[Bioperl-l] Bioperl 1.5.2 RC2

Chris Fields cjfields at uiuc.edu
Tue Oct 17 13:52:36 EDT 2006


What do you get when you run the SearchIO.t test by itself using 'perl -I.
t/SearchIO.t'?  It looks like something pretty catastrophic happened.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Paul Boutros
> Sent: Tuesday, October 17, 2006 11:57 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bioperl 1.5.2 RC2
> 
> 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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