[Bioperl-l] SCF installation

Scott Cain scott at scottcain.net
Fri Aug 21 13:05:25 UTC 2009 

Hi Bernd,

Just so you know, you don't need Bio::SCF for Bio::Graphics either,  
unless you want to display ABI trace glyphs.  It is a suggested  
("recommends" in Module::Build parlance) module.

Scott

On Aug 21, 2009, at 5:30 AM, Bernd Jagla wrote:

> 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
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> 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>
> _______________________________________________
> 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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