[Bioperl-l] Install help errors

Chris Fields cjfields at uiuc.edu
Fri Jul 4 11:01:15 EDT 2008

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

>>>>>> "SB" == Sendu Bala  writes:
> [...]
> SB> Yup, thanks for doing that.
>>> Incidentally why is 1.5.2 still called a "developer" release and
>>> 1.4 "stable", it just confuses users who tend to assume that the
>>> "stable" release is the one they should install (and Linux
>>> distributions for that matter).  1.5.2 is now already 3 or so years
>>> old, so it should be considered the default release by now.
> SB> See
> SB> http://www.bioperl.org/wiki/FAQ#What_is_the_difference_between_1.5.2_and_1.4.0.3F_What_do_you_mean_developer_release.3F
> Ok, but it needs to be made upfront on the download section to new
> users (i.e. those that don't have any existing scripts that might not
> be compatible with the new API in 1.5.2) that even though it is a
> "developer" release, they should still get 1.5.2 as I've seen a few
> several threads on this mailing list that go like this:
> 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

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

> SB> While I've got you, what are your thoughts on this?:
> SB> http://article.gmane.org/gmane.comp.lang.perl.bio.general/17282
> SB> Is this still an issue with recent version of Fedora? Does the
> SB> problem indeed come and go with different versions? Why does
> SB> Fedora suffer the problem at all?
> I don't know exactly what "the problem" is that you are referring to.
> Which version of Fedora and what version of perl-bioperl?  Is this an
> issue with bioperl-sql?  That bit isn't packaged yet.
> The current version of Task::Weaken package (in F-8, at least) is:
> perl-Task-Weaken-1.02-2.fc8
> And looking at http://search.cpan.org/dist/Task-Weaken/ it seems to be
> the most recent.  I never saw a requirement for that package in the
> original Build.PL, should it be made a requirement for bioperl (core)
> or bioperl-run?
> If it is a "soft requirement", then it should be able to be installed
> using yum:
> yum install perl-Task-Weaken
> Also, I would never recommend overwriting the files from RPMs with the
> files from manually-compiled CPAN Perl packages, it will cause endless
> headaches down the road.  The cleanest way to "overwrite" non-RPM
> packaged CPAN packages is to first remove the Fedora RPM:
> yum remove perl-foobar
> then install the CPAN package using the perl system, but make sure
> that they are installed in /usr/local/ not /usr to avoid stepping on
> any system-managed files.
> Alex

The problem is actually with Scalar::Util and weaken().  The link to  
Task::Weaken describes the problem: some versions of Red Hat Linux  
(and I'm assuming Fedora as well) ship with a broken version of  
Scalar::Util that does not pass tests due to issues with the XS-based  
weaken().  The only option is to add Task::Weaken as a dependency,  
which catches the problem if it exists and indicates the next possible  
step (generally to reinstall Scalar::Util or install a user-specific  
version of perl).

I'm surprised we haven't seen this more often, but IIRC the user in  
that link was using a newer version of Fedora.


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