[Bioperl-l] Bioperl 1.5.2 RC2

Paul Boutros paul.boutros at utoronto.ca
Tue Oct 17 13:59:33 EDT 2006


Hi Chris,

Here it is:
pcboutro at ccb690[643] >> perl -I. t/SearchIO.t
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.


Quoting Chris Fields <cjfields at uiuc.edu>:

> 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.
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>





More information about the Bioperl-l mailing list