dpkg-buildpackage -rfakeroot -D -us -uc dpkg-buildpackage: warning: using a gain-root-command while being root dpkg-buildpackage: source package biococoa dpkg-buildpackage: source version 2.2.2-1build1 dpkg-buildpackage: source changed by Matthias Klose dpkg-source --before-build biococoa-2.2.2 dpkg-buildpackage: host architecture i386 fakeroot debian/rules clean test -x debian/rules dh_testroot rm -f debian/stamp-makefile-build debian/stamp-makefile-install GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 -k clean This is gnustep-make 2.6.2. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2' rm -rf ./*~ ./obj Making clean in subprojects of framework BioCocoa... make[2]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' rm -rf ./*~ ./obj Making clean in subprojects of subproject BCFoundation... make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' rm -rf ./*~ ./obj make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' make[2]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making clean for framework BioCocoa... rm -rf \ \ ./BioCocoa.framework ./derived_src make[1]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2' dh_clean rm -f debian/libbiococoa2.install rm -f debian/libbiococoa-dev.install /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/var/www/debian/biococoa/biococoa-2.2.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \ fi Removing patch link-libs.patch Restoring GNUmakefile No patches applied rm -rf ./.pc rm -f debian/stamp-patch* dpkg-source -b biococoa-2.2.2 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: patches are not applied, applying them now dpkg-source: info: applying link-libs.patch dpkg-source: info: building biococoa using existing ./biococoa_2.2.2.orig.tar.gz dpkg-source: info: building biococoa in biococoa_2.2.2-1build1.debian.tar.gz dpkg-source: info: building biococoa in biococoa_2.2.2-1build1.dsc debian/rules build test -x debian/rules mkdir -p "." /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2' cd . && QUILT_PATCHES=/var/www/debian/biococoa/biococoa-2.2.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2 File series fully applied, ends at patch link-libs.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2' GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 This is gnustep-make 2.6.2. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2' Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... /usr/share/GNUstep/Makefiles/mkinstalldirs ../../BioCocoa.framework/Versions/2/Headers /usr/bin/install -c -p -m 644 BCPairwiseAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCPairwiseAlignment.h /usr/bin/install -c -p -m 644 BCScoreMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCScoreMatrix.h /usr/bin/install -c -p -m 644 BCSequenceAlignment.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceAlignment.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... /usr/bin/install -c -p -m 644 BCMCP.h ../../BioCocoa.framework/Versions/2/Headers/BCMCP.h /usr/bin/install -c -p -m 644 BCSuffixArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSuffixArray.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... /usr/bin/install -c -p -m 644 BCSeries.h ../../BioCocoa.framework/Versions/2/Headers/BCSeries.h /usr/bin/install -c -p -m 644 BCSample.h ../../BioCocoa.framework/Versions/2/Headers/BCSample.h /usr/bin/install -c -p -m 644 BCPlatform.h ../../BioCocoa.framework/Versions/2/Headers/BCPlatform.h /usr/bin/install -c -p -m 644 BCParseSOFT.h ../../BioCocoa.framework/Versions/2/Headers/BCParseSOFT.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... /usr/bin/install -c -p -m 644 BCCodonDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonDNA.h /usr/bin/install -c -p -m 644 BCCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCCodon.h /usr/bin/install -c -p -m 644 BCCodonRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCCodonRNA.h /usr/bin/install -c -p -m 644 BCGeneticCode.h ../../BioCocoa.framework/Versions/2/Headers/BCGeneticCode.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... /usr/bin/install -c -p -m 644 BCAtom.h ../../BioCocoa.framework/Versions/2/Headers/BCAtom.h /usr/bin/install -c -p -m 644 BCProteinStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCProteinStructure.h /usr/bin/install -c -p -m 644 BCSecondaryStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSecondaryStructure.h /usr/bin/install -c -p -m 644 BCChain.h ../../BioCocoa.framework/Versions/2/Headers/BCChain.h /usr/bin/install -c -p -m 644 BCResidue.h ../../BioCocoa.framework/Versions/2/Headers/BCResidue.h /usr/bin/install -c -p -m 644 BCSequenceStructure.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... /usr/bin/install -c -p -m 644 BCAnnotation.h ../../BioCocoa.framework/Versions/2/Headers/BCAnnotation.h /usr/bin/install -c -p -m 644 BCSequence.h ../../BioCocoa.framework/Versions/2/Headers/BCSequence.h /usr/bin/install -c -p -m 644 BCSequenceArray.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h /usr/bin/install -c -p -m 644 BCSequenceCodon.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... /usr/bin/install -c -p -m 644 BCSequenceReader.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h /usr/bin/install -c -p -m 644 BCSequenceWriter.