Checking if your kit is complete... Looks good Warning: prerequisite Bio::SeqIO::abi 0 not found. Writing Makefile for Bio::Ext::Align Please tell us where your Staden io_lib "read" library is installed: [/usr/local/lib] /usr/local/lib Please tell us where your Staden io_lib "Read.h" header is installed: [/usr/local/include/io_lib] /usr/local/include/io_lib Writing Makefile for Bio::SeqIO::staden::read Writing Makefile for Bio cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h cp Bio/Ext/Align/libs/linesubs.h blib/lib/Bio/Ext/Align/libs/linesubs.h cp Bio/Ext/Align/libs/probability.c blib/lib/Bio/Ext/Align/libs/probability.c cp Bio/Ext/Align/test.pl blib/lib/Bio/Ext/Align/test.pl cp Bio/Ext/Align/libs/wiseoverlay.h blib/lib/Bio/Ext/Align/libs/wiseoverlay.h cp Bio/Ext/Align/libs/proteinsw.h blib/lib/Bio/Ext/Align/libs/proteinsw.h cp Bio/Ext/Align/libs/wisebase.h blib/lib/Bio/Ext/Align/libs/wisebase.h cp Bio/Ext/Align/libs/seqaligndisplay.h blib/lib/Bio/Ext/Align/libs/seqaligndisplay.h cp Bio/Ext/Align/libs/dyna.h blib/lib/Bio/Ext/Align/libs/dyna.h cp Bio/Ext/Align/libs/wiseerror.c blib/lib/Bio/Ext/Align/libs/wiseerror.c cp Bio/Ext/Align/libs/commandline.h blib/lib/Bio/Ext/Align/libs/commandline.h cp Bio/Ext/Align/libs/aln.c blib/lib/Bio/Ext/Align/libs/aln.c cp Bio/Ext/Align/libs/packaln.c blib/lib/Bio/Ext/Align/libs/packaln.c cp Bio/Ext/Align/libs/dpenvelope.c blib/lib/Bio/Ext/Align/libs/dpenvelope.c cp Bio/Ext/Align/libs/complexsequence.c blib/lib/Bio/Ext/Align/libs/complexsequence.c cp Bio/Ext/Align/libs/wisestring.h blib/lib/Bio/Ext/Align/libs/wisestring.h cp Bio/Ext/Align/libs/codon.c blib/lib/Bio/Ext/Align/libs/codon.c cp Bio/Ext/Align/libs/linspc.c blib/lib/Bio/Ext/Align/libs/linspc.c cp Bio/Ext/Align/libs/probability.h blib/lib/Bio/Ext/Align/libs/probability.h cp Bio/Ext/Align/Align.xs blib/lib/Bio/Ext/Align/Align.xs cp Bio/Ext/Align/libs/packaln.h blib/lib/Bio/Ext/Align/libs/packaln.h cp Bio/Ext/Align/libs/dynlibcross.c blib/lib/Bio/Ext/Align/libs/dynlibcross.c cp Bio/Ext/Align/libs/sequencedb.c blib/lib/Bio/Ext/Align/libs/sequencedb.c cp Bio/Ext/Align/libs/sw_wrap.c blib/lib/Bio/Ext/Align/libs/sw_wrap.c cp Bio/Ext/Align/libs/wiseerror.h blib/lib/Bio/Ext/Align/libs/wiseerror.h cp Bio/Ext/Align/Makefile.PL blib/lib/Bio/Ext/Align/Makefile.PL cp Bio/Ext/Align/libs/complexsequence.h blib/lib/Bio/Ext/Align/libs/complexsequence.h cp Bio/Ext/Align/libs/wiseconfig.h blib/lib/Bio/Ext/Align/libs/wiseconfig.h cp Bio/Ext/Align/libs/dynlibcross.h blib/lib/Bio/Ext/Align/libs/dynlibcross.h cp Bio/Ext/Align/libs/complexevalset.c blib/lib/Bio/Ext/Align/libs/complexevalset.c cp Bio/Ext/Align/libs/complexevalset.h blib/lib/Bio/Ext/Align/libs/complexevalset.h