[Bioperl-l] releasing next week

Barry Moore bmoore at genetics.utah.edu
Wed Sep 14 20:41:02 EDT 2005


Sorry for the slow reply - temporarily abandoned my e-mail due to a
deadline.  My mistake on the file error - I was running the test script
from within the t directory, so it couldn't create t/tmp.  When I moved
back to bioperl-live directory it works fine.  This was hiding the real
failure in my RestrictionIO.t which.  Test 10 is failing.  The error is:

# Test 10 got: '9' (t/RestrictionIO.t at line 53)
#    Expected: '11'

Test 10 reads rebase.withrefm file.  This file has a couple of multiple
site cutters.  It correctly reads the first multi site cutter, and adds
it to the object, but fails to add the last two rest enzymes in the file
(another multi-site cutter and a single site cutter).  Oddly, if I step
into  Bio::Restriction::IO::base::_make_multisites method with the
debugger while parsing the second multi site cutter (the one that is
failing to get parsed correctly)  - not changing anything, just stepping
one line into the method - it parses fine, the object contains all the
re's and the test passes just fine.  That one's got me stumped.  If
anyone has suggestions for debugging that let me know.


-----Original Message-----
From: Brian Osborne [mailto:brian_osborne at cognia.com] 
Sent: Friday, September 09, 2005 12:43 PM
To: Barry Moore; Jason Stajich; bioperl-l
Subject: Re: [Bioperl-l] releasing next week


my $tmpdir = "t/tmp";

So this fails for you? What about:

mkdir $tmpdir


Brian O.

On 9/9/05 12:16 AM, "Barry Moore" <bmoore at genetics.utah.edu> wrote:

> Jason,
> BioDBGFF.t failed cause I gave it the wrong Postgres login detail -
> can't remember my damn password!
> RemoteBlast.t passed when run individually.
> RestrictionIO.t failed to open an output file because the directory
> didn't exist, and it wasn't clear to me why it should.
> Didn't look into tutorial.t failures.
> System is Debian Woody, Perl 5.6.1, and fresh live bioperl.
> Failed Test       Stat Wstat Total Fail  Failed  List of Failed
> -------
> t/BioDBGFF.t                   138  138 100.00%  1-138
> t/RemoteBlast.t      2   512     6    1  16.67%  2
> t/RestrictionIO.t               14    1   7.14%  10
> t/tutorial.t       255 65280    21    6  28.57%  19-21
> 122 subtests skipped.
> Failed 4/215 test scripts, 98.14% okay. 143/9892 subtests failed,
> okay.
> Barry
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Jason
> Stajich
> Sent: Thursday, September 08, 2005 3:30 PM
> To: bioperl-l List
> Cc: Scott Cain
> Subject: [Bioperl-l] releasing next week
> All tests pass for me on two different machines.
> If you have any reason for the 1.5.1 release to not happen next week,
> please speak up now.  I'm trying to time it with the GMOD Gbrowse
> release so people can feel comfortable upgrading to bioperl 1.5 and
> the latest Gbrowse at the same time.
> The only test failing for me to DBCUTG.t this seems  to be a
> webserver error - perhaps they have changed their interface?  This is
> rather minor so I won't let it hold up the release if no one looks at
> it before next week.
> I'm choosing to ignore the "" overloading in SeqFeature/Annotation
> objects for 1.5.1.  Similarly, adding additional seqfeature tests are
> going to be on the backburner for this release but need to be done
> before the 1.6 release.
> I'd like to see if we can help Brian with the SeqIO test overhaul.
> This seems like the only other outstanding issue.
> My feeling is the TypedSeqFeature implementation can wait, perhaps in
> a future 1.5.x in prep for 1.6.
> I'm thinking I will try and put a release candidate up by Monday and
> release as soon as a few people have tested it out.  Please do me a
> favor and do a fresh CVS checkout and run make test on your own
> machines to see what else still needs work.
> -jason
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
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