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h /usr/bin/install -c -p -m 644 BCCachedSequenceFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h /usr/bin/install -c -p -m 644 BCCachedFastaFile.h ../../BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... /usr/bin/install -c -p -m 644 BCAminoAcid.h ../../BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h /usr/bin/install -c -p -m 644 BCNucleotide.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotide.h /usr/bin/install -c -p -m 644 BCSymbol.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbol.h /usr/bin/install -c -p -m 644 BCNucleotideDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h /usr/bin/install -c -p -m 644 BCNucleotideRNA.h ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h /usr/bin/install -c -p -m 644 BCSymbolSet.h ../../BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... /usr/bin/install -c -p -m 644 BCSequenceTool.h ../../BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h /usr/bin/install -c -p -m 644 BCToolDigest.h ../../BioCocoa.framework/Versions/2/Headers/BCToolDigest.h /usr/bin/install -c -p -m 644 BCToolHydropathyCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h /usr/bin/install -c -p -m 644 BCToolMassCalculator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h /usr/bin/install -c -p -m 644 BCToolComplement.h ../../BioCocoa.framework/Versions/2/Headers/BCToolComplement.h /usr/bin/install -c -p -m 644 BCToolSequenceFinder.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h /usr/bin/install -c -p -m 644 BCToolSymbolCounter.h ../../BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h /usr/bin/install -c -p -m 644 BCToolTranslator.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h /usr/bin/install -c -p -m 644 BCToolTranslatorDNA.h ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... /usr/bin/install -c -p -m 644 BCDataMatrix.h ../../BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h /usr/bin/install -c -p -m 644 BCUtilData.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilData.h /usr/bin/install -c -p -m 644 BCUtilStrings.h ../../BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... /usr/bin/install -c -p -m 644 BCFoundation.h ../BioCocoa.framework/Versions/2/Headers/BCFoundation.h /usr/bin/install -c -p -m 644 BCFoundationDefines.h ../BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h /usr/bin/install -c -p -m 644 BCStringDefinitions.h ../BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h /usr/bin/install -c -p -m 644 BCPreferences.h ../BioCocoa.framework/Versions/2/Headers/BCPreferences.h make[2]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs ./derived_src; \ touch derived_src/.stamp /usr/share/GNUstep/Makefiles/mkinstalldirs BioCocoa.framework/Versions/2/Resources cd ./BioCocoa.framework/Versions; \ rm -f Current; \ ln -s 2 Current cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of framework BioCocoa... make[2]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all in subprojects of subproject BCFoundation... make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCAlignment... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCAlignment.obj/ gcc BCPairwiseAlignment.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCAlignment.obj/BCPairwiseAlignment.m.o gcc BCScoreMatrix.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCAlignment.obj/BCScoreMatrix.m.o gcc BCSequenceAlignment.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCAlignment.obj/BCSequenceAlignment.m.o gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCAlignment.obj/BCPairwiseAlignment.m.o obj/BCAlignment.obj/BCScoreMatrix.m.o obj/BCAlignment.obj/BCSequenceAlignment.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCAnalysis... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCAnalysis.obj/ gcc BCMCP.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCAnalysis.obj/BCMCP.m.o BCMCP.m: In function '-[BCMCP intersectToFile:withMCP:]': BCMCP.m:486:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:487:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:489:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:490:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:514:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:515:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:517:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:518:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:735:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:736:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:738:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:739:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:762:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:763:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:765:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:766:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP