[Bioperl-l] Bio::Graphics dependencies

Alex Lancaster alexl at users.sourceforge.net
Thu Jan 29 12:03:49 UTC 2009

>>>>> 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:


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

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/.
relocation R_X86_64_32 against `a local symbol' can not be used when
making a shared object; recompile with -fPIC
could not read symbols: Bad value

The full build log is here:


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:


Would it be possible to update the meta-data for the CPAN module:


and clarify the license is the usual Perl one, or if not, change to



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