[Bioperl-l] Bio::Graphics dependencies

[Chris Fields]

Lincoln,

You could probably use auto_features to check for the module  
beforehand, then maybe indicate the module is optional if it isn't  
installed (or optionally add it to the recommends list, with a default  
of 'no').  There is a decent example of using auto_features with  
SVN::Notify::Mirror (which checks for the module and adds optional  
test scripts on the fly):

http://search.cpan.org/~ewilhelm/Module-Build-0.31012/lib/Module/Build/Cookbook.pm#EXAMPLES_ON_CPAN

chris

On Jan 29, 2009, at 9:17 AM, Lincoln Stein wrote:

> Hi Alex,
>
> Is there an easy trick in the Module::Build system to selectively  
> disable
> installation of certain modules? That would be very handy.
>
> I will update the Bio-SCF module's license; the module is very old  
> and has
> no primary developer (I sort of inherited it).
>
> Lincoln
>
> On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster <alexl at users.sourceforge.net
>> wrote:
>
>>>>>>> Lincoln Stein  writes:
>>
>>> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on
>>> Bio::Graphics::Browser::Util was spurious and has been removed. The
>>> Bio::Graphics::Glyph::trace module implements an ABI sequencing
>>> trace display, and does require an external module called
>>> Bio::SCF. This module is on CPAN, but it in turn requires a binary
>>> library called io-lib from the STADEN
>>> (http://staden.sourceforge.net/) package. So I have made this into a
>>> "recommendation" in the META.yml file.
>>
>> Thanks Lincoln,
>>
>> I updated to the latest CPAN module and rebuilt the Fedora package:
>>
>> http://koji.fedoraproject.org/koji/buildinfo?buildID=80541
>>
>> which no longer has the requirement on GBrowse and temporarily  
>> removed
>> the .pm from the install.  (Could you possibly disable the
>> installation of modules for which optional dependencies are not
>> found?)
>>
>> I looked into packaging Bio::SCF, but got stuck at link time.  This
>> may be related to the io-lib package (which is called staden-io-lib  
>> in
>> Fedora, as io-lib was deemed too generic):
>>
>> gcc  -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -DPERL_USE_SAFE_PUTENV SCF.o  -o blib/arch/auto/Bio/SCF/SCF.so \
>>  -lstaden-read -lz  \
>>
>> /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/.
>> ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o):
>> relocation R_X86_64_32 against `a local symbol' can not be used when
>> making a shared object; recompile with -fPIC
>> /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden- 
>> read.a:
>> could not read symbols: Bad value
>> c
>>
>> The full build log is here:
>>
>> http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log
>>
>> This may because the Fedora package doesn't provide a shared library
>> for libstaden-read.
>>
>> Lastly regarding the Bio::SCF package, I notice that the only license
>> listed is "Artistic", is this really intended to be the Perl license
>> (i.e. GPL + Artistic)?  The original Artistic 1.0 license alone is  
>> not
>> acceptable for Fedora:
>>
>> http://fedoraproject.org/wiki/Licensing#Bad_Licenses
>>
>> Would it be possible to update the meta-data for the CPAN module:
>>
>> http://search.cpan.org/dist/Bio-SCF/
>>
>> and clarify the license is the usual Perl one, or if not, change to
>> it?
>>
>> Thanks,
>>
>> Alex
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>> Bioperl-l at lists.open-bio.org
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>>
>
>
>
> -- 
> Lincoln D. Stein
>
> 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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