unionToFile:withMCP:]': BCMCP.m:910:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:911:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:913:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:914:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:936:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:937:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:939:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:940:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1093:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1094:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1096:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1097:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1123:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1124:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1126:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1127:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1167:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1168:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1170:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1171:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1186:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1187:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1189:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1190:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1222:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1223:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1225:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1226:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1239:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1240:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1242:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1243:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP trimToFile:]': BCMCP.m:1272:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1273:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1275:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1276:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '-[BCMCP outputFormat:withMinimumLength:]': BCMCP.m:1481:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1482:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1485:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1486:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1603:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1604:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1606:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:1607:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m: In function '+[BCMCP mcpToFile:suffixArray:withSuffixArray:lowerBound:]': BCMCP.m:160:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:161:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:163:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:164:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:334:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:335:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:352:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:353:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:358:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:359:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:366:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCMCP.m:367:16: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc BCSuffixArray.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCAnalysis.obj/BCSuffixArray.m.o BCSuffixArray.m: In function '-[BCSuffixArray constructFromSequenceArray:strand:]': BCSuffixArray.m:487:13: warning: ignoring return value of 'mktemp', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:513:13: warning: ignoring return value of 'mktemp', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m: In function '-[BCSuffixArray dumpSuffixArray]': BCSuffixArray.m:896:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:897:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:932:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:933:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m: In function '-[BCSuffixArrayUnionEnumerator nextSuffixPosition:sequence:suffixArray:]': BCSuffixArray.m:1464:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1465:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1598:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCSuffixArray.m:1599:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCAnalysis.obj/BCMCP.m.o obj/BCAnalysis.obj/BCSuffixArray.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneExpression... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCGeneExpression.obj/ gcc BCSeries.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCGeneExpression.obj/BCSeries.m.o gcc BCSample.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCGeneExpression.obj/BCSample.m.o gcc BCPlatform.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCGeneExpression.obj/BCPlatform.m.o gcc BCParseSOFT.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCGeneExpression.obj/BCParseSOFT.m.o gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCGeneExpression.obj/BCSeries.m.o obj/BCGeneExpression.obj/BCSample.m.o obj/BCGeneExpression.obj/BCPlatform.m.o obj/BCGeneExpression.obj/BCParseSOFT.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCGeneticCode... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCGeneticCode.obj/ gcc BCCodonDNA.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCGeneticCode.obj/BCCodonDNA.m.o gcc BCCodon.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCGeneticCode.obj/BCCodon.m.o gcc BCCodonRNA.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCGeneticCode.obj/BCCodonRNA.m.o gcc BCGeneticCode.