[Bioperl-l] SCF installation

[Bernd Jagla]

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