[Bioperl-l] bioperl-ext installation issue

[Paolo Pavan]

Hi everybody,
I have problems installing the bioperl-ext package, any help is much
appreciated.
1)

   - I start trying with cpan i /bioperl-ext/ the only resource available is
   /B/BI/BIRNEY/bioperl-ext-1.4 (is it ok?)
   - I install Inline::MakeMaker and Inline::C then
   - i/BIRNEY/bioperl-ext-1.4/ fails bacause I don't have staden package

2) I try to install io_lib-1.8.10.tar as suggested by the README (
ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/), installation fails after:
...
gcc -g -O2 -o makeSCF makeSCF.o ../read/.libs/libread.a -lz -lm
../read/.libs/libread.a(compress.o): In function `fopen_compressed':
/root/Download/staden/io_lib-1.8.10/utils/compress.c:321: warning: the use
of `tempnam' is dangerous, better use `mkstemp'
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf
-I../ztr -I../plain -I../scf -I../exp_file -I../utils  -I/usr/local/include
-g -O2 -c -o extract_seq.o `test -f extract_seq.c || echo './'`extract_seq.c
/bin/sh ../libtool --mode=link gcc  -g -O2   -o extract_seq  extract_seq.o
../read/libread.la
gcc -g -O2 -o extract_seq extract_seq.o ../read/.libs/libread.a -lz -lm
../read/.libs/libread.a(compress.o): In function `fopen_compressed':
/root/Download/staden/io_lib-1.8.10/utils/compress.c:321: warning: the use
of `tempnam' is dangerous, better use `mkstemp'
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf
-I../ztr -I../plain -I../scf -I../exp_file -I../utils  -I/usr/local/include
-g -O2 -c -o index_tar.o `test -f index_tar.c || echo './'`index_tar.c
index_tar.c: In function âmainâ:
index_tar.c:12: error: two or more data types in declaration specifiers
make[2]: *** [index_tar.o] Error 1
make[2]: Leaving directory `/home/root/Download/staden/io_lib-1.8.10/progs'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/root/Download/staden/io_lib-1.8.10'
make: *** [all-recursive-am] Error 2

3) I give up staden, because I actually need pSW, and try to install from
Makefile.PL in Bio/Ext/Align but installation fails after:
...
Align.xs:18: warning: ânot_hereâ defined but not used
Running Mkbootstrap for Bio::Ext::Align ()
chmod 644 Align.bs
rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so
gcc  -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Align.o  -o
../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a    \
           -lm          \

/usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `a local
symbol' can not be used when making a shared object; recompile with -fPIC
libs/libsw.a: could not read symbols: 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/root/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-ext-1.4/Bio/Ext/Align'
make: *** [subdirs] Error 2

I have also made some other tries such force install Bio::Ext:Align without
success but I'm sure I miss something trivial that I can't catch.
Can someone help me?

Thank you,
Paolo