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCGeneticCode.obj/BCGeneticCode.m.o BCGeneticCode.m: In function '+[BCGeneticCode priv:createCodonArraysFromDictionary:]': BCGeneticCode.m:221:23: warning: variable 'RNACodon' set but not used [-Wunused-but-set-variable] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCGeneticCode.obj/BCCodonDNA.m.o obj/BCGeneticCode.obj/BCCodon.m.o obj/BCGeneticCode.obj/BCCodonRNA.m.o obj/BCGeneticCode.obj/BCGeneticCode.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCProteinStructure... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCProteinStructure.obj/ gcc BCAtom.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCProteinStructure.obj/BCAtom.m.o gcc BCProteinStructure.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCProteinStructure.obj/BCProteinStructure.m.o gcc BCSecondaryStructure.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCProteinStructure.obj/BCSecondaryStructure.m.o gcc BCChain.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCProteinStructure.obj/BCChain.m.o gcc BCResidue.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCProteinStructure.obj/BCResidue.m.o gcc BCSequenceStructure.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCProteinStructure.obj/BCSequenceStructure.m.o gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCProteinStructure.obj/BCAtom.m.o obj/BCProteinStructure.obj/BCProteinStructure.m.o obj/BCProteinStructure.obj/BCSecondaryStructure.m.o obj/BCProteinStructure.obj/BCChain.m.o obj/BCProteinStructure.obj/BCResidue.m.o obj/BCProteinStructure.obj/BCSequenceStructure.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequence... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSequence.obj/ gcc BCAnnotation.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSequence.obj/BCAnnotation.m.o BCAnnotation.m: In function '-[BCAnnotation isEqualToAnnotation:]': BCAnnotation.m:214:2: warning: 'NSObject' may not respond to '-isEqualTo:' [enabled by default] BCAnnotation.m:214:2: warning: (Messages without a matching method signature [enabled by default] BCAnnotation.m:214:2: warning: will be assumed to return 'id' and accept [enabled by default] BCAnnotation.m:214:2: warning: '...' as arguments.) [enabled by default] BCAnnotation.m:214:2: warning: return makes integer from pointer without a cast [enabled by default] gcc BCSequence.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSequence.obj/BCSequence.m.o gcc BCSequenceArray.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSequence.obj/BCSequenceArray.m.o gcc BCSequenceCodon.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSequence.obj/BCSequenceCodon.m.o BCSequenceCodon.m: In function '-[BCSequenceCodon openReadingFramesLongerThanCutoff:]': BCSequenceCodon.m:301:16: warning: 'inORF' may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCSequence.obj/BCAnnotation.m.o obj/BCSequence.obj/BCSequence.m.o obj/BCSequence.obj/BCSequenceArray.m.o obj/BCSequence.obj/BCSequenceCodon.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSequenceIO... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSequenceIO.obj/ gcc BCSequenceReader.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSequenceIO.obj/BCSequenceReader.m.o BCSequenceReader.m: In function '-[BCSequenceReader readFileUsingText:]': BCSequenceReader.m:167:3: warning: no '-initWithRTF:documentAttributes:' method found [enabled by default] BCSequenceReader.m:167:3: warning: (Messages without a matching method signature [enabled by default] BCSequenceReader.m:167:3: warning: will be assumed to return 'id' and accept [enabled by default] BCSequenceReader.m:167:3: warning: '...' as arguments.) [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readMacVectorFile:]': BCSequenceReader.m:651:18: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:782:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m:798:3: warning: passing argument 2 of 'scanUpToString:intoString:' from incompatible pointer type [enabled by default] BCSequenceReader.m:798:3: note: expected 'struct NSString **' but argument is of type 'id' BCSequenceReader.m: In function '-[BCSequenceReader readGDEFile:]': BCSequenceReader.m:891:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readPirFile:]': BCSequenceReader.m:976:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readPhylipFile:]': BCSequenceReader.m:1130:9: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m:1113:31: warning: variable 'annotationsArray' set but not used [-Wunused-but-set-variable] BCSequenceReader.m: In function '-[BCSequenceReader readRawFile:]': BCSequenceReader.m:1195:3: warning: passing argument 1 of 'isEqualTo:' from distinct Objective-C type [enabled by default] BCSequenceReader.m: In function '-[BCSequenceReader readSwissProtFile:]': BCSequenceReader.m:426:15: warning: 'sequenceString' may be used uninitialized in this function [-Wmaybe-uninitialized] BCSequenceReader.m: In function '-[BCSequenceReader readClustalFile:]': BCSequenceReader.m:822:18: warning: 'sequenceRange.location' may be used uninitialized in this function [-Wmaybe-uninitialized] BCSequenceReader.m: In function '-[BCSequenceReader readFASTQFile:]': BCSequenceReader.m:1310:18: warning: 'seqData' may be used uninitialized in this function [-Wmaybe-uninitialized] gcc BCSequenceWriter.