[Bioperl-l] 1.2-alpha-1 tar file built

[Nash, John]

As requested, on a Pentium/Linux box, running Redhat 7.3, Redhat Perl 5.6.1
installation, all Bundle::BioPerl modules installed ok, including the latest
GD module, and libgd (2.0.9, I think - it was a 10 minute old install from
www.boutell.com's lates version).  I can list all my Perl modules if it's
necessary.

I ran "perl Makefile.PL" without the mysql tests (because mysql is not
installed yet on this box); followed by "make", and "make test".  I have
included the "non all ok" tests.

I hope this is useful,
John

< snip

PERL_DL_NONLAZY=1 /usr/local/bin/perl -Iblib/arch -Iblib/lib
-I/usr/lib/perl5/5.6.1/i386-linux -I/usr/lib/perl5/5.6.1 -e 'use
Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t

t/DB................ok, 1/78 skipped: unknown reason

t/game..............Use of uninitialized value in pattern match (m//) at
/usr/lib/perl5/site_perl/5.6.1/XML/Writer.pm line 307.
Use of uninitialized value in print at
/usr/lib/perl5/5.6.1/i386-linux/IO/Handle.pm line 394.
ok

t/SearchIO..........Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 192, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 192, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in sprintf at
Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
line 447, <GEN31> line 353.
Use of uninitialized value in addition (+) at Bio/Search/SearchUtils.pm line
154, <GEN37> line 353.
Use of uninitialized value in addition (+) at Bio/Search/SearchUtils.pm line
154, <GEN37> line 353.
Use of uninitialized value in numeric eq (==) at Bio/Search/SearchUtils.pm
line 300, <GEN37> line 353.
Use of uninitialized value in numeric eq (==) at Bio/Search/SearchUtils.pm
line 300, <GEN37> line 353.
Use of uninitialized value in concatenation (.) or string at
Bio/Search/SearchUtils.pm line 227, <GEN37> line 353.
Use of uninitialized value in concatenation (.) or string at
Bio/Search/SearchUtils.pm line 228, <GEN37> line 353.
Use of uninitialized value in concatenation (.) or string at
Bio/Search/SearchUtils.pm line 229, <GEN37> line 353.
Use of uninitialized value in concatenation (.) or string at
Bio/Search/SearchUtils.pm line 227, <GEN37> line 353.
Use of uninitialized value in concatenation (.) or string at
Bio/Search/SearchUtils.pm line 228, <GEN37> line 353.
Use of uninitialized value in concatenation (.) or string at
Bio/Search/SearchUtils.pm line 229, <GEN37> line 353.
ok

t/SeqIO.............ok, 3/146 skipped: unknown reason

All tests successful, 4 subtests skipped.
Files=132, Tests=5948, 120 wallclock secs (64.13 cusr +  3.91 csys = 68.04
CPU)
PERL_DL_NONLAZY=1 /usr/local/bin/perl -Iblib/arch -Iblib/lib
-I/usr/lib/perl5/5.6.1/i386-linux -I/usr/lib/perl5/5.6.1 test.pl



-----Original Message-----
From: Ewan Birney [mailto:birney@ebi.ac.uk]
Sent: Tuesday, December 17, 2002 12:45 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] 1.2-alpha-1 tar file built



I know that for alot of people checking things out of cvs is one too many 
speed-bump to learn for testing, so I have built a tar file available at


  ftp://bioperl.org/pub/birney

called

  bioperl-1.2-alpha-1.tar.gz


If people could pick this up, untar it and then go


   perl Makefile.PL
  
and 

   make test




please send results (just the ones the fail) or all pass, OS and perl 
version (ideally I think to the list to encourage untested archs to try 
the test)




-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------


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