[Bioperl-l] Bioperl 1.5.2 RC2

Paul Boutros paul.boutros at utoronto.ca
Tue Oct 17 12:57:19 EDT 2006


Hi,
Here's a quick make test on AIX 5.2 with Perl 5.8.8.  I get two failed  
tests, the first seems to be just a result of me not having DBD::mysql  
installed.
Paul

Test Summary
============

Failed Test               Stat Wstat Total Fail  List of Failed
-------------------------------------------------------------------------------
t/BioDBSeqFeature_mysql.t               46   46  1-46
t/SearchIO.t                22  5632  1337 2671  2-1337
2 tests and 106 subtests skipped.
Failed 2/236 test scripts. 1382/11688 subtests failed.
Files=236, Tests=11688, 259 wallclock secs (139.47 cusr + 20.14 csys =  
159.61 CPU)

BioDBSeqFeature_mysql
=====================
pcboutro at ccb690[674] >> perl -w t/BioDBSeqFeature_mysql.t
1..46
install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (@INC  
contains: /home/pcboutro/cvswork/bioperl-live/ . .. ./blib/lib t  
/db2blast/perl/lib/5.8.8/aix-thread-multi /db2blast/perl/lib/5.8.8  
/db2blast/perl/lib/site_perl/5.8.8/aix-thread-multi  
/db2blast/perl/lib/site_perl/5.8.8 /db2blast/perl/lib/site_perl) at  
(eval 37) line 3.
Perhaps the DBD::mysql perl module hasn't been fully installed,
or perhaps the capitalisation of 'mysql' isn't right.
Available drivers: DB2, DBM, ExampleP, File, Proxy, Sponge.
  at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 208

SearchIO
========
pcboutro at ccb690[670] >> perl -w t/SearchIO.t | more
1..1337
ok 1

-------------------- WARNING ---------------------
MSG: XML::SAX::Expat not currently supported; must have local copies  
of NCBI DTD docs!
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: error in parsing a report:

404 File `/home/pcboutro/tmp/bioperl-1.5.2-RC2/NCBI_BlastOutput.dtd'  
does not exist  
file:///home/pcboutro/tmp/bioperl-1.5.2-RC2/NCBI_BlastOutput.dtd
Handler couldn't resolve external entity at line 2, column 82, byte 104
error in processing external entity reference at line 2, column 82,  
byte 104 at  
/db2blast/perl/lib/site_perl/5.8.8/aix-thread-multi/XML/Parser.pm line  
187

---------------------------------------------------
not ok 2
# Failed test 2 in t/SearchIO.t at line 68
Can't call method "database_name" on an undefined value at  
t/SearchIO.t line 69.

------------------------------

Message: 10
Date: Tue, 17 Oct 2006 11:32:54 +0100
From: Sendu Bala <bix at sendu.me.uk>
Subject: [Bioperl-l] Bioperl 1.5.2 RC2
To: bioperl-l at bioperl.org
Message-ID: <4534B156.4090501 at sendu.me.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Bioperl 1.5.2 Release Candidate 2 is ready and available for testing.
See http://www.bioperl.org/wiki/Release_1.5.2 for
instructions on getting and testing this RC.

Developers:
    This should be the last RC before release ~next monday. Now would
    be a good time for last minute documentaiton updates and additions.

Users:
    Even though 1.5.2 is a 'developer' release, we consider it the most
    stable and capable version of Bioperl, and recommend that you use
    it in all but the most critical production environments. Please
    try it out and let us know of any problems or difficulties you run
    into.


Thank you,
Sendu.





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