[Bioperl-l] Need Help: 0.7.2 and 0.9.1 tests and preparations

Jason Eric Stajich jason@cgt.mc.duke.edu
Tue, 30 Oct 2001 14:03:35 -0500 (EST)

Looks good - these are no different that those that failed in 0.7.1
release =)

>From the MTYWTK category - here is my assesment of these bugs if anyone
wants to help and fix.

The GDB error is likely because of missing LWP::UserAgent or HTML::Parser
- I've added more verification of these being installed in the tests which
will be pushed out in new candidate tonight.

The Index problem has always been there when I did try this out on Win98,
I think it has to do with filehandles versus IO::File.  We're going to
need someone to step up and be perl + windows guru in order for us to
track any of these that appear to be OS specific issues.

DB::GenBank is also typical of NCBI dropping repeated connections and/or
changes in their CGI script, not sure we will get to this.

SearchDist is the missing Compile/SW extension which must be built
separated - not sure if anyone has ever done this on Windows.

BLAST is likely the gzip dependancy - I think Steve even has a note in
there that says "this will not work on non-unix". We should auto-detect OS
and not run these tests in fact I'm sure we've done that somewhere else,
have to see...

Will see if someone can look at the BPpsilite File::Temp - I know that
there is a known bug with the tempfiles in 0.7 that is not correctable on
stable branch (requires an API change).

Will make sure all of these are added as known BUGS in the release file if
they aren't addressable at this time.

On Tue, 30 Oct 2001, Jurgen Pletinckx wrote:

> # I've put 0.7.2 candidate in
> # ftp://bioperl.org/pub/jason/bioperl-0.7.2-candidate.tar.gz
> Let's see. NT 4.0, perl 5.6.0, build 623
> Blast: skipped 5/29
> BPsilite: problem with File::Temp
> DB: skipped 8/47 (Couldn't connect to genBank with Bio::DB::GenBank)
> GDB : failed 3-6, 8-11
> Index: failed 6-10
> SearchDist: skipped 3/3
> clustalw, blast or tcoffee still not installed on this box
> Total : failed 13 subtests, skipped 37 subtests
> Cheers,

Jason Stajich
Duke University