[Bioperl-l] Re: [Bug 1837] Bio::Ext::Align
Brian Osborne
osborne1 at optonline.net
Fri Dec 23 16:12:57 EST 2005
Jouni,
I've been playing a bit with bioperl-ext on Mac OS X, I found that the 'make
install' of SeqIO/staden/* was not working unless I performed the 'make' and
'make install' from within the bioperl-ext/Bio/SeqIO/staden directory.
Perhaps you're seeing the same thing - can you try 'make clean', 'perl
Makefile.PL', 'make', 'make test', and then the 'make install' from within
bioperl-ext/Bio/Ext/Align and see what happens?
Brian O.
On 12/22/05 12:13 PM, "Brian Osborne" <osborne1 at optonline.net> wrote:
> Jouni,
>
> I suggest you show this error to bioperl-l, I'm unable to debug this package
> because of problems with "make", unrelated to the problems that you've seen.
>
> Brian O.
>
>
> On 12/19/05 10:30 AM, "Jouni Valiaho" <Jouni.Valiaho at uta.fi> wrote:
>
>> Brian,
>>
>> Thanks, again!
>>
>> Now the make goes through (prompt attached the end of email).
>> I run "make test" (as a normal user) and got an error at the end of
>> test (see prompt attached the end of email).
>> Despite of that, I run "make install" (as root, prompt attached the end
>> of email).
>> After it i run simple test:
>> $ perl -e 'use Bio::Ext::Align;'
>> Can't locate Bio/Ext/Align.pm in @INC (@INC contains:
>> /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi
>> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
>> /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi
>> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
>> /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
>> /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3
>> /usr/lib/perl5/site_perl
>> /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
>> /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3
>> /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.6/i386-linux-thread-multi
>> /usr/lib/perl5/5.8.6 .) at -e line 1.
>> BEGIN failed--compilation aborted at -e line 1.
>>
>> As you see the INC contains the path /usr/lib/perl5/site_perl/5.8.6,
>> where the ext modules were installed.
>> Do you have any suggestions what can I do?
>>
>> Jouni
>>
>> Quoting Brian Osborne <osborne1 at optonline.net>:
>>
>>> Jouni,
>>>
>>> Hmm. What happens when you change:
>>>
>>> use vars qw(@ISA $VERSION $HAS_INLINE);
>>> VERSION => '0.01',
>>>
>>> To
>>>
>>> use vars qw(@ISA $VERSION $HAS_INLINE);
>>> VERSION => '1.51',
>>>
>>> As well?
>>>
>>> You probably want to start from the beginning with "make clean" etc.
>>>
>>> BIO
>>>
>>>
>>> On 12/19/05 3:30 AM, "Jouni Valiaho" <Jouni.Valiaho at uta.fi> wrote:
>>>
>>>> Brian,
>>>>
>>>> Thanks, I changed "1.5.1" to "1.51" in Bio/SeqIO/staden/read.pm.
>>>> It fixed the problem. Here is the command prompt.
>>>>
>>>> $ perl Makefile.PL
>>>> 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.
>>>>
>>>> Then I perform the make command (as a normal user, not as super user).
