[Bioperl-l] Bioperl 1.5.2 RC2

Chris Fields cjfields at uiuc.edu
Tue Oct 17 14:31:51 EDT 2006


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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