[root@guyver-1 xuying]# perl -MCPAN -e shell cpan shell -- CPAN exploration and modules installation (v1.61) ReadLine support available (try 'install Bundle::CPAN') cpan> look Bio::SeqIO::staden CPAN: Storable loaded ok Going to read /root/.cpan/Metadata Database was generated on Thu, 16 Dec 2004 22:50:19 GMT CPAN: LWP::UserAgent loaded ok Fetching with LWP: ftp://ftp.perl.org/pub/CPAN/authors/01mailrc.txt.gz Going to read /root/.cpan/sources/authors/01mailrc.txt.gz CPAN: Compress::Zlib loaded ok Fetching with LWP: ftp://ftp.perl.org/pub/CPAN/modules/02packages.details.txt.gz Going to read /root/.cpan/sources/modules/02packages.details.txt.gz Database was generated on Sat, 18 Dec 2004 00:49:18 GMT There's a new CPAN.pm version (v1.76) available! [Current version is v1.61] You might want to try install Bundle::CPAN reload cpan without quitting the current session. It should be a seamless upgrade while we are running... Fetching with LWP: ftp://ftp.perl.org/pub/CPAN/modules/03modlist.data.gz Going to read /root/.cpan/sources/modules/03modlist.data.gz Going to write /root/.cpan/Metadata Warning: Cannot look Bio::SeqIO::staden, don't know what it is. Try the command i /Bio::SeqIO::staden/ to find objects with matching identifiers. cpan>quit [root@guyver-1 bioperl-ext-1.4]# make clean cd Bio/Ext/Align && test -f Makefile && make clean make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' rm -rf Align.c libs/*.o libs/*.a ./blib Makefile.aperl ../blib/arch/auto/Bio/Ext/Align/extralibs.all perlmain.c tmon.out mon.out so_locations pm_to_blib *.o *.a perl.exe perl perl Align.bs Align.bso Align.def libAlign.def Align.exp Align.x core core.*perl.*.? *perl.core mv Makefile Makefile.old > /dev/null 2>&1 make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' cd Bio/SeqIO/staden && test -f Makefile && make clean make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' rm -rf _Inline read.inl ./blib Makefile.aperl ../blib/arch/auto/Bio/SeqIO/staden/read/extralibs.all perlmain.c tmon.out mon.out so_locations pm_to_blib *.o *.a perl.exe perl perl read.bso read.def libread.def read.exp read.x core core.*perl.*.? *perl.core mv Makefile Makefile.old > /dev/null 2>&1 make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' rm -rf ./blib Makefile.aperl blib/arch/auto/Bio/extralibs.all perlmain.c tmon.out mon.out so_locations pm_to_blib *.o *.a perl.exe perl perl Bio.bso Bio.def libBio.def Bio.exp Bio.x core core.*perl.*.? *perl.core mv Makefile Makefile.old > /dev/null 2>&1 [xuying@guyver-1 bioperl-ext-1.4]$ perl Makefile.PL Checking if your kit is complete... Looks good Writing Makefile for Bio::Ext::Align Found Staden io_lib "libread" in /usr/local/lib ... Automatically using the Read.h found in /usr/local/include/io_lib ... Writing Makefile for Bio::SeqIO::staden::read Writing Makefile for Bio One or more DATA sections were not processed by Inline. [xuying@guyver-1 bioperl-ext-1.4]$ make;make test 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/commandline.h blib/lib/Bio/Ext/Align/libs/commandline.h cp Bio/Ext/Align/libs/wiseerror.c blib/lib/Bio/Ext/Align/libs/wiseerror.c cp Bio/Ext/Align/libs/aln.c blib/lib/Bio/Ext/Align/libs/aln.c cp Bio/Ext/Align/libs/dpenvelope.c blib/lib/Bio/Ext/Align/libs/dpenvelope.c cp Bio/Ext/Align/libs/packaln.c blib/lib/Bio/Ext/Align/libs/packaln.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/Makefile.old blib/lib/Bio/Ext/Align/Makefile.old cp Bio/Ext/Align/libs/packaln.h blib/lib/Bio/Ext/Align/libs/packaln.h 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/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/Makefile.PL blib/lib/Bio/Ext/Align/Makefile.PL cp Bio/Ext/Align/libs/wiseerror.h blib/lib/Bio/Ext/Align/libs/wiseerror.h 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/complexevalset.c blib/lib/Bio/Ext/Align/libs/complexevalset.c cp Bio/Ext/Align/libs/dynlibcross.h blib/lib/Bio/Ext/Align/libs/dynlibcross.h cp Bio/Ext/Align/libs/complexevalset.h blib/lib/Bio/Ext/Align/libs/complexevalset.h cp Bio/Ext/Align/libs/wisefile.c blib/lib/Bio/Ext/Align/libs/wisefile.c cp Bio/Ext/Align/libs/wiseconfig.c blib/lib/Bio/Ext/Align/libs/wiseconfig.c cp Bio/Ext/Align/libs/alnconvert.c blib/lib/Bio/Ext/Align/libs/alnconvert.c cp Bio/Ext/Align/typemap blib/lib/Bio/Ext/Align/typemap 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/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/hscore.c blib/lib/Bio/Ext/Align/libs/hscore.c cp Bio/Ext/Align/libs/complexconsensi.c blib/lib/Bio/Ext/Align/libs/complexconsensi.