>>>>
>>
>> #################################
>> $ make
>> #################################
>> $ make
>> cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h
>> cp Bio/Ext/Align/libs/probability.c blib/lib/Bio/Ext/Align/libs/probability.c
>> cp Bio/Ext/Align/libs/linesubs.h blib/lib/Bio/Ext/Align/libs/linesubs.h
>> 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/HMM/hmm.h blib/lib/Bio/Ext/HMM/hmm.h
>> 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/SeqIO/staden/read.pm.ori blib/lib/Bio/SeqIO/staden/read.pm.ori
>> 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/blosum45.mat blib/lib/Bio/Ext/Align/blosum45.mat
>> 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/HMM/Makefile.PL blib/lib/Bio/Ext/HMM/Makefile.PL
>> 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/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/HMM/typemap blib/lib/Bio/Ext/HMM/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/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/blosum62.mat blib/lib/Bio/Ext/Align/blosum62.mat
>> 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/blosum50.mat blib/lib/Bio/Ext/Align/blosum50.mat
>> 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/libs/complexconsensi.h
>> blib/lib/Bio/Ext/Align/libs/complexconsensi.h
>> 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/HMM/hmmlib.c blib/lib/Bio/Ext/HMM/hmmlib.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/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/wisetime.c blib/lib/Bio/Ext/Align/libs/wisetime.c
>> cp Bio/Ext/HMM/test.pl blib/lib/Bio/Ext/HMM/test.pl
>> 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/linesubs.c blib/lib/Bio/Ext/Align/libs/linesubs.c
>> cp Bio/Ext/Align/libs/compmat.c blib/lib/Bio/Ext/Align/libs/compmat.c
>> cp Bio/Ext/Align/libs/proteindb.c blib/lib/Bio/Ext/Align/libs/proteindb.c
>> cp Bio/Ext/Align/libs/codon.h blib/lib/Bio/Ext/Align/libs/codon.h
>> 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/wiserandom.h blib/lib/Bio/Ext/Align/libs/wiserandom.h
>> cp Bio/Ext/Align/libs/dnamatrix.h blib/lib/Bio/Ext/Align/libs/dnamatrix.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/HMM/HMM.pm blib/lib/Bio/Ext/HMM/HMM.pm
>> cp Bio/Ext/HMM/HMM.xs blib/lib/Bio/Ext/HMM/HMM.xs
>> 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/md_20.mat blib/lib/Bio/Ext/Align/md_20.mat
>> 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/wisetime.h blib/lib/Bio/Ext/Align/libs/wisetime.h
>> cp Bio/Ext/Align/libs/protein.c blib/lib/Bio/Ext/Align/libs/protein.c
>> cp Bio/Ext/Align/libs/wiseoverlay.c blib/lib/Bio/Ext/Align/libs/wiseoverlay.c
>> cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h
>> 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
>> make[1]: Entering directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align'
>> cp Align.pm ../blib/lib/Bio/Ext/Align.pm
>> DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; CFLAGS='-D_REENTRANT
>> -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm'; export DEFINE INC CC CFLAGS; \
>> cd libs && make CC='gcc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBUGGING
>> -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPOSIX -DNOERROR'
>> DEFINE='-DPOSIX -DNOERROR' libsw.a -e
>> make[2]: Entering directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align/libs'
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o aln.o aln.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o alnconvert.o alnconvert.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o alnrange.o alnrange.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o asciibtcanvas.o
>> asciibtcanvas.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o basematrix.o basematrix.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o btcanvas.o btcanvas.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o commandline.o
>> commandline.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o complexconsensi.o
>> complexconsensi.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o complexevalset.o
>> complexevalset.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o complexsequence.o
>> complexsequence.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o compmat.o compmat.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o codon.o codon.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o dna.o dna.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o dnamatrix.o dnamatrix.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o dpenvelope.o dpenvelope.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o dynlibcross.o
>> dynlibcross.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o histogram.o histogram.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o hscore.o hscore.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o linesubs.o linesubs.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o packaln.o packaln.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o probability.o
>> probability.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o protein.o protein.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o proteindb.o proteindb.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o proteinsw.o proteinsw.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o seqaligndisplay.o
>> seqaligndisplay.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o sequence.o sequence.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o sequencedb.o sequencedb.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o sw_wrap.o sw_wrap.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o wiseerror.o wiseerror.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o wisefile.o wisefile.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o wisememman.o wisememman.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o wiseoverlay.o