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSequenceIO.obj/BCSequenceWriter.m.o gcc BCCachedSequenceFile.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o gcc BCCachedFastaFile.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSequenceIO.obj/BCCachedFastaFile.m.o BCCachedFastaFile.m: In function '-[BCCachedFastaFile initWithContentsOfFile:]': BCCachedFastaFile.m:58:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:73:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:76:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m:97:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m: In function '-[BCCachedFastaFile symbols:ForCurrentSequenceAtPosition:ofLength:]': BCCachedFastaFile.m:149:10: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BCCachedFastaFile.m: In function '-[BCCachedFastaFile initWithContentsOfFile:]': BCCachedFastaFile.m:104:3: warning: 'filePos' may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCSequenceIO.obj/BCSequenceReader.m.o obj/BCSequenceIO.obj/BCSequenceWriter.m.o obj/BCSequenceIO.obj/BCCachedSequenceFile.m.o obj/BCSequenceIO.obj/BCCachedFastaFile.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCSymbol... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCSymbol.obj/ gcc BCAminoAcid.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSymbol.obj/BCAminoAcid.m.o gcc BCNucleotide.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSymbol.obj/BCNucleotide.m.o gcc BCSymbol.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSymbol.obj/BCSymbol.m.o gcc BCNucleotideDNA.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSymbol.obj/BCNucleotideDNA.m.o gcc BCNucleotideRNA.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSymbol.obj/BCNucleotideRNA.m.o gcc BCSymbolSet.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCSymbol.obj/BCSymbolSet.m.o gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCSymbol.obj/BCAminoAcid.m.o obj/BCSymbol.obj/BCNucleotide.m.o obj/BCSymbol.obj/BCSymbol.m.o obj/BCSymbol.obj/BCNucleotideDNA.m.o obj/BCSymbol.obj/BCNucleotideRNA.m.o obj/BCSymbol.obj/BCSymbolSet.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCTools... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCTools.obj/ gcc BCSequenceTool.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCSequenceTool.m.o gcc BCToolDigest.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCToolDigest.m.o gcc BCToolHydropathyCalculator.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCToolHydropathyCalculator.m.o gcc BCToolMassCalculator.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCToolMassCalculator.m.o gcc BCToolComplement.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCToolComplement.m.o gcc BCToolSequenceFinder.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCToolSequenceFinder.m.o gcc BCToolSymbolCounter.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCToolSymbolCounter.m.o gcc BCToolTranslator.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCToolTranslator.m.o gcc BCToolTranslatorDNA.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCTools.obj/BCToolTranslatorDNA.m.o gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCTools.obj/BCSequenceTool.m.o obj/BCTools.obj/BCToolDigest.m.o obj/BCTools.obj/BCToolHydropathyCalculator.m.o obj/BCTools.obj/BCToolMassCalculator.m.o obj/BCTools.obj/BCToolComplement.m.o obj/BCTools.obj/BCToolSequenceFinder.m.o obj/BCTools.obj/BCToolSymbolCounter.m.o obj/BCTools.obj/BCToolTranslator.m.o obj/BCTools.obj/BCToolTranslatorDNA.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj Making all for subproject BCUtils... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCUtils.obj/ gcc BCDataMatrix.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCUtils.obj/BCDataMatrix.m.o gcc BCUtilData.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCUtils.obj/BCUtilData.m.o gcc BCUtilStrings.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCUtils.obj/BCUtilStrings.m.o BCUtilStrings.m: In function '-[NSString(StringAdditions) stringBeginsWithTwoNumbers]': BCUtilStrings.m:98:2: warning: passing argument 1 of 'scanInt:' from incompatible pointer type [enabled by default] BCUtilStrings.m:98:2: note: expected 'int *' but argument is of type 'id' BCUtilStrings.m:100:3: warning: passing argument 1 of 'scanInt:' from incompatible pointer type [enabled by default] BCUtilStrings.m:100:3: note: expected 'int *' but argument is of type 'id' gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCUtils.obj/BCDataMatrix.m.o obj/BCUtils.obj/BCUtilData.m.o obj/BCUtils.obj/BCUtilStrings.m.o ; make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BCFoundation.obj/ gcc BCStringDefinitions.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCFoundation.obj/BCStringDefinitions.m.o gcc BCPreferences.m -c \ -MMD -MP -D_FORTIFY_SOURCE=2 -Wno-import -Wno-unknown-pragmas -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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/include/GNUstep \ -o obj/BCFoundation.obj/BCPreferences.m.o gcc -nostdlib -r -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./obj/subproject.o obj/BCFoundation.obj/BCStringDefinitions.m.o obj/BCFoundation.obj/BCPreferences.m.o BCAlignment/obj/subproject.o BCAnalysis/obj/subproject.o BCGeneExpression/obj/subproject.o BCGeneticCode/obj/subproject.o BCProteinStructure/obj/subproject.o BCSequence/obj/subproject.o BCSequenceIO/obj/subproject.o BCSymbol/obj/subproject.o BCTools/obj/subproject.o BCUtils/obj/subproject.o ; make[2]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... cd .; \ /usr/share/GNUstep/Makefiles/mkinstalldirs ./obj/BioCocoa.obj/ classes=""; \ for object_file in ./BCFoundation/obj/subproject.o __dummy__; do \ if [ "$object_file" != "__dummy__" ]; then \ sym=`nm -Pg $object_file | sed -n -e '/^__objc_class_name_[A-Za-z0-9_.]