[Bioperl-l] SCF installation

Thu Aug 20 14:30:33 UTC 2009

Hi Bernd,

Bio::SCF isn't technically part of BioPerl, but I have installed it  
before so I'll take a shot: do you have the Staden io-lib installed?   
It is a prereq for Bio::SCF.  If you did install it, is it in a normal  
library path, and did you run ldconfig (if appropriate for your  
system) after installing it?

io-lib can be obtained here:

   http://staden.sourceforge.net/

If you do have all of those things in place, what version of io-lib  
are you using?  I wonder if there is an incompatibility between  
Bio::SCF and your version.  The INSTALL doc for Bio::SCF indicates  
that you should have version 0.9, but io-lib is now at 1.11.5.  That  
jump to a whole number may have broken an api call that Bio::SCF  
depends on.

Scott

On Aug 20, 2009, at 4:46 AM, 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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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research