[Bioperl-l] Package status for 1.5.2

Brian Osborne osborne1 at optonline.net
Sun Sep 24 16:15:59 EDT 2006


Sendu,

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?

Brian O.


On 9/24/06 11:55 AM, "Sendu Bala" <bix at sendu.me.uk> wrote:

> Brian Osborne wrote:
>> Sendu,
>> 
>> Did you test the latest version of bioperl-network? Perhaps part of the
>> issue is that one doesn't just require Graph, you have to have at least v.
>> 70 of Graph. Let me amend the *t's...
> 
> Yes, the latest network from cvs. I only installed Graph today - built
> from J/JH/JHI/Graph-0.78.tar.gz by cpan, which tests all ok and seems to
> install fine (though ends up with CPAN_VERSION 0.78 vs INST_VERSION
> 0.20101 when I look at 'i Graph' - is that expected?).
> 
> After your recent commits I get:
> 
> make test
> PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/Edge...........ok
> t/Graph-MD5......Can't locate object method "new" via package
> "Graph::Undirected" (perhaps you forgot to load "Graph::Undirected"?) at
> t/Graph-MD5.t line 44.
> t/Graph-MD5......dubious
>          Test returned status 2 (wstat 512, 0x200)
>          after all the subtests completed successfully
> t/Graph-Seq......ok 1/18Use 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 "seq" on an undefined value at t/Graph-Seq.t line 56.
> t/Graph-Seq......dubious
>          Test returned status 255 (wstat 65280, 0xff00)
>          after all the subtests completed successfully
> t/Interaction....ok 1/17Can't locate object method "add_interaction" via
> package "Graph::Undirected" at t/Interaction.t line 59.
> t/Interaction....dubious
>          Test returned status 255 (wstat 65280, 0xff00)
>          after all the subtests completed successfully
> t/IO_dip_tab.....ok 1/16Can't locate object method "get_nodes_by_id" via
> package "Graph::Undirected" at
> /mnt/data_local/os_homes/linux/src/bioperl/network/blib/lib/Bio/Network/IO/dip
> _tab.pm 
> line 141, <GEN1> line 1.
> t/IO_dip_tab.....dubious
>          Test returned status 9 (wstat 2304, 0x900)
>          after all the subtests completed successfully
> t/IO_psi.........ok 2/21Can't locate object method "add_node" via
> package "Graph::Undirected" at
> /mnt/data_local/os_homes/linux/src/bioperl/network/blib/lib/Bio/Network/IO/psi
> .pm 
> line 346.
> t/IO_psi.........dubious
>          Test returned status 255 (wstat 65280, 0xff00)
>          after all the subtests completed successfully
> t/Node...........ok
> t/ProteinNet.....ok 1/168Can't locate object method "get_nodes_by_id"
> via package "Graph::Undirected" at
> /mnt/data_local/os_homes/linux/src/bioperl/network/blib/lib/Bio/Network/IO/dip
> _tab.pm 
> line 141, <GEN1> line 1.
> t/ProteinNet.....dubious
>          Test returned status 9 (wstat 2304, 0x900)
>          after all the subtests completed successfully
> Failed Test     Stat Wstat Total Fail  Failed  List of Failed
> 
------------------------------------------------------------------------------>
-
> t/Graph-MD5.t      2   512    19    0   0.00%  ??
> t/Graph-Seq.t    255 65280    18    0   0.00%  ??
> t/IO_dip_tab.t     9  2304    16    0   0.00%  ??
> t/IO_psi.t       255 65280    21    0   0.00%  ??
> t/Interaction.t  255 65280    17    0   0.00%  ??
> t/ProteinNet.t     9  2304   168    0   0.00%  ??
> 252 subtests skipped.
> Failed 6/8 test scripts, 25.00% okay. 0/296 subtests failed, 100.00% okay.
> make: *** [test_dynamic] Error 9
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