[Bioperl-l] Install help errors

Chris Fields cjfields at uiuc.edu
Fri Jul 4 23:41:15 EDT 2008

On Jul 4, 2008, at 9:13 PM, Alex Lancaster wrote:

>>>>>> "CF" == Chris Fields  writes:
>>> ...
> CF> That happens anyway regardless of where we put a notice.
> Not necessarily, the notice needs to be made much more prominent in
> the section:
> http://www.bioperl.org/wiki/Getting_BioPerl#Bioperl_1.5.2.2C_Developer_Release
> however, because people are unlikely to click on FAQ page because
> (especially experienced) users will think they already know the
> difference between developer and stable.  Perhaps something like:
> Which version should I get?
> 1. If you are just starting with bioperl, you should download the
>    developer release as it is the most currently maintained release.
> 2. If you have older scripts and are concerned about API
>    compatibility, you may want install the stable bioperl.

Added to the wiki.

> ...
> CF> The problem is actually with Scalar::Util and weaken().  The link
> CF> to Task::Weaken describes the problem: some versions of Red Hat
> CF> Linux (and I'm assuming Fedora as well) ship with a broken version
> CF> of Scalar::Util that does not pass tests due to issues with the
> CF> XS-based weaken().  The only option is to add Task::Weaken as a
> CF> dependency, which catches the problem if it exists and indicates
> CF> the next possible step (generally to reinstall Scalar::Util or
> CF> install a user-specific version of perl).
> If this is still a major issue in Fedora 9 (F-9) or rawhide, then
> the best way to handle this would be to open up a bug on:
> http://bugzilla.redhat.com/
> and file it against the perl component, which appears to provide
> Scalar::Util:
> $ rpm -q --whatprovides 'perl(Scalar::Util)'
> perl-5.10.0-27.fc9.i386
> Feel free to Cc me on the bug.  Once fixed in perl 5.10, we could look
> into backporting the fix to F-8 which still ships with perl 5.8.
> CF> I'm surprised we haven't seen this more often, but IIRC the user
> CF> in that link was using a newer version of Fedora.
> F-9 ships with perl-5.10.  Not sure if this is still a problem in that
> version.
> Alex

Scalar::Util bug reports have already been posted several times, both  
with Fedora 8 and RHEL 5:


The first bug apparently is still pending.  This doesn't include  
duplicate reports either.

Unfortunately this appears to be a common issue with Fedora/RH.  I'm  
not sure why they consistently ship perl with an apparently broken  
Scalar::Util (which is part of the perl core lib since 5.8 and is  
tested for weaken() and other XS-based methods, so should fail).  The  
module apparently compiles w/o problems.


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