cp Bio/Ext/Align/libs/wiseconfig.c blib/lib/Bio/Ext/Align/libs/wiseconfig.c cp Bio/Ext/Align/libs/wisefile.c blib/lib/Bio/Ext/Align/libs/wisefile.c cp Bio/Ext/Align/libs/alnconvert.c blib/lib/Bio/Ext/Align/libs/alnconvert.c cp Bio/Ext/Align/libs/histogram.h blib/lib/Bio/Ext/Align/libs/histogram.h cp Bio/Ext/Align/libs/makefile blib/lib/Bio/Ext/Align/libs/makefile cp Bio/Ext/Align/typemap blib/lib/Bio/Ext/Align/typemap cp Bio/Ext/Align/libs/proteindb.h blib/lib/Bio/Ext/Align/libs/proteindb.h cp Bio/Ext/Align/libs/btcanvas.c blib/lib/Bio/Ext/Align/libs/btcanvas.c cp Bio/Ext/Align/libs/complexconsensi.c blib/lib/Bio/Ext/Align/libs/complexconsensi.c cp Bio/Ext/Align/libs/hscore.c blib/lib/Bio/Ext/Align/libs/hscore.c cp Bio/Ext/Align/libs/alnrange.c blib/lib/Bio/Ext/Align/libs/alnrange.c cp Bio/Ext/Align/libs/dpenvelope.h blib/lib/Bio/Ext/Align/libs/dpenvelope.h cp Bio/Ext/Align/libs/sequence.h blib/lib/Bio/Ext/Align/libs/sequence.h cp Bio/Ext/Align/libs/asciibtcanvas.h blib/lib/Bio/Ext/Align/libs/asciibtcanvas.h cp Bio/SeqIO/staden/read.pm blib/lib/Bio/SeqIO/staden/read.pm cp Bio/Ext/Align/blosum62.bla blib/lib/Bio/Ext/Align/blosum62.bla cp Bio/Ext/Align/libs/protein.h blib/lib/Bio/Ext/Align/libs/protein.h cp Bio/Ext/Align/libs/sequencedb.h blib/lib/Bio/Ext/Align/libs/sequencedb.h cp Bio/Ext/Align/Align.pm blib/lib/Bio/Ext/Align/Align.pm cp Bio/Ext/Makefile.PL blib/lib/Bio/Ext/Makefile.PL cp Bio/Ext/Align/libs/complexconsensi.h blib/lib/Bio/Ext/Align/libs/complexconsensi.h cp Bio/Ext/Align/libs/dna.c blib/lib/Bio/Ext/Align/libs/dna.c cp Bio/Ext/Align/libs/sw.h blib/lib/Bio/Ext/Align/libs/sw.h cp Bio/SeqIO/staden/test.pl blib/lib/Bio/SeqIO/staden/test.pl cp Bio/SeqIO/staden/Makefile.PL blib/lib/Bio/SeqIO/staden/Makefile.PL cp Bio/Ext/Align/libs/wisestring.c blib/lib/Bio/Ext/Align/libs/wisestring.c cp Bio/Ext/Align/libs/sw_wrap.h blib/lib/Bio/Ext/Align/libs/sw_wrap.h cp Bio/Ext/Align/libs/alnrange.h blib/lib/Bio/Ext/Align/libs/alnrange.h cp Bio/Ext/Align/libs/dpalign.c blib/lib/Bio/Ext/Align/libs/dpalign.c cp Bio/Ext/Align/libs/database.h blib/lib/Bio/Ext/Align/libs/database.h cp Bio/Ext/Align/libs/wisetime.c blib/lib/Bio/Ext/Align/libs/wisetime.c cp Bio/Ext/Align/libs/dpalign.h blib/lib/Bio/Ext/Align/libs/dpalign.h cp Bio/Ext/Align/libs/proteinsw.c blib/lib/Bio/Ext/Align/libs/proteinsw.c cp Bio/Ext/Align/libs/wiserandom.c blib/lib/Bio/Ext/Align/libs/wiserandom.c cp Bio/Ext/Align/libs/btcanvas.h blib/lib/Bio/Ext/Align/libs/btcanvas.h cp Bio/Ext/Align/libs/proteindb.c blib/lib/Bio/Ext/Align/libs/proteindb.c cp Bio/Ext/Align/libs/linesubs.c blib/lib/Bio/Ext/Align/libs/linesubs.c cp Bio/Ext/Align/libs/codon.h blib/lib/Bio/Ext/Align/libs/codon.h