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/Ext/Align/blosum62.bla blib/lib/Bio/Ext/Align/blosum62.bla cp Bio/SeqIO/staden/read.pm blib/lib/Bio/SeqIO/staden/read.pm 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/Makefile.PL blib/lib/Bio/Ext/Makefile.PL cp Bio/Ext/Align/Align.pm blib/lib/Bio/Ext/Align/Align.pm cp Bio/Ext/Align/libs/dna.c blib/lib/Bio/Ext/Align/libs/dna.c cp Bio/Ext/Align/libs/complexconsensi.h blib/lib/Bio/Ext/Align/libs/complexconsensi.h cp Bio/Ext/Align/libs/sw.h blib/lib/Bio/Ext/Align/libs/sw.h cp Bio/Ext/Align/libs/wisestring.c blib/lib/Bio/Ext/Align/libs/wisestring.c 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/alnrange.h blib/lib/Bio/Ext/Align/libs/alnrange.h cp Bio/Ext/Align/libs/sw_wrap.h blib/lib/Bio/Ext/Align/libs/sw_wrap.h cp Bio/Ext/Align/libs/dpalign.c blib/lib/Bio/Ext/Align/libs/dpalign.c cp Bio/SeqIO/staden/Makefile.old blib/lib/Bio/SeqIO/staden/Makefile.old cp Bio/Ext/Align/libs/database.h blib/lib/Bio/Ext/Align/libs/database.h cp Bio/Ext/Align/libs/proteinsw.c blib/lib/Bio/Ext/Align/libs/proteinsw.c 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/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/codon.h blib/lib/Bio/Ext/Align/libs/codon.h cp Bio/Ext/Align/libs/linesubs.c blib/lib/Bio/Ext/Align/libs/linesubs.c cp Bio/Ext/Align/libs/proteindb.c blib/lib/Bio/Ext/Align/libs/proteindb.c 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/dnamatrix.h blib/lib/Bio/Ext/Align/libs/dnamatrix.h cp Bio/Ext/Align/libs/histogram.c blib/lib/Bio/Ext/Align/libs/histogram.c 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/dna.h blib/lib/Bio/Ext/Align/libs/dna.h 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/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/asciibtcanvas.c blib/lib/Bio/Ext/Align/libs/asciibtcanvas.c cp Bio/Ext/Align/libs/dnamatrix.c blib/lib/Bio/Ext/Align/libs/dnamatrix.c cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' 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 make[2]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align/libs' 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 make[2]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align/libs' /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap Align.xs > Align.xsc && mv Align.xsc Align.c gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fpic "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so LD_RUN_PATH="/lib" gcc -shared -L/usr/local/lib Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read -e1 0.01 ../blib/arch Starting Build Prepocess Stage Finished Build Prepocess Stage Starting Build Parse Stage Finished Build Parse Stage Starting Build Glue 1 Stage Finished Build Glue 1 Stage Starting Build Glue 2 Stage Finished Build Glue 2 Stage Starting Build Glue 3 Stage Finished Build Glue 3 Stage Starting Build Compile Stage Starting "perl Makefile.PL" Stage Writing Makefile for Bio::SeqIO::staden::read Finished "perl Makefile.PL" Stage Starting "make" Stage make[2]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv read.xsc read.c gcc -c -I/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fpic "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c In file included from /usr/local/include/io_lib/os.h:4, from /usr/local/include/io_lib/Read.h:43, from read.xs:5: /usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined read.c:1:1: warning: this is the location of the previous definition read.xs: In function `staden_write_trace': read.xs:32: warning: assignment from incompatible pointer type Running Mkbootstrap for Bio::SeqIO::staden::read () chmod 644 read.bs rm -f blib/arch/auto/Bio/SeqIO/staden/read/read.so LD_RUN_PATH="/usr/local/lib" gcc -shared -L/usr/local/lib read.o -o blib/arch/auto/Bio/SeqIO/staden/read/read.so -L/usr/local/lib -lread chmod 755 blib/arch/auto/Bio/SeqIO/staden/read/read.so cp read.bs blib/arch/auto/Bio/SeqIO/staden/read/read.bs chmod 644 blib/arch/auto/Bio/SeqIO/staden/read/read.bs make[2]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' Finished "make" Stage Starting "make install" Stage make[2]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' Installing /home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.so Installing /home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bs Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Writing /home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/.packlist make[2]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' Finished "make install" Stage Starting Cleaning Up Stage Finished Cleaning Up Stage Finished Build Compile Stage Manifying ../blib/man3/Bio::SeqIO::staden::read.3pm make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' Manifying blib/man3/Bio::SeqIO::staden::read.3pm make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/basic....ok All tests successful. Files=1, Tests=1, 0 wallclock secs ( 0.06 cusr + 0.00 csys = 0.06 CPU) make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl 1..2 ok 1 2..2 Testing bp_sw with a protein alignment... ProteinSW Matrix calculation: [ 0] Cells 0% one 1 WLGQRNLVSSTGGNLLNVWLKDW W+G RN+V NLLNVW +DW two 1 WMGNRNVV-----NLLNVWFRDW ok 2 make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, '../blib/lib', '../blib/arch')" test.pl test....ok 7/94# Failed test 7 in test.pl at line 110 *TODO*: We don't have the ability to write files for abi format test....ok 8/94# Failed test 8 in test.pl at line 110 fail #2 *TODO*: We don't have the ability to write files for abi format test....ok 9/94# Failed test 9 in test.pl at line 110 fail #3 *TODO*: We don't have the ability to write files for abi format test....ok 10/94# Failed test 10 in test.pl at line 110 fail #4 *TODO*: We don't have the ability to write files for abi format test....ok 11/94# Failed test 11 in test.pl at line 110 fail #5 *TODO*: We don't have the ability to write files for abi format test....ok 12/94# Failed test 12 in test.pl at line 110 fail #6 *TODO*: We don't have the ability to write files for abi format test....ok 13/94# Failed test 13 in test.pl at line 110 fail #7 *TODO*: We don't have the ability to write files for abi format test....ok 14/94# Failed test 14 in test.pl at line 62 *TODO*: Still missing test files for alf format test....ok 15/94# Failed test 15 in test.pl at line 62 fail #2 *TODO*: Still missing test files for alf format test....ok 16/94# Failed test 16 in test.pl at line 62 fail #3 *TODO*: Still missing test files for alf format test....ok 17/94# Failed test 17 in test.pl at line 62 fail #4 *TODO*: Still missing test files for alf format test....ok 18/94# Failed test 18 in test.pl at line 62 fail #5 *TODO*: Still missing test files for alf format test....ok 19/94# Failed test 19 in test.pl at line 62 fail #6 *TODO*: Still missing test files for alf format test....ok 20/94# Failed test 20 in test.pl at line 62 fail #7 *TODO*: Still missing test files for alf format test....ok 21/94# Failed test 21 in test.pl at line 62 fail #8 *TODO*: Still missing test files for alf format test....ok 22/94# Failed test 22 in test.pl at line 62 fail #9 *TODO*: Still missing test files for alf format test....ok 23/94# Failed test 23 in test.pl at line 62 fail #10 *TODO*: Still missing test files for alf format test....ok 24/94# Failed test 24 in test.pl at line 62 fail #11 *TODO*: Still missing test files for alf format test....ok 25/94# Failed test 25 in test.pl at line 62 fail #12 *TODO*: Still missing test files for alf format test....ok 31/94# Failed test 31 in test.pl at line 107 *TODO*: Can't write valid ctf files until we have a trace object test....ok 32/94# Failed test 32 in test.pl at line 107 fail #2 *TODO*: Can't write valid ctf files until we have a trace object test....ok 33/94# Failed test 33 in test.pl at line 107 fail #3 *TODO*: Can't write valid ctf files until we have a trace object test....ok 34/94# Failed test 34 in test.pl at line 107 fail #4 *TODO*: Can't write valid ctf files until we have a trace object test....ok 35/94# Failed test 35 in test.pl at line 107 fail #5 *TODO*: Can't write valid ctf files until we have a trace object test....ok 36/94# Failed test 36 in test.pl at line 107 fail #6 *TODO*: Can't write valid ctf files until we have a trace object test....ok 37/94# Failed test 37 in test.pl at line 107 fail #7 *TODO*: Can't write valid ctf files until we have a trace object test....ok All tests successful. Files=1, Tests=94, 8 wallclock secs ( 5.58 cusr + 0.08 csys = 5.66 CPU) make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' [root@guyver-1 bioperl-ext-1.4]# make install make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Entering directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' make[1]: Leaving directory `/home/xuying/bioperl-ext-1.4/Bio/SeqIO/staden' Writing /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/auto/Bio/.packlist Appending installation info to /usr/lib/perl5/5.8.0/i386-linux-thread-multi/perllocal.pod