools/BCSequenceTools > -I../BCTools/BCTranslation -I../BCUtils -I./../../derived_src -I. > -I/usr/local/include/GNUstep -I/usr/include/GNUstep \ > -o obj/BCAlignment.obj/BCPairwiseAlignment.m.o > BCPairwiseAlignment.m: In function '+[BCSequenceAlignment(PairwiseAlignment) > needlemanWunschAlignmentWithSequences:properties:]': > BCPairwiseAlignment.m:179:2: error: unknown type name 'BCSequence' > BCSequence *alnA = [BCSequence sequenceWithString:[NSString > stringWithCString:an length:k]]; > ^~~~~~~~~~ > > BCPairwiseAlignment.m:179:2: note: use 'struct' keyword to refer to the type > BCPairwiseAlignment.m:179:21: warning: initialization from incompatible > pointer type [-Wincompatible-pointer-types] > BCSequence *alnA = [BCSequence sequenceWithString:[NSString > stringWithCString:an length:k]]; > ^ > > BCPairwiseAlignment.m:183:2: warning: passing argument 1 of > 'arrayWithObjects:' from incompatible pointer type > [-Wincompatible-pointer-types] > return [[[BCSequenceAlignment alloc] initWithSequenceArray:[NSArray > arrayWithObjects:alnA,alnB,nil]] autorelease]; > ^~~~~~ > > BCPairwiseAlignment.m:183:2: note: expected 'id' but argument is of type 'int > *' > In file included from /usr/include/GNUstep/Foundation/Foundation.h:117:0, > from BCSequenceAlignment.h:36, > from BCPairwiseAlignment.m:31: > At top level: > /usr/include/GNUstep/Foundation/NSTextCheckingResult.h:34:33: warning: > 'NSTextCheckingTypeRegularExpression' defined but not used > [-Wunused-const-variable] > static const NSTextCheckingType NSTextCheckingTypeRegularExpression = > 1ULL<<10; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > In file included from /usr/include/GNUstep/Foundation/Foundation.h:106:0, > from BCSequenceAlignment.h:36, > from BCPairwiseAlignment.m:31: > /usr/include/GNUstep/Foundation/NSRegularExpression.h:66:32: warning: > 'NSMatchingWithoutAnchoringBounds' defined but not used > [-Wunused-const-variable] > static const NSMatchingOptions NSMatchingWithoutAnchoringBounds = 1<<4; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:65:32: warning: > 'NSMatchingWithTransparentBounds' defined but not used > [-Wunused-const-variable] > static const NSMatchingOptions NSMatchingWithTransparentBounds = 1<<3; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:64:32: warning: > 'NSMatchingAnchored' defined but not used [-Wunused-const-variable] > static const NSMatchingOptions NSMatchingAnchored = 1<<2; > ^~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:63:32: warning: > 'NSMatchingReportCompletion' defined but not used [-Wunused-const-variable] > static const NSMatchingOptions NSMatchingReportCompletion = 1<<1; > ^~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:62:32: warning: > 'NSMatchingReportProgress' defined but not used [-Wunused-const-variable] > static const NSMatchingOptions NSMatchingReportProgress = 1<<0; > ^~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:59:30: warning: > 'NSMatchingInternalError' defined but not used [-Wunused-const-variable] > static const NSMatchingFlags NSMatchingInternalError = 1<<4; > ^~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:58:30: warning: > 'NSMatchingRequiredEnd' defined but not used [-Wunused-const-variable] > static const NSMatchingFlags NSMatchingRequiredEnd = 1<<3; > ^~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:57:30: warning: > 'NSMatchingHitEnd' defined but not used [-Wunused-const-variable] > static const NSMatchingFlags NSMatchingHitEnd = 1<<2; > ^~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:56:30: warning: > 'NSMatchingCompleted' defined but not used [-Wunused-const-variable] > static const NSMatchingFlags NSMatchingCompleted = 1<<1; > ^~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:55:30: warning: > 'NSMatchingProgress' defined but not used [-Wunused-const-variable] > static const NSMatchingFlags NSMatchingProgress = 1<<0; > ^~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:52:3: warning: > 'NSRegularExpressionUseUnicodeWordBoundaries' defined but not used > [-Wunused-const-variable] > NSRegularExpressionUseUnicodeWordBoundaries = 1<<6; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:50:3: warning: > 'NSRegularExpressionUseUnixLineSeparators' defined but not used > [-Wunused-const-variable] > NSRegularExpressionUseUnixLineSeparators = 1<<5; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:48:3: warning: > 'NSRegularExpressionAnchorsMatchLines' defined but not used > [-Wunused-const-variable] > NSRegularExpressionAnchorsMatchLines = 1<<4; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:46:3: warning: > 'NSRegularExpressionDotMatchesLineSeparators' defined but not used > [-Wunused-const-variable] > NSRegularExpressionDotMatchesLineSeparators = 1<<3; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:44:3: warning: > 'NSRegularExpressionIgnoreMetacharacters' defined but not used > [-Wunused-const-variable] > NSRegularExpressionIgnoreMetacharacters = 1<<2; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:42:3: warning: > 'NSRegularExpressionAllowCommentsAndWhitespace' defined but not used > [-Wunused-const-variable] > NSRegularExpressionAllowCommentsAndWhitespace = 1<<1; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/include/GNUstep/Foundation/NSRegularExpression.h:40:3: warning: > 'NSRegularExpressionCaseInsensitive' defined but not used > [-Wunused-const-variable] > NSRegularExpressionCaseInsensitive = 1<<0; > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > /usr/share/GNUstep/Makefiles/rules.make:468: recipe for target > 'obj/BCAlignment.obj/BCPairwiseAlignment.m.o' failed > make[5]: *** [obj/BCAlignment.obj/BCPairwiseAlignment.m.o] Error 1 -- Martin Michlmayr Linux for HPE Helion, Hewlett Packard Enterprise
