[Bioperl-l] Bio::Graphics dependencies

[Alex Lancaster]

>>>>> 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