[Bioperl-l] Install help errors

Alex Lancaster alexl at users.sourceforge.net
Fri Jul 4 22:13:05 EDT 2008

>>>>> "CF" == Chris Fields  writes:

CF> On Jul 4, 2008, at 5:01 AM, Alex Lancaster wrote:

>>>>>> "SB" == Sendu Bala  writes:


>> User: something doesn't work in bioperl!  Dev: what version are you
>> using?  U: I'm using bioperl 1.4!  D: what!?  that's way old, you
>> should be using 1.5.2 U: but I'm using the stable version listed:
>> 1.4

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:


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.

CF> I don't think we can dump the 'stable' vs. 'dev' versioning
CF> systemjust for aesthetic reasons.  However, I think we could fix a
CF> minimal set of problems at this point (bugs, etc) and release a
CF> new stable version fairly quickly.  I would be up for that.

Sure, sounds good.


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:


and file it against the perl component, which appears to provide

$ rpm -q --whatprovides 'perl(Scalar::Util)'

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


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