cp Bio/Ext/Align/libs/compmat.c blib/lib/Bio/Ext/Align/libs/compmat.c cp Bio/Ext/Align/libs/basematrix.h blib/lib/Bio/Ext/Align/libs/basematrix.h cp Bio/Ext/Align/libs/histogram.c blib/lib/Bio/Ext/Align/libs/histogram.c cp Bio/Ext/Align/libs/dnamatrix.h blib/lib/Bio/Ext/Align/libs/dnamatrix.h cp Bio/Ext/Align/libs/wiserandom.h blib/lib/Bio/Ext/Align/libs/wiserandom.h cp Bio/Ext/Align/libs/wisememman.c blib/lib/Bio/Ext/Align/libs/wisememman.c cp Bio/Ext/Align/libs/seqaligndisplay.c blib/lib/Bio/Ext/Align/libs/seqaligndisplay.c cp Bio/Ext/Align/libs/commandline.c blib/lib/Bio/Ext/Align/libs/commandline.c cp Bio/Ext/Align/libs/alnconvert.h blib/lib/Bio/Ext/Align/libs/alnconvert.h cp Bio/Ext/Align/libs/compmat.h blib/lib/Bio/Ext/Align/libs/compmat.h cp Bio/Ext/Align/libs/dna.h blib/lib/Bio/Ext/Align/libs/dna.h cp Bio/Ext/Align/libs/basematrix.c blib/lib/Bio/Ext/Align/libs/basematrix.c cp Bio/Ext/Align/libs/aln.h blib/lib/Bio/Ext/Align/libs/aln.h cp Bio/Ext/Align/libs/sequence.c blib/lib/Bio/Ext/Align/libs/sequence.c cp Bio/Ext/Align/libs/wisememman.h blib/lib/Bio/Ext/Align/libs/wisememman.h cp Bio/Ext/Align/libs/protein.c blib/lib/Bio/Ext/Align/libs/protein.c cp Bio/Ext/Align/libs/wisetime.h blib/lib/Bio/Ext/Align/libs/wisetime.h cp Bio/Ext/Align/libs/wiseoverlay.c blib/lib/Bio/Ext/Align/libs/wiseoverlay.c cp Bio/Ext/Align/libs/dnamatrix.c blib/lib/Bio/Ext/Align/libs/dnamatrix.c cp Bio/Ext/Align/libs/asciibtcanvas.c blib/lib/Bio/Ext/Align/libs/asciibtcanvas.c cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h cp Align.pm ../blib/lib/Bio/Ext/Align.pm DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ cd libs && make CC=gcc libsw.a -e gcc -c -O -c -o aln.o aln.c gcc -c -O -c -o alnconvert.o alnconvert.c gcc -c -O -c -o alnrange.o alnrange.c gcc -c -O -c -o asciibtcanvas.o asciibtcanvas.c gcc -c -O -c -o basematrix.o basematrix.c gcc -c -O -c -o btcanvas.o btcanvas.c gcc -c -O -c -o commandline.o commandline.c gcc -c -O -c -o complexconsensi.o complexconsensi.c gcc -c -O -c -o complexevalset.o complexevalset.c gcc -c -O -c -o complexsequence.o complexsequence.c gcc -c -O -c -o compmat.o compmat.c gcc -c -O -c -o codon.o codon.c gcc -c -O -c -o dna.o dna.c gcc -c -O -c -o dnamatrix.o dnamatrix.c gcc -c -O -c -o dpenvelope.o dpenvelope.c gcc -c -O -c -o dynlibcross.o dynlibcross.c gcc -c -O -c -o histogram.o histogram.c gcc -c -O -c -o hscore.o hscore.c gcc -c -O -c -o linesubs.o linesubs.c gcc -c -O -c -o packaln.o packaln.c gcc -c -O -c -o probability.o probability.c gcc -c -O -c -o protein.o protein.c gcc -c -O -c -o proteindb.o proteindb.c gcc -c -O -c -o proteinsw.o proteinsw.c gcc -c -O -c -o seqaligndisplay.o seqaligndisplay.c