>> wiseoverlay.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o wiserandom.o wiserandom.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o wisestring.o wisestring.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o wisetime.o wisetime.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -c -o dpalign.o dpalign.c
>> gcc -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe
>> -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> -I/usr/include/gdbm -DPOSIX -DNOERROR -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 libsw.a
>> make[2]: Leaving directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align/libs'
>> /usr/bin/perl /usr/lib/perl5/5.8.6/ExtUtils/xsubpp -typemap
>> /usr/lib/perl5/5.8.6/ExtUtils/typemap -typemap typemap Align.xs >
>> Align.xsc && mv Align.xsc Align.c
>> gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING
>> -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4
>> -fasynchronous-unwind-tables -DVERSION=\"1.5.1\"
>> -DXS_VERSION=\"1.5.1\" -fPIC
>> "-I/usr/lib/perl5/5.8.6/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
>> 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/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align'
>> make[1]: Entering directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/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 1.51 ../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/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden/_Inline/build/Bio/Se>>
q
>> IO/staden/read'
>> /usr/bin/perl /usr/lib/perl5/5.8.6/ExtUtils/xsubpp -typemap
>> /usr/lib/perl5/5.8.6/ExtUtils/typemap read.xs > read.xsc && mv
>> read.xsc read.c
>> gcc -c -I/home/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden
>> -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING
>> -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4
>> -fasynchronous-unwind-tables -DVERSION=\"1.51\" -DXS_VERSION=\"1.51\"
>> -fPIC "-I/usr/lib/perl5/5.8.6/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
>> <command line>:1:1: warning: this is the location of the previous definition
>> Running Mkbootstrap for Bio::SeqIO::staden::read ()
>> chmod 644 read.bs
>> rm -f blib/arch/auto/Bio/SeqIO/staden/read/read.so
>> gcc -shared -L/usr/local/lib read.o -o
>> blib/arch/auto/Bio/SeqIO/staden/read/read.so -L/usr/local/lib -lread
>> -lz
>> 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/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden/_Inline/build/Bio/Se>>
q
>> IO/staden/read'
>> Finished "make" Stage
>>
>> Starting "make install" Stage
>> make[2]: Entering directory
>>
`/home/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden/_Inline/build/Bio/Se>>
q
>> IO/staden/read'
>> Installing
>>
/home/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden/../blib/arch/auto/Bio>>
/
>> SeqIO/staden/read/read.so
>> Installing
>>
/home/java/perl_code/bioperl-ext-1.5.1/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/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden/../blib/arch/auto/Bio>>
/
>> SeqIO/staden/read/.packlist
>> make[2]: Leaving directory
>>
`/home/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden/_Inline/build/Bio/Se>>
q
>> IO/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/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden'
>> Manifying blib/man3/Bio::SeqIO::staden::read.3pm
>>
>>
>> ###########################################
>> $make test
>> ###########################################
>> $ make test
>> make[1]: Entering directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align'
>> make[1]: Leaving directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align'
>> make[1]: Entering directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden'
>> make[1]: Leaving directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/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 ( 0.03 cusr + 0.01 csys = 0.04 CPU)
>> make[1]: Entering directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align'
>> PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
>> 1..9
>> # Running under perl version 5.008006 for linux
>> # Current time local: Mon Dec 19 16:56:07 2005
>> # Current time GMT: Mon Dec 19 14:56:07 2005
>> # Using Test.pm version 1.25
>> ok 1
>> ok 2
>> ok 3
>> ok 4
>> ProteinSW Matrix calculation: [ 0] Cells 0%
>> ok 5
>> ok 6
>> ok 7
>> ok 8
>> ok 9
>> *** glibc detected *** /usr/bin/perl: double free or corruption (top):
>> 0x08f2add0 ***
>> ======= Backtrace: =========
>> /lib/libc.so.6[0x385124]
>> /lib/libc.so.6(__libc_free+0x77)[0x38565f]
>>
../blib/arch/auto/Bio/Ext/Align/Align.so(XS_Bio__Ext__Align__SequenceProfile_>>
D
>> ESTROY+0xfc)[0xef08d6]
>>
/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so(Perl_pp_entersub>>
+
>> 0x3a5)[0x9d7bcc]
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so[0x967bbe]
>>
/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so(Perl_call_sv+0x7>>
3
>> 6)[0x96c251]
>>
/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so(Perl_sv_clear+0x>>
1
>> 19)[0x9dcc3b]
>>
/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so(Perl_sv_free+0x1>>
0
>> c)[0x9dd5e2]
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so[0x9ddb98]
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so[0x9dabbe]
>>
/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so(Perl_sv_clean_ob>>
j
>> s+0x36)[0x9dac88]
>>
/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so(perl_destruct+0x>>
1
>> 2f3)[0x96e367]
>> /usr/bin/perl(main+0xda)[0x804939e]
>> /lib/libc.so.6(__libc_start_main+0xdf)[0x336d5f]
>> /usr/bin/perl[0x8049241]
>> ======= Memory map: ========
>> 00111000-0012f000 r-xp 00000000 03:03 737502
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/auto/POSIX/POSIX.so
>> 0012f000-00130000 rwxp 0001d000 03:03 737502
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/auto/POSIX/POSIX.so
>> 00281000-00285000 r-xp 00000000 03:03 737497
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/auto/IO/IO.so
>> 00285000-00286000 rwxp 00003000 03:03 737497
