[Bioperl-l] Trouble again while installing Bioperl-Ext-1.4 & dpAlign

[jany]

Hi, all:
Today I tried to re-install bioperl-Ext module, since
yesterday it does not work.:-( And I met different
errors. This time make does not success. Please help!
Thanks,
Nan
[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
gcc -c   -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=\"0.08.0\"
-DXS_VERSION=\"0.08.0\" -fPIC
"-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" 
 Bio/Ext/Align/libs/linspc.c
cp Bio/Ext/Align/libs/codon.o
blib/lib/Bio/Ext/Align/libs/codon.o
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/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
make[1]: Entering directory
`/home/jiangnan/bioperl/bioperl-ext/Bio/Ext/Align'
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
Align.c: In function
`XS_Bio__Ext__Align__AlnBlock_bit_ascii_AlnBlock':
Align.c:102: warning: initialization from incompatible
pointer type
Align.c: In function
`XS_Bio__Ext__Align__AlnBlock_dump_ascii_AlnBlock':
Align.c:117: warning: initialization from incompatible
pointer type
Align.c: In function
`XS_Bio__Ext__Align__CompMat_write_Blast_CompMat':
Align.c:2246: warning: initialization from
incompatible pointer type
......(more warnings here)
Align.c: In function
`XS_Bio__Ext__Align__FileSource_input':
Align.c:5319: warning: passing arg 8 of `Perl_do_open'
from incompatible pointer type
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
/usr/bin/ld: warning: unknown architecture of input
file `libs/libsw.a(aln.o)' is incompatible with i386
output
/usr/bin/ld: warning: unknown architecture of input
file `libs/libsw.a(alnrange.o)' is incompatible with
i386 output
..... (more warnings here)
/usr/bin/ld: warning: unknown architecture of input
file `libs/libsw.a(alnconvert.o)' is incompatible with
i386 output
/usr/bin/ld: warning: unknown architecture of input
file `libs/libsw.a(dpenvelope.o)' is incompatible with
i386 output
/usr/bin/ld: final link failed: Bad value
collect2: ld returned 1 exit status
make[1]: ***
[../blib/arch/auto/Bio/Ext/Align/Align.so] Error 1
make[1]: Leaving directory
`/home/jiangnan/bioperl/bioperl-ext/Bio/Ext/Align'
make: *** [subdirs] Error 2




	
	
		
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