[Bioperl-l] bioperl-ext installation

boyang zhe zheboyang at gmail.com
Sat Oct 22 01:38:56 UTC 2011 

I try to install bioperl-ext. But I failed.

So I try the method suggested by JMF< jeanmarc.frigerio at gmail.com>.

made a patch to the Bio/
Ext/Align/Makefile.PL to make the compiler happy, just by changing:

 'MYEXTLIB'  => 'libs/libsw$(LIB_EXT)',
to
'MYEXTLIB'  => '\'-fPIC libs/libsw$(LIB_EXT)\''

Then I run make.
It seems ok for compilation.

However, it generate errors when I run make test. No any of the 20 tests
passed.

it seems that because " Can't load
'../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align:
../blib/arch/auto/Bio/Ext/Align/Align.so"
I did not see any Align.so file at those directory. In fact, I can only find
a blank directory of blib/arch/auto/Bio/Ext.

Hope for your help. It is really hard for me.

Thank you very much.
boyang

info as below:
make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE
-DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \
cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR'
DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \
    : libsw.a
make[2]: Entering directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE
-DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \
cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR'
DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \
    : libsw.a
make[2]: Entering directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so
cc  -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o  -o
../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \
   -lm   \

chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so
make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align'
make[1]: Entering directory
`/home/bji/Software/bioperl-ext/Bio/SeqIO/staden'
make[1]: Leaving directory `/home/bji/Software/bioperl-ext/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.t .. ok
All tests successful.
Files=1, Tests=1,  0 wallclock secs ( 0.04 usr  0.00 sys +  0.04 cusr  0.00
csys =  0.08 CPU)
Result: PASS
make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE
-DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \
cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR'
DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \
    : libsw.a
make[2]: Entering directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE
-DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \
cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR'
DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \
    : libsw.a
make[2]: Entering directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so
cc  -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o  -o
../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \
   -lm   \

chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..20
not ok 1 - use Bio::Ext::Align;
#   Failed test 'use Bio::Ext::Align;'
#   at test.pl line 15.
#     Tried to use 'Bio::Ext::Align'.
#     Error:  Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for
module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined
symbol: bp_sw_access_name_CompMat at /usr/lib/perl/5.10/DynaLoader.pm line
193.
#  at (eval 4) line 2
# Compilation failed in require at (eval 4) line 2.
# BEGIN failed--compilation aborted at (eval 4) line 2.

The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has
not been installed.
 Please install the bioperl-ext package

# Looks like you planned 20 tests but ran 1.
# Looks like you failed 1 test of 1 run.
# Looks like your test exited with 1 just after 1.
make[1]: *** [test_dynamic] Error 1
make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align'
make: *** [subdirs-test] Error 2

