[Bioperl-l] Install help errors

Alex Lancaster alexl at users.sourceforge.net
Fri Jul 4 06:01:00 EDT 2008

>>>>> "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

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:


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.


More information about the Bioperl-l mailing list