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Id: 32850
Status: new
Priority: 0/
Queue: Bio-SCF

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Owner: Nobody in particular
Requestors: meyniel [...] cervi-lyon.inserm.fr
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Subject: Problem with Bio::SCF install (libread.a, debian amd64)
Date: Fri, 01 Feb 2008 12:02:45 +0100
To: bug-Bio-SCF [...] rt.cpan.org
From: meyniel laurene <meyniel [...] cervi-lyon.inserm.fr>
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Hi, 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 server (Mandriva), thanks for your help a few weeks ago). 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? Thanks in advance, Best regards, Laurène MEYNIEL


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