* [^U]/ {s/^__objc_class_name_\([A-Za-z0-9_.]*\) [^U].*/\1/p;}'`; \ classes="$classes $sym"; \ fi; \ done; \ classlist=""; \ classarray=""; \ for f in $classes __dummy__ ; do \ if [ "$f" != "__dummy__" ]; then \ if [ "$classlist" = "" ]; then \ classlist="@\"$f\""; \ classarray="(\"$f\""; \ else \ classlist="$classlist, @\"$f\""; \ classarray="$classarray, \"$f\""; \ fi; \ fi; \ done; \ if [ "$classlist" = "" ]; then \ classlist="NULL"; \ classarray="()"; \ else \ classlist="$classlist, NULL"; \ classarray="$classarray)"; \ fi; \ echo "$classarray" > ./derived_src/BioCocoa-class-list; \ echo "#include " > derived_src/NSFramework_BioCocoa.m; \ echo "@interface NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion;" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses;" >> derived_src/NSFramework_BioCocoa.m; \ echo "@end" >> derived_src/NSFramework_BioCocoa.m; \ echo "@implementation NSFramework_BioCocoa" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkEnv { return nil; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkPath { return @\"/usr/lib/GNUstep/Frameworks\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *)frameworkVersion { return @\"2\"; }" >> derived_src/NSFramework_BioCocoa.m; \ echo "static NSString *allClasses[] = {$classlist};" >> derived_src/NSFramework_BioCocoa.m; \ echo "+ (NSString *const*)frameworkClasses { return allClasses; }" >> derived_src/NSFramework_BioCocoa.m;\ echo "@end" >> derived_src/NSFramework_BioCocoa.m gcc derived_src/NSFramework_BioCocoa.m -c -MMD -MP -D_FORTIFY_SOURCE=2 -DGNUSTEP -DGNUSTEP_BASE_LIBRARY=1 -DGNU_GUI_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./derived_src -I. -I/usr/include/GNUstep -o obj/BioCocoa.obj/NSFramework_BioCocoa.o \ gcc -shared -Wl,-soname,libBioCocoa.so.2 -rdynamic -Wl,-z,defs -Wl,--as-needed -pthread -shared-libgcc -fexceptions -o ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 obj/BioCocoa.obj/NSFramework_BioCocoa.o BCFoundation/obj/subproject.o -L/usr/lib -lgnustep-base -lobjc && (cd ./BioCocoa.framework/Versions/2/.; rm -f libBioCocoa.so; if [ "libBioCocoa.so.2" != "libBioCocoa.so.2.2.2" ]; then rm -f libBioCocoa.so.2; ln -s libBioCocoa.so.2.2.2 libBioCocoa.so.2; fi; ln -s libBioCocoa.so.2 libBioCocoa.so; ) || rm -f ./BioCocoa.framework/Versions/2/./libBioCocoa.so.2.2.2 ; \ (cd ./BioCocoa.framework/Versions/2/.; \ rm -f BioCocoa; \ ln -s libBioCocoa.so BioCocoa) \ for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f $f -o -d $f ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: $f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done (echo "{"; echo ' NOTE = "Automatically generated, do not edit!";'; \ echo " NSExecutable = \"BioCocoa\";"; \ echo " NSMainNibFile = \"\";"; \ echo " NSPrincipalClass = \"BioCocoa\";"; \ echo " Classes = "; \ cat ./derived_src/BioCocoa-class-list; \ echo " ;"; \ echo "}") >BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist if [ -r "BioCocoaInfo.plist" ]; then \ plmerge BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist BioCocoaInfo.plist; \ fi cd ./BioCocoa.framework/.; \ rm -f BioCocoa libBioCocoa.so; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./BioCocoa short` \ BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh . \ Versions/Current/./libBioCocoa.so short` \ libBioCocoa.so make[1]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks fakeroot debian/rules binary test -x debian/rules dh_testroot dh_clean -k dh_clean: dh_clean -k is deprecated; use dh_prep instead dh_installdirs -A sed -e "s:@GNUSTEP_SYSTEM_LIBRARIES@:/usr/lib:g" -e "s:@GNUSTEP_SYSTEM_LIBRARY@:/usr/lib/GNUstep:g" -e "s:@GNUSTEP_SYSTEM_HEADERS@:/usr/include/GNUstep:g" -e "s/@FRAMEWORK@/BioCocoa/g; s/@FRAMEWORKVER@/2/g" < /usr/share/GNUstep/debian/frameworklib.install.in > debian/libbiococoa2.install sed -e "s:@GNUSTEP_SYSTEM_LIBRARIES@:/usr/lib:g" -e "s:@GNUSTEP_SYSTEM_LIBRARY@:/usr/lib/GNUstep:g" -e "s:@GNUSTEP_SYSTEM_HEADERS@:/usr/include/GNUstep:g" -e "s/@FRAMEWORK@/BioCocoa/g; s/@FRAMEWORKVER@/2/g" < /usr/share/GNUstep/debian/frameworkdev.install.in > debian/libbiococoa-dev.install mkdir -p "." DEB_MAKE_CHECK_TARGET unset, not running checks GNUSTEP_MAKEFILES=/usr/share/GNUstep/Makefiles /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,defs -Wl,--as-needed" OPTFLAG=-O2 install DESTDIR=/var/www/debian/biococoa/biococoa-2.2.2/debian/tmp/ GNUSTEP_INSTALLATION_DOMAIN=SYSTEM This is gnustep-make 2.6.2. Type 'make print-gnustep-make-help' for help. make[1]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2' Making build-headers in subprojects of framework BioCocoa... make[2]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making build-headers in subprojects of subproject BCFoundation... make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' Making build-headers for subproject BCAlignment... