[Bioperl-l] Bio::Graphics dependencies

Lincoln Stein lincoln.stein at gmail.com
Thu Jan 29 10:17:19 EST 2009

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).


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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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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