gcc -c -O -c -o sequence.o sequence.c gcc -c -O -c -o sequencedb.o sequencedb.c gcc -c -O -c -o sw_wrap.o sw_wrap.c gcc -c -O -c -o wiseerror.o wiseerror.c gcc -c -O -DNOERROR wisefile.c gcc -c -O -c -o wisememman.o wisememman.c gcc -c -O -c -o wiseoverlay.o wiseoverlay.c gcc -c -O -c -o wiserandom.o wiserandom.c gcc -c -O -c -o wisestring.o wisestring.c gcc -c -O -c -o wisetime.o wisetime.c gcc -c -O -c -o dpalign.o dpalign.c gcc -c -O -c -o linspc.o linspc.c ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o btcanvas.o commandline.o complexconsensi.o complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o ar: creating archive libsw.a /Users/cpanrun/pristine/5.8.7/bin/perl /Users/cpanrun/pristine/5.8.7/lib/5.8.7/ExtUtils/xsubpp -typemap /Users/cpanrun/pristine/5.8.7/lib/5.8.7/ExtUtils/typemap -typemap typemap Align.xs > Align.xsc && mv Align.xsc Align.c gcc -c -I./libs -fno-common -DPERL_DARWIN -no-cpp-precomp -arch ppc -arch i386 -nostdinc -B/Developer/SDKs/MacOSX10.4u.sdk/usr/include/gcc -B/Developer/SDKs/MacOSX10.4u.sdk/usr/lib/gcc -isystem/Developer/SDKs/MacOSX10.4u.sdk/usr/include -F/Developer/SDKs/MacOSX10.4u.sdk/System/Library/Frameworks -mmacosx-version-min=10.3 -DUSE_SITECUSTOMIZE -DNO_HASH_SEED -fno-strict-aliasing -pipe -O3 -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" "-I/Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.bundle LD_RUN_PATH="" env MACOSX_DEPLOYMENT_TARGET=10.3 cc -bundle -undefined dynamic_lookup -arch ppc -arch i386 -Wl,-search_paths_first -Wl,-syslibroot,/Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.3 Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.bundle libs/libsw.a -lm /usr/bin/ld: for architecture i386 /usr/bin/ld: warning libs/libsw.a archive's cputype (18, architecture ppc) does not match cputype (7) for specified -arch flag: i386 (can't load from it) chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.bundle cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm /Users/cpanrun/pristine/5.8.7/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read -e1 0.01 ../blib/arch Can't locate Bio/Root/Root.pm in @INC (@INC contains: /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-ext/Bio/SeqIO/staden/../blib/arch /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-ext/Bio/SeqIO/staden/../blib/lib /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-ext/Bio/SeqIO/staden/../blib/lib/Bio/SeqIO/staden/read.pm line 64. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-ext/Bio/SeqIO/staden/../blib/lib/Bio/SeqIO/staden/read.pm line 64. Compilation failed in require. BEGIN failed--compilation aborted. make[1]: *** [read.inl] Error 2 make: *** [subdirs] Error 2