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' Making build-headers for subproject BCAnalysis... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making build-headers for subproject BCGeneExpression... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making build-headers for subproject BCGeneticCode... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making build-headers for subproject BCProteinStructure... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' Making build-headers for subproject BCSequence... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making build-headers for subproject BCSequenceIO... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' Making build-headers for subproject BCSymbol... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' Making build-headers for subproject BCTools... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCUtils... make[4]: Nothing to be done for `internal-subproject-build-headers'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making build-headers for subproject BCFoundation... make[3]: Nothing to be done for `internal-subproject-build-headers'. make[2]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making build-headers for framework BioCocoa... cd ./BioCocoa.framework; \ if [ ! -h "Resources" ]; then \ rm -f Resources; \ ln -s Versions/Current/Resources Resources; \ fi; \ if [ ! -h "Headers" ]; then \ rm -f Headers; \ ln -s Versions/Current/Headers Headers; \ fi cd ./derived_src; \ if [ ! -h "BioCocoa" ]; then \ rm -f ./BioCocoa; \ ln -s ../BioCocoa.framework/Headers \ ./BioCocoa; \ fi Making all in subprojects of framework BioCocoa... make[2]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making all in subprojects of subproject BCFoundation... make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' Making all for subproject BCAlignment... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' Making all for subproject BCAnalysis... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making all for subproject BCGeneExpression... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making all for subproject BCGeneticCode... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making all for subproject BCProteinStructure... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' Making all for subproject BCSequence... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making all for subproject BCSequenceIO... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' Making all for subproject BCSymbol... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' Making all for subproject BCTools... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCUtils... make[5]: Nothing to be done for `internal-subproject-compile'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making all for subproject BCFoundation... make[4]: Nothing to be done for `internal-subproject-compile'. make[2]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making all for framework BioCocoa... make[3]: Nothing to be done for `internal-framework-compile'. for f in BCFoundation/BCSymbol/SymbolTemplates/nucleotides.plist BCFoundation/BCSymbol/SymbolTemplates/aminoacids.plist; do \ if [ -f $f -o -d $f ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ else \ echo "Warning: $f not found - ignoring"; \ fi; \ done for subproject in BCFoundation; do \ if [ -d $subproject/Resources/Subproject ]; then \ for f in $subproject/Resources/Subproject/*; do \ if [ $f != $subproject'/Resources/Subproject/*' ]; then \ cp -fr $f ./BioCocoa.framework/Versions/2/Resources/; \ fi; \ done; \ fi; \ done Making install in subprojects of framework BioCocoa... make[2]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making install in subprojects of subproject BCFoundation... make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' Making install for subproject BCAlignment... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAlignment' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' Making install for subproject BCAnalysis... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCAnalysis' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' Making install for subproject BCGeneExpression... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneExpression' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' Making install for subproject BCGeneticCode... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCGeneticCode' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' Making install for subproject BCProteinStructure... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCProteinStructure' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' Making install for subproject BCSequence... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequence' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' Making install for subproject BCSequenceIO... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSequenceIO' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' Making install for subproject BCSymbol... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCSymbol' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' Making install for subproject BCTools... