[Bioperl-l] SCF installation

[Joel Martin]

Hello,
   Bio::SCF isn't a pre-requisite of samtools or Bio::Samtools,
and neither is actually related to Bioperl.  samtools has a 
pretty active mailing list at sourceforge, you might try asking
there.

http://sourceforge.net/mailarchive/forum.php?forum_name=samtools-help 

I use samtools all the time w/o either of those modules.

Joel

On Thu, Aug 20, 2009 at 10:46:52AM +0200, Bernd Jagla wrote:
> Hi,
> 
>  
> 
> I am trying to install SCF (a prerequisite to samtools).
> 
> I installed libread and the compilation seems to be working, only test is
> failing:
> 
>  
> 
> zoppel:Bio-SCF-1.01 bernd$ perl Makefile.PL 
> 
> Checking if your kit is complete...
> 
> Looks good
> 
> Writing Makefile for Bio::SCF
> 
>  
> 
> zoppel:Bio-SCF-1.01 bernd$ make
> 
> cp SCF.pm blib/lib/Bio/SCF.pm
> 
> cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm
> 
> /opt/local/bin/perl /opt/local/lib/perl5/5.8.9/ExtUtils/xsubpp  -typemap
> /opt/local/lib/perl5/5.8.9/ExtUtils/typemap  SCF.xs > SCF.xsc && mv SCF.xsc
> SCF.c
> 
> Please specify prototyping behavior for SCF.xs (see perlxs manual)
> 
> /usr/bin/gcc-4.0 -c   -fno-common -DPERL_DARWIN -I/opt/local/include
> -no-cpp-precomp -fno-strict-aliasing -pipe -I/usr/local/include
> -I/opt/local/include -O3   -DVERSION=\"1.01\" -DXS_VERSION=\"1.01\"
> "-I/opt/local/lib/perl5/5.8.9/darwin-2level/CORE"  -DLITTLE_ENDIAN SCF.c
> 
> Running Mkbootstrap for Bio::SCF ()
> 
> chmod 644 SCF.bs
> 
> rm -f blib/arch/auto/Bio/SCF/SCF.bundle
> 
> LD_RUN_PATH="/opt/local/lib" env MACOSX_DEPLOYMENT_TARGET=10.3
> /usr/bin/gcc-4.0  -L/opt/local/lib -bundle -undefined dynamic_lookup
> -L/usr/local/lib SCF.o  -o blib/arch/auto/Bio/SCF/SCF.bundle         \
> 
>                -lread -lz         \
> 
>               
> 
> chmod 755 blib/arch/auto/Bio/SCF/SCF.bundle
> 
> cp SCF.bs blib/arch/auto/Bio/SCF/SCF.bs
> 
> chmod 644 blib/arch/auto/Bio/SCF/SCF.bs
> 
> Manifying blib/man3/Bio::SCF.3pm
> 
>  
> 
>  
> 
> zoppel:Bio-SCF-1.01 bernd$ make test
> 
> PERL_DL_NONLAZY=1 /opt/local/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> 
> t/scf.t .. get_scf_pointer(...) : failed on read_scf(./test.scf)
> 
> t/scf.t .. Dubious, test returned 2 (wstat 512, 0x200)
> 
> Failed 18/18 subtests 
> 
>  
> 
> Test Summary Report
> 
> -------------------
> 
> t/scf.t (Wstat: 512 Tests: 0 Failed: 0)
> 
>   Non-zero exit status: 2
> 
>   Parse errors: Bad plan.  You planned 18 tests but ran 0.
> 
> Files=1, Tests=0,  0 wallclock secs ( 0.02 usr  0.00 sys +  0.08 cusr  0.01
> csys =  0.11 CPU)
> 
> Result: FAIL
> 
> Failed 1/1 test programs. 0/0 subtests failed.
> 
> make: *** [test_dynamic] Error 2
> 
>  
> 
>  
> 
>  
> 
>  
> 
> Any idea what might be going wrong?
> 
>  
> 
> Please not that in the directory there are some file empty:
> 
>  
> 
> ls -ltr
> 
> -rw-r--r--   1 bernd  staff  167468 23 sep  1999 test.scf
> 
> -rw-r--r--   1 bernd  staff    1131 31 jan  2006 DISCLAIMER
> 
> -rw-r--r--   1 bernd  staff     532 17 mai  2006 README
> 
> -rw-r--r--   1 bernd  staff     525 17 mai  2006 INSTALL
> 
> -rw-r--r--   1 bernd  staff     396 17 mai  2006 Makefile.PL
> 
> -rw-r--r--   1 bernd  staff    9308 17 mai  2006 SCF.xs
> 
> -rw-r--r--   1 bernd  staff   12438 17 mai  2006 SCF.pm
> 
> drwxr-xr-x   3 bernd  staff     102 17 mai  2006 t
> 
> drwxr-xr-x   6 bernd  staff     204 17 mai  2006 eg
> 
> drwxr-xr-x   3 bernd  staff     102 17 mai  2006 SCF
> 
> -rw-r--r--   1 bernd  staff     290 17 mai  2006 META.yml
> 
> -rw-r--r--   1 bernd  staff     255 17 mai  2006 MANIFEST
> 
> drwxr-xr-x   4 bernd  staff     136 20 ao 10:12 ..
> 
> -rw-r--r--   1 bernd  staff   27915 20 ao 10:13 Makefile.old
> 
> -rw-r--r--   1 bernd  staff   27915 20 ao 10:16 Makefile
> 
> -rw-r--r--   1 bernd  staff       0 20 ao 10:17 pm_to_blib
> 
> drwxr-xr-x   8 bernd  staff     272 20 ao 10:17 blib
> 
> -rw-r--r--   1 bernd  staff       0 20 ao 10:17 SCF.bs
> 
> -rw-r--r--   1 bernd  staff   14580 20 ao 10:18 SCF.o
> 
> -rw-r--r--   1 bernd  staff   15125 20 ao 10:18 SCF.c
> 
> drwxr-xr-x  21 bernd  staff     714 20 ao 10:18 .
> 
>  
> 
>  
> 
> Thanks,
> 
>  
> 
> Bernd
> 
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