Hi all,
I failed to install Bio::SCF (in order to see traces) on a new server
two weeks ago, so I sent a message describing my problem to
[EMAIL PROTECTED] I have received no response and have not found
a solution so far, so I turn to you, if someone could bring me some help :
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I'm trying to install Bio::SCF 1.01 for traces visualization with
Gbrowse on a new server
(Debian) (it works well on the first Mandriva server).
Here are informations about the new server :
# uname - a :
Linux xxxxx 2.6.22-3-vserver-amd64 #1 SMP Sun Nov 4 18:41:00 UTC 2007
x86_64 GNU/Linux
The Staden Package (1.6.0), io-lib 1.11 and zlib 1.2.3 are well
installed (I hope so!).
I have downloaded Bio-SCF-1.01 from CPAN and then began to install it
from my home directory, with
root privileges :
# perl Makefile.PL :
OK
# make :
cc -c -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBIAN
-fno-strict-aliasing
-pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-O2 -DVERSION=\"1.01\" -DXS_VERSION=\"1.01\" -fPIC
"-I/usr/lib/perl/5.8/CORE" -DLITTLE_ENDIAN SCF.c
SCF.xs: In function 'XS_Bio__SCF_get_scf_pointer':
SCF.xs:57: warning: cast from pointer to integer of different size
SCF.xs: In function 'XS_Bio__SCF_get_scf_fpointer':
SCF.xs:80: warning: cast from pointer to integer of different size
SCF.xs: In function 'XS_Bio__SCF_scf_free':
SCF.xs:89: warning: cast to pointer from integer of different size
SCF.xs: In function 'XS_Bio__SCF_get_comments':
SCF.xs:95: warning: cast to pointer from integer of different size
SCF.xs: In function 'XS_Bio__SCF_set_comments':
SCF.xs:108: warning: cast to pointer from integer of different size
SCF.xs: In function 'XS_Bio__SCF_scf_write':
SCF.xs:121: warning: cast to pointer from integer of different size
SCF.xs: In function 'XS_Bio__SCF_scf_fwrite':
SCF.xs:137: warning: cast to pointer from integer of different size
SCF.xs: In function 'XS_Bio__SCF_get_from_header':
SCF.xs:159: warning: cast to pointer from integer of different size
SCF.xs: In function 'XS_Bio__SCF_get_at':
SCF.xs:186: warning: cast to pointer from integer of different size
SCF.xs: In function 'XS_Bio__SCF_set_base_at':
SCF.xs:242: warning: cast to pointer from integer of different size
SCF.xs: In function 'XS_Bio__SCF_set_at':
SCF.xs:255: warning: cast to pointer from integer of different size
Running Mkbootstrap for Bio::SCF ()
chmod 644 SCF.bs
rm -f blib/arch/auto/Bio/SCF/SCF.so
cc -shared -L/usr/local/lib SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \
-lread -lz \
/usr/bin/ld: /usr/local/lib/libread.a(libread_a-misc_scf.o): relocation
R_X86_64_32
against `a local symbol' can not be used when making a shared object;
recompile with -fPIC
/usr/local/lib/libread.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [blib/arch/auto/Bio/SCF/SCF.so] Erreur 1
I found several indications on the Web :
- problems during compilation for Debian with 64 bits processors....
(independant from
Bio::SCF)
- problem with the libread (io-lib) library : I installed the 1.09
(minimum required by
Gbrowse) version, nothing changed.
When I search for libread.a into the server architecture, it answers me :
/home/meyniel/io_lib-1.9.0/read/libread.a
/home/meyniel/io_lib-1.11.0b3/read/libread.a
/usr/local/lib/libread.a
I tested the # make after creating the environment variable
LD_LIBRARY_PATH =
/usr/local/lib/:/home/meyniel/io_lib-1.9.0/read/, without surprise it
failed too.
Please, have you got an idea or have you ever seen the same problem?
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Thanks in advance,
Best regards,
Laurène MEYNIEL
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