This is the info for 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/SeqIO/staden/CHANGES blib/lib/Bio/SeqIO/staden/CHANGES
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/SeqIO/staden/t/staden/data/readtest.exp
blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.exp
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/Align/libs/complexsequence.h
blib/lib/Bio/Ext/Align/libs/complexsequence.h
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/wiseconfig.h blib/lib/Bio/Ext/Align/libs/wiseconfig.h
cp Bio/SeqIO/staden/t/staden/data/readtestabi.fa
blib/lib/Bio/SeqIO/staden/t/staden/data/readtestabi.fa
cp Bio/Ext/Align/libs/dynlibcross.h
blib/lib/Bio/Ext/Align/libs/dynlibcross.h
cp Bio/SeqIO/staden/t/staden/data/readtest.pln
blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.pln
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/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/SeqIO/staden/README blib/lib/Bio/SeqIO/staden/README
cp Bio/SeqIO/staden/read.xs blib/lib/Bio/SeqIO/staden/read.xs
cp Bio/SeqIO/staden/t/staden/data/readtest.abi
blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.abi
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/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/t/staden/data/readtestref.scf
blib/lib/Bio/SeqIO/staden/t/staden/data/readtestref.scf
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/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/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/SeqIO/staden/META.yml blib/lib/Bio/SeqIO/staden/META.yml
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/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/wisetime.c blib/lib/Bio/Ext/Align/libs/wisetime.c
cp Bio/Ext/Align/libs/proteinsw.c blib/lib/Bio/Ext/Align/libs/proteinsw.c
cp Bio/SeqIO/staden/MANIFEST blib/lib/Bio/SeqIO/staden/MANIFEST
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/compmat.c blib/lib/Bio/Ext/Align/libs/compmat.c
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/SeqIO/staden/t/staden/data/readtest.ctf
blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ctf
cp Bio/SeqIO/staden/t/staden/data/readtest.ztr
blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ztr
cp Bio/Ext/Align/libs/basematrix.h blib/lib/Bio/Ext/Align/libs/basematrix.h
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/histogram.c blib/lib/Bio/Ext/Align/libs/histogram.c
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/md_20.mat blib/lib/Bio/Ext/Align/md_20.mat
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/scores.lst blib/lib/Bio/Ext/Align/scores.lst
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/SeqIO/staden/t/staden_read.t
blib/lib/Bio/SeqIO/staden/t/staden_read.t
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
make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align'
cp Align.pm ../blib/lib/Bio/Ext/Align.pm
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE
-DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \
cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR'
DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \
    : libsw.a
make[2]: Entering directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o aln.o aln.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o alnconvert.o alnconvert.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o alnrange.o alnrange.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o asciibtcanvas.o
asciibtcanvas.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o basematrix.o basematrix.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o btcanvas.o btcanvas.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o commandline.o commandline.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o complexconsensi.o
complexconsensi.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o complexevalset.o
complexevalset.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o complexsequence.o
complexsequence.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o compmat.o compmat.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o codon.o codon.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o dna.o dna.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o dnamatrix.o dnamatrix.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o dpenvelope.o dpenvelope.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o dynlibcross.o dynlibcross.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o histogram.o histogram.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o hscore.o hscore.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o linesubs.o linesubs.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o packaln.o packaln.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o probability.o probability.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o protein.o protein.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o proteindb.o proteindb.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o proteinsw.o proteinsw.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o seqaligndisplay.o
seqaligndisplay.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o sequence.o sequence.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o sequencedb.o sequencedb.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o sw_wrap.o sw_wrap.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o wiseerror.o wiseerror.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o wisefile.o wisefile.c
wisefile.dy: In function ‘bp_sw_myfclose’:
wisefile.dy:66: warning: format ‘%d’ expects type ‘int’, but argument 3 has
type ‘struct FILE *’
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o wisememman.o wisememman.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o wiseoverlay.o wiseoverlay.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o wiserandom.o wiserandom.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o wisestring.o wisestring.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o wisetime.o wisetime.c
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR   -c -o dpalign.o dpalign.c
dpalign.c: In function ‘dpAlign_fatal’:
dpalign.c:43: warning: format not a string literal and no format arguments
cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -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/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE
-DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \
cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR'
DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \
    : libsw.a
make[2]: Entering directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
make[2]: `libsw.a' is up to date.
make[2]: Leaving directory
`/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs'
/usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp  -typemap
/usr/share/perl/5.10/ExtUtils/typemap -typemap typemap  Align.xs > Align.xsc
&& mv Align.xsc Align.c
cc -c  -I./libs -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing
-pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.6.0\" -DXS_VERSION=\"1.6.0\"
-fPIC "-I/usr/lib/perl/5.10/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
cc  -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o  -o
../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC 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/bji/Software/bioperl-ext/Bio/Ext/Align'
make[1]: Entering directory
`/home/bji/Software/bioperl-ext/Bio/SeqIO/staden'
cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm
/usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp  -typemap
/usr/share/perl/5.10/ExtUtils/typemap  read.xs > read.xsc && mv read.xsc
read.c
cc -c  -I/usr/local/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"1.007000\"
-DXS_VERSION=\"1.007000\" -fPIC "-I/usr/lib/perl/5.10/CORE"   read.c
read.xs: In function ‘staden_write_trace’:
read.xs:17: warning: cast to pointer from integer of different size
read.xs:22: warning: cast to pointer from integer of different size
read.xs: In function ‘staden_read_graph’:
read.xs:204: warning: passing argument 2 of ‘Perl_newRV’ from incompatible
pointer type
/usr/lib/perl/5.10/CORE/proto.h:2166: note: expected ‘struct SV *’ but
argument is of type ‘struct AV *’
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" cc  -shared -O2 -g -L/usr/local/lib
-fstack-protector read.o  -o ../blib/arch/auto/Bio/SeqIO/staden/read/read.so
\
   -L/usr/local/lib -lz -lm -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
Manifying ../blib/man3/Bio::SeqIO::staden::read.3pm
make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden'
Manifying blib/man3/Bio::SeqIO::staden::read.3pm

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