[Bioperl-l] SCF installation

Bernd Jagla bernd.jagla at gmail.com
Fri Aug 21 09:30:27 UTC 2009 

Hi,

I have installed io_lib-1.9.0. This produces libread.a. I am working on a
Mac OSX 10.5.7. I just recompiled io-lib and didn't see any error message. I
don't really know how to test that it is working.

I am trying to install Bio-SCF-1.01.

It seems that the test.scf file cannot be read. Is there another way using
some other tools to see if that is working?

(Sorry for misrepresenting samtools. I was actually trying to install
Bio-Graphics, which was asking for Bio::SCF).

Thanks,

Bernd


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Lincoln Stein
Sent: Thursday, August 20, 2009 6:07 PM
To: scott at scottcain.net
Cc: bioperl-l at lists.open-bio.org; Bernd Jagla
Subject: Re: [Bioperl-l] SCF installation

It is all a bit confusing. On the download page for Staden, there is a
release 1.12, but the home page hasn't been updated and still reads 1.11. If
you download and install Staden 1.12, you'll get a library named
libstaden-read rather than libread; Bio::SCF hasn't been updated for the
name change, and so you will have to open up the Makefile.PL and change
"-lread" to "-lstaden-read" in order for it to compile.

This being said, your log indicates that Bio::SCF compiled and linked just
fine, but the test failed, so it may be more of a problem than just getting
the staden library installed.

Lincoln

On Thu, Aug 20, 2009 at 10:30 AM, Scott Cain <cain.cshl at gmail.com> wrote:

> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> -----------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
>
>
>
>
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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