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/auto/IO/IO.so
>> 002ec000-002ee000 r-xp 00000000 03:03 7242199 /lib/libutil-2.3.5.so
>> 002ee000-002ef000 r-xp 00001000 03:03 7242199 /lib/libutil-2.3.5.so
>> 002ef000-002f0000 rwxp 00002000 03:03 7242199 /lib/libutil-2.3.5.so
>> 00304000-0031e000 r-xp 00000000 03:03 7241779 /lib/ld-2.3.5.so
>> 0031e000-0031f000 r-xp 00019000 03:03 7241779 /lib/ld-2.3.5.so
>> 0031f000-00320000 rwxp 0001a000 03:03 7241779 /lib/ld-2.3.5.so
>> 00322000-00445000 r-xp 00000000 03:03 7242154 /lib/libc-2.3.5.so
>> 00445000-00447000 r-xp 00123000 03:03 7242154 /lib/libc-2.3.5.so
>> 00447000-00449000 rwxp 00125000 03:03 7242154 /lib/libc-2.3.5.so
>> 00449000-0044b000 rwxp 00449000 00:00 0
>> 0044d000-00470000 r-xp 00000000 03:03 7242168 /lib/libm-2.3.5.so
>> 00470000-00471000 r-xp 00022000 03:03 7242168 /lib/libm-2.3.5.so
>> 00471000-00472000 rwxp 00023000 03:03 7242168 /lib/libm-2.3.5.so
>> 00474000-00476000 r-xp 00000000 03:03 7242162 /lib/libdl-2.3.5.so
>> 00476000-00477000 r-xp 00001000 03:03 7242162 /lib/libdl-2.3.5.so
>> 00477000-00478000 rwxp 00002000 03:03 7242162 /lib/libdl-2.3.5.so
>> 00576000-00584000 r-xp 00000000 03:03 6914064 /lib/libpthread-2.3.5.so
>> 00584000-00585000 r-xp 0000d000 03:03 6914064 /lib/libpthread-2.3.5.so
>> 00585000-00586000 rwxp 0000e000 03:03 6914064 /lib/libpthread-2.3.5.so
>> 00586000-00588000 rwxp 00586000 00:00 0
>> 0076c000-00775000 r-xp 00000000 03:03 3833859
>> /lib/libgcc_s-4.0.2-20051126.so.1
>> 00775000-00776000 rwxp 00009000 03:03 3833859
>> /lib/libgcc_s-4.0.2-20051126.so.1
>> 007ff000-00804000 r-xp 00000000 03:03 737890
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/auto/Socket/Socket.so
>> 00804000-00805000 rwxp 00004000 03:03 737890
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/auto/Socket/Socket.so
>> 00946000-00a84000 r-xp 00000000 03:03 737470
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so
>> 00a84000-00a8f000 rwxp 0013d000 03:03 737470
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE/libperl.so
>> 00a8f000-00a91000 rwxp 00a8f000 00:00 0
>> 00aa9000-00aac000 r-xp 00000000 03:03 737492
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/auto/Fcntl/Fcntl.so
>> 00aac000-00aad000 rwxp 00002000 03:03 737492
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/auto/Fcntl/Fcntl.so
>> 00bf1000-00c00000 r-xp 00000000 03:03 7242170 /lib/libresolv-2.3.5.so
>> 00c00000-00c01000 r-xp 0000e000 03:03 7242170 /lib/libresolv-2.3.5.so
>> 00c01000-00c02000 rwxp 0000f000 03:03 7242170 /lib/libresolv-2.3.5.so
>> 00c02000-00c04000 rwxp 00c02000 00:00 0
>> 00c95000-00c96000 r-xp 00c95000 00:00 0 [vdso]
>> 00dd1000-00de3000 r-xp 00000000 03:03 7242158 /lib/libnsl-2.3.5.so
>> 00de3000-00de4000 r-xp 00011000 03:03 7242158 /lib/libnsl-2.3.5.so
>> 00de4000-00de5000 rwxp 00012000 03:03 7242158 /lib/libnsl-2.3.5.so
>> 00de5000-00de7000 rwxp 00de5000 00:00 0
>> 00e99000-00f30000 r-xp 00000000 03:03 1736935
>>
/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/blib/arch/auto/Bio/Ext/Align/A>>
l
>> ign.so
>> 00f30000-00f32000 rwxp 00096000 03:03 1736935
>>
/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/blib/arch/auto/Bio/Ext/Align/A>>
l
>> ign.so
>> 075e1000-075e6000 r-xp 00000000 03:03 7242164 /lib/libcrypt-2.3.5.so
>> 075e6000-075e7000 r-xp 00004000 03:03 7242164 /lib/libcrypt-2.3.5.so
>> 075e7000-075e8000 rwxp 00005000 03:03 7242164 /lib/libcrypt-2.3.5.so
>> 075e8000-0760f000 rwxp 075e8000 00:00 0
>> 08048000-0804b000 r-xp 00000000 03:03 41930 /usr/bin/perl
>> 0804b000-0804d000 rw-p 00002000 03:03 41930 /usr/bin/perl
>> 08913000-08f47000 rw-p 08913000 00:00 0 [heap]
>> b7b00000-b7b21000 rw-p b7b00000 00:00 0
>> b7b21000-b7c00000 ---p b7b21000 00:00 0
>> b7cfe000-b7d1f000 rw-p b7cfe000 00:00 0
>> b7d1f000-b7f1f000 r--p 00000000 03:03 48867
>> /usr/lib/locale/locale-archive
>> b7f1f000-b7f22000 rw-p b7f1f000 00:00 0
>> b7f3a000-b7f3b000 rw-p b7f3a000 00:00 0
>> bff25000-bff3b000 rw-p bff25000 00:00 0 [stack]
>> make[1]: *** [test_dynamic] Aborted
>> make[1]: Leaving directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align'
>> make: *** [test] Error 2
>>
>>
>> ################################################
>> $make install
>> ################################################
>> make install
>> make[1]: Entering directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align'
>> make[1]: Leaving directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/Ext/Align'
>> make[1]: Entering directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden'
>> make[1]: Leaving directory
>> `/home/java/perl_code/bioperl-ext-1.5.1/Bio/SeqIO/staden'
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/blosum62.mat
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/test.pl
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/blosum50.mat
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/blosum45.mat
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/blosum62.bla
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/typemap
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/md_20.mat
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/Makefile.PL
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/Align.pm
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/Align.xs
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/aln.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisetime.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wiserandom.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dpenvelope.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/codon.c
>> Installing
