[Bioperl-l] Bioperl 1.5.2 RC2

Paul Boutros paul.boutros at utoronto.ca
Tue Oct 17 19:49:52 EDT 2006


Hi Chris,

Yup, that's it.  I installed XML::SAX::ExpatXS (make test output  
below).  Should there be a note somewhere in the INSTALL docs saying  
basically what you just wrote?  Or maybe it's already there somewhere  
and I missed it.

Also, I'd propose changing BioDBSeqFeature_mysql.t so that it checks  
if DBD::mysql can be loaded, and if not doesn't run the test.  Since  
the file is only one-line long, here's the modified file rather than a  
patch:
################################################################
BEGIN {
         # DBD::mysql is required
         eval {
                 require DBD::mysql;
                 };
         if ( $@ ) {
                 use Test::More skip_all => "DBD::mysql is not  
installed or is installed incorrectly - skipping BioDBSeqFeature
_mysql.t";
                 exit(0);
                 }
         }

system "perl t/BioDBSeqFeature.t -adaptor DBI::mysql -create 1 -temp 1  
-dsn test";
################################################################

And when I run it I get:
t/BioDBSeqFeature_mysql......skipped
         all skipped: DBD::mysql is not installed or is installed  
incorrectly - skipping BioDBSeqFeature_mysql.t

And for the overall make test:
All tests successful, 3 tests and 106 subtests skipped.
Files=236, Tests=11642, 247 wallclock secs (143.85 cusr + 20.39 csys =  
164.24 CPU)

Hope this helps,
Paul


Quoting Chris Fields <cjfields at uiuc.edu>:

> Your local copy of XML::SAX has XML::SAX::Expat set as the default SAX
> backend parser.  For some reason BLAST XML parsing doesn't work with that
> parser (it tries to verify the XML first before parsing, hence the DTD
> error).  I may try getting this to work again, but so far I haven't found an
> easy way to prevent XML verification via XML::SAX::Expat.
>
> There are two options: 1) install XML::SAX::ExpatXS (the better option),
> which works AND is 4x faster than XML::SAX::Expat, or  2) set the default
> parser in the PareserDetails.ini file in your local to use
> XML::SAX::PurePerl.
>
> BTW, XML::SAX::ExpatXS is intended to replace XML::SAX::Expat (it just
> hasn't officially happened yet); the latter hasn't had significant
> development in about three years.
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>> -----Original Message-----
>> From: Paul Boutros [mailto:paul.boutros at utoronto.ca]
>> Sent: Tuesday, October 17, 2006 1:00 PM
>> To: Chris Fields
>> Cc: bioperl-l at lists.open-bio.org
>> Subject: RE: [Bioperl-l] Bioperl 1.5.2 RC2
>>
>> 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
>> >
>> >
>>
>
>
>





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