[Bioperl-l] Package status for 1.5.2

[Sendu Bala]

Brian Osborne wrote:
> Let's take these one at a time, starting with t/Graph-MD5 (I'm not seeing
> any of these errors so you'll have to test, sorry about that). I've changed
> 'eval { require Graph; };' to 'eval { require Graph::Undirected; };'. Does
> this help?

I compared my copy of Graph.pm (my command-line CPAN claims that 0.78 is 
the latest version) to the one I could find via search.cpan.org (v0.80) 
and they're nothing alike. Mine is just

$VERSION = 0.20101;
@ISA = qw(Graph::Directed Graph::Base);

And nothing else, which is obviously why Graph::Undirected wasn't being 
loaded. How do I install whatever variant of Graph you expect? The 
network INSTALL file is pretty vague on that front. "bioperl-network 
also depends on Perl's Graph package. See CPAN at www.perl.org for 
instructions on downloading and installing Graph, use Graph version .70 
or greater." CPAN is at www.cpan.org or cpan.perl.org, and there are no 
download or install 'instructions' for things on CPAN (just a download 
link as far as I can see).

Anyway, new results following your commit:


perl -w t/Graph-MD5.t
1..19
# Running under perl version 5.008008 for linux
# Current time local: Mon Sep 25 09:00:31 2006
# Current time GMT:   Mon Sep 25 08:00:31 2006
# Using Test.pm version 1.25
ok 1
Use of uninitialized value in hash slice at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 66.
Use of uninitialized value in exists at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 332.
Use of uninitialized value in hash element at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 338.
Use of uninitialized value in hash element at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 339.
Use of uninitialized value in hash element at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 342.
Use of uninitialized value in hash element at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 310.
Use of uninitialized value in hash element at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 315.
Use of uninitialized value in hash element at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 316.
Use of uninitialized value in hash element at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 360.
Use of uninitialized value in hash element at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 361.
Use of uninitialized value in sort at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 96.
Use of uninitialized value in sort at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 96.
Use of uninitialized value in sort at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 96.
Use of uninitialized value in sort at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 96.
Use of uninitialized value in sort at 
/usr/lib64/perl5/vendor_perl/5.8.8/Graph/Base.pm line 96.
Can't call method "add" on an undefined value at t/Graph-MD5.t line 59.
ok 2 # skip Missing dependencies. Skipping tests
ok 3 # skip Missing dependencies. Skipping tests
ok 4 # skip Missing dependencies. Skipping tests
ok 5 # skip Missing dependencies. Skipping tests
ok 6 # skip Missing dependencies. Skipping tests
ok 7 # skip Missing dependencies. Skipping tests
ok 8 # skip Missing dependencies. Skipping tests
ok 9 # skip Missing dependencies. Skipping tests
ok 10 # skip Missing dependencies. Skipping tests
ok 11 # skip Missing dependencies. Skipping tests
ok 12 # skip Missing dependencies. Skipping tests
ok 13 # skip Missing dependencies. Skipping tests
ok 14 # skip Missing dependencies. Skipping tests
ok 15 # skip Missing dependencies. Skipping tests
ok 16 # skip Missing dependencies. Skipping tests
ok 17 # skip Missing dependencies. Skipping tests
ok 18 # skip Missing dependencies. Skipping tests
ok 19 # skip Missing dependencies. Skipping tests

(That's a bad skip message btw, given that it isn't true)