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCTools' make[3]: Entering directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCUtils... make[4]: Nothing to be done for `internal-subproject-install'. make[3]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation/BCUtils' Making install for subproject BCFoundation... make[3]: Nothing to be done for `internal-subproject-install'. make[2]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2/BCFoundation' Making install for framework BioCocoa... /usr/share/GNUstep/Makefiles/mkinstalldirs /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks /usr/share/GNUstep/Makefiles/mkinstalldirs /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/include/GNUstep rm -rf /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework; \ (cd .; tar cfX - /usr/share/GNUstep/Makefiles/tar-exclude-list BioCocoa.framework) | (cd /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks; tar xf -) cd /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/include/GNUstep; \ rm -f BioCocoa; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/include/GNUstep /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Headers short` BioCocoa; \ cd /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/.; \ rm -f libBioCocoa.so; \ rm -f libBioCocoa.so.2; \ rm -f libBioCocoa.so.2.2.2; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/. /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so short` libBioCocoa.so; \ if test -r "/var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2"; then \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/. /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2 short` libBioCocoa.so.2; \ fi; \ ln -s `/usr/share/GNUstep/Makefiles/relative_path.sh /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/. /var/www/debian/biococoa/biococoa-2.2.2/debian/tmp///usr/lib/GNUstep/Frameworks/BioCocoa.framework/Versions/Current/./libBioCocoa.so.2.2.2 short` libBioCocoa.so.2.2.2 make[1]: Leaving directory `/var/www/debian/biococoa/biococoa-2.2.2' touch debian/stamp-makefile-install Adding cdbs dependencies to debian/libbiococoa-dev.substvars dh_installdirs -plibbiococoa-dev Adding cdbs dependencies to debian/libbiococoa2.substvars dh_installdirs -plibbiococoa2 dh_installdocs -plibbiococoa-dev dh_installexamples -plibbiococoa-dev dh_installman -plibbiococoa-dev dh_installinfo -plibbiococoa-dev dh_installmenu -plibbiococoa-dev dh_installcron -plibbiococoa-dev dh_installinit -plibbiococoa-dev dh_installdebconf -plibbiococoa-dev dh_installemacsen -plibbiococoa-dev dh_installcatalogs -plibbiococoa-dev dh_installpam -plibbiococoa-dev dh_installlogrotate -plibbiococoa-dev dh_installlogcheck -plibbiococoa-dev dh_installchangelogs -plibbiococoa-dev ./ChangeLog dh_installudev -plibbiococoa-dev dh_lintian -plibbiococoa-dev dh_bugfiles -plibbiococoa-dev dh_install -plibbiococoa-dev --sourcedir=/var/www/debian/biococoa/biococoa-2.2.2/debian/tmp/ dh_link -plibbiococoa-dev dh_installmime -plibbiococoa-dev dh_installgsettings -plibbiococoa-dev gsdh_gnustep -plibbiococoa-dev dh_link -plibbiococoa-dev rm -f debian/libbiococoa-dev//usr/lib/GNUstep/Frameworks/*.framework/Versions/Current dh_installdocs -plibbiococoa2 dh_installexamples -plibbiococoa2 dh_installman -plibbiococoa2 dh_installinfo -plibbiococoa2 dh_installmenu -plibbiococoa2 dh_installcron -plibbiococoa2 dh_installinit -plibbiococoa2 dh_installdebconf -plibbiococoa2 dh_installemacsen -plibbiococoa2 dh_installcatalogs -plibbiococoa2 dh_installpam -plibbiococoa2 dh_installlogrotate -plibbiococoa2 dh_installlogcheck -plibbiococoa2 dh_installchangelogs -plibbiococoa2 ./ChangeLog dh_installudev -plibbiococoa2 dh_lintian -plibbiococoa2 dh_bugfiles -plibbiococoa2 dh_install -plibbiococoa2 --sourcedir=/var/www/debian/biococoa/biococoa-2.2.2/debian/tmp/ dh_link -plibbiococoa2 dh_installmime -plibbiococoa2 dh_installgsettings -plibbiococoa2 gsdh_gnustep -plibbiococoa2 dh_link -plibbiococoa2 dh_strip -plibbiococoa-dev dh_compress -plibbiococoa-dev dh_fixperms -plibbiococoa-dev dh_makeshlibs -plibbiococoa-dev dh_strip -plibbiococoa2 dh_compress -plibbiococoa2 dh_fixperms -plibbiococoa2 dh_makeshlibs -plibbiococoa2 --noscripts dh_installdeb -plibbiococoa-dev dh_perl -plibbiococoa-dev dh_shlibdeps -plibbiococoa-dev dh_installdeb -plibbiococoa2 dh_perl -plibbiococoa2 dh_shlibdeps -plibbiococoa2 dh_gencontrol -plibbiococoa-dev dh_md5sums -plibbiococoa-dev dh_builddeb -plibbiococoa-dev dpkg-deb: building package `libbiococoa-dev' in `../libbiococoa-dev_2.2.2-1build1_i386.deb'. dh_gencontrol -plibbiococoa2 dh_md5sums -plibbiococoa2 dh_builddeb -plibbiococoa2 dpkg-deb: building package `libbiococoa2' in `../libbiococoa2_2.2.2-1build1_i386.deb'. dpkg-genchanges >../biococoa_2.2.2-1build1_i386.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build biococoa-2.2.2 dpkg-source: info: unapplying link-libs.patch dpkg-buildpackage: binary and diff upload (original source NOT included) Now running lintian... warning: the authors of lintian do not recommend running it with root privileges! W: biococoa source: out-of-date-standards-version 3.9.1 (current is 3.9.3) Finished running lintian. Now signing changes and any dsc files... signfile biococoa_2.2.2-1build1.dsc Matthias Klose gpg: skipped "Matthias Klose ": secret key not available gpg: /tmp/debsign.DRDohgUG/biococoa_2.2.2-1build1.dsc: clearsign failed: secret key not available debsign: gpg error occurred! Aborting....