[Debian-med-packaging] Bug#811711: biococoa: FTBFS with GCC 6: unknown type name
Martin Michlmayr
tbm at hpe.com
Wed Jan 20 01:32:40 UTC 2016
Package: biococoa
Version: 2.2.2-2
Severity: important
User: debian-gcc at lists.debian.org
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
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