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/complexsequence.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dynlibcross.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/asciibtcanvas.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/proteindb.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/protein.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wiserandom.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dyna.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisestring.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/histogram.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wiseerror.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dna.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wiseconfig.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/sequencedb.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/proteinsw.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/basematrix.c
>> Installing
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/seqaligndisplay.c
>> Installing
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/seqaligndisplay.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/sequence.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/sequencedb.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/complexevalset.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dpenvelope.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wiseoverlay.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/probability.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wiseoverlay.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/sw_wrap.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dpalign.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/alnconvert.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/histogram.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dynlibcross.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/sw.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/protein.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisefile.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/probability.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/commandline.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisememman.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/alnrange.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/basematrix.h
>> Installing
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/complexconsensi.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dpalign.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisememman.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/btcanvas.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisebase.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/compmat.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisefile.c
>> Installing
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/complexsequence.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/hscore.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/linesubs.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wiseerror.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wiseconfig.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/hscore.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/packaln.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/aln.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/alnconvert.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dna.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/proteindb.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/proteinsw.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisestring.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/alnrange.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/sw_wrap.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dnamatrix.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/wisetime.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/makefile
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/btcanvas.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/dnamatrix.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/codon.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/complexevalset.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/asciibtcanvas.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/compmat.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/linspc.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/linesubs.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/packaln.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/commandline.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/sequence.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/database.h
>> Installing
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/Align/libs/complexconsensi.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/HMM/hmmlib.c
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/HMM/test.pl
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/HMM/HMM.pm
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/HMM/HMM.xs
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/HMM/typemap
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/HMM/hmm.h
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/Ext/HMM/Makefile.PL
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/SeqIO/staden/test.pl
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/SeqIO/staden/read.pm
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/SeqIO/staden/read.pm.ori
>> Installing /usr/lib/perl5/site_perl/5.8.6/Bio/SeqIO/staden/Makefile.PL
>> Installing /usr/share/man/man3/Bio::SeqIO::staden::read.3pm
>> Writing
>> /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi/auto/Bio/.packlist
>> Appending installation info to
>> /usr/lib/perl5/5.8.6/i386-linux-thread-multi/perllocal.pod
>>
>>
>>
>> --------------------------------------------------------------------
>> Jouni Väliaho, Research scientist Phone: +358-3-215 8916
>> Institute of Medical Technology Fax: +358-3-215 7710
>> FI-33014 University of Tampere E-mail: jouni.valiaho at uta.fi
>> Finland http://bioinf.uta.fi/
>> --------------------------------------------------------------------
>>
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