[Bioperl-l] Package status for 1.5.2

Sendu Bala bix at sendu.me.uk
Sun Sep 24 11:55:08 EDT 2006


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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