[Bioperl-l] Trouble install Bioperl-Ext-1.4 & dpAlign

jany janynannan at yahoo.co.uk
Tue Jun 8 09:07:45 EDT 2004 

Hello, All:
I tried to install bioperl-ext-1.4 in Redhat9. I get
errors on running make. I found Barry met the similar
problems in January, but I failed on make test. Could
anybody know how to solve it?
Many thanks,
Nan
The errors are attched below. Since it is too long, I
delete some to shorten the mail.

[root at localhost bioperl-ext]# 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.
 
[root at localhost bioperl-ext]# make
cp Bio/Ext/Align/libs/hscore.h
blib/lib/Bio/Ext/Align/libs/hscore.h
.....
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/jiangnan/download/bioperl-ext/Bio/Ext/Align'
cp Align.pm ../blib/lib/Bio/Ext/Align.pm
DEFINE='-DPOSIX -DNOERROR'; CC='gcc';
CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
-DDEBUGGING -fno-strict-aliasing -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 -DTHREADS_HAVE_PIDS -DDEBUGGING
-fno-strict-aliasing -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/jiangnan/download/bioperl-ext/Bio/Ext/Align/libs'
gcc -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
-DDEBUGGING -fno-strict-aliasing -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 -DTHREADS_HAVE_PIDS
-DDEBUGGING -fno-strict-aliasing -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 -DTHREADS_HAVE_PIDS
-DDEBUGGING -fno-strict-aliasing -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
make[2]: Leaving directory
`/home/jiangnan/download/bioperl-ext/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
-DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing
-I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2
-march=i386 -mcpu=i686 -g   -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/jiangnan/download/bioperl-ext/Bio/Ext/Align'
make[1]: Entering directory
`/home/jiangnan/download/bioperl-ext/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 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/jiangnan/download/bioperl-ext/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/jiangnan/download/bioperl-ext/Bio/SeqIO/staden
-I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE
-DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing
-I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2
-march=i386 -mcpu=i686 -g   -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/jiangnan/download/bioperl-ext/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read'
  Finished "make" Stage
 
  Starting "make install" Stage
make[2]: Entering directory
`/home/jiangnan/download/bioperl-ext/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read'
Installing
/home/jiangnan/download/bioperl-ext/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.so
Installing
/home/jiangnan/download/bioperl-ext/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/jiangnan/download/bioperl-ext/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/.packlist
make[2]: Leaving directory
`/home/jiangnan/download/bioperl-ext/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/jiangnan/download/bioperl-ext/Bio/SeqIO/staden'
Manifying blib/man3/Bio::SeqIO::staden::read.3pm
Manifying
blib/man3/Bio::Ext::Align::Bio::Tools::dpAlign.3pm

[root at localhost bioperl-ext]# make test
make[1]: Entering directory
`/home/jiangnan/download/bioperl-ext/Bio/Ext/Align'
make[1]: Leaving directory
`/home/jiangnan/download/bioperl-ext/Bio/Ext/Align'
make[1]: Entering directory
`/home/jiangnan/download/bioperl-ext/Bio/SeqIO/staden'
make[1]: Leaving directory
`/home/jiangnan/download/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....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/jiangnan/download/bioperl-ext/Bio/Ext/Align'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib"
"-I../blib/arch" test.pl
1..2
Not enough arguments for
Bio::Ext::Align::Align_Protein_Sequences at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/dpAlign.pm
line 300, near "'blosum62')"
Not enough arguments for
Bio::Ext::Align::Align_Protein_Sequences at
/usr/lib/perl5/site_perl/5.8.0/Bio/Tools/dpAlign.pm
line 355, near "'blosum62')"
Compilation failed in require at test.pl line 11.
BEGIN failed--compilation aborted at test.pl line 11.
not ok 1
make[1]: *** [test_dynamic] Error 255
make[1]: Leaving directory
`/home/jiangnan/download/bioperl-ext/Bio/Ext/Align'
make: *** [test] Error 2



	
	
		
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