[Bioperl-l] Re: RedHat/DBM (was Re: Bioperl volunteering)

Tue, 17 Apr 2001 15:12:06 -0400 (EDT)

t_coffee link should be embedded in Cedric's HTML doc page, if not I can
dig it up for you.  We need someone to write a RPM for this one day, and
a FreeBSD port.  It is equivalent to clustalw in many ways, but I find it
nice to have multiple views of MSA sometimes so I added it.

The standaloneblast test requires you to have installed the ecoli.nt
blastabledb.  Look at the test file StandAloneBlast.t -- we need to give
some more documentation here for people setting up bioperl and running
make test.  Perhaps just in the README?  Or a README.externalprograms?

Steve, I am bring this discussions on list because I know it is helpful to
other people to see how to debug some of these types of problems.

-jason
On Tue, 17 Apr 2001, Steve Lane wrote:

> hi all, i managed to get this one working this morning.
> here's what i did:
>
> - i started by looking at DB_File.  i had looked at this
>   before, because i saw it in Bio/Index/Abstract.pm.  i
>   tried to update it from CPAN, and got the error on
>   not finding db.h.  i didn't pursue then because i wasn't
>   sure that DB_File was really related to the problem.
>
> - after Jason's letter of Monday, i tried harder with
>   DB_File.  its README has notes about both Berkeley DB
>   and problems with RedHat Linux.
>
> - i installed Berkeley DB 3.2.9 from sleepycat.
>
> - i then installed DB_File, after editing its config.in.
>
> now t/Index.t passes all tests.  the non-passes i get now are:
>
> t/Clustalw..........FAILED tests
> 5-6
>         Failed 2/9 tests, 77.78% okay
> t/StandAloneBlast...ok 2/8[blastall] WARNING: Could not find index files
> for database /usr/local/blast/data/ecoli.nt
> [blastall] WARNING: Test Could not find index files for database
> /usr/local/blast/data/ecoli.nt
> -------------------- EXCEPTION --------------------
> MSG: blastall call crashed: 256 /usr/local/blast/blastall -p  blastn
> -d  /usr/local/blast/data/ecoli.nt  -i  t/test.txt  -o  blastreport.out
>
> STACK Bio::Tools::Run::StandAloneBlast::_runblast
> blib/lib/Bio/Tools/Run/StandAloneBlast.pm:569
> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> blib/lib/Bio/Tools/Run/StandAloneBlast.pm:541
> STACK Bio::Tools::Run::StandAloneBlast::blastall
> blib/lib/Bio/Tools/Run/StandAloneBlast.pm:429
> STACK toplevel t/StandAloneBlast.t:70
> -------------------------------------------
> t/StandAloneBlast...dubious
>         Test returned status 1 (wstat 256, 0x100)
> DIED. FAILED tests 3-8
>         Failed 6/8 tests, 25.00% okay
> t/TCoffee...........ok 4/9tcoffee program not found. Skipping tests 5 to
> 9.
> t/TCoffee...........ok, 5/9 skipped: unknown
> reason
>
> i'll give these a try shortly... i bet i can figure them all
> out.  i may need some help in actually finding t_coffee, though.
> the perldoc page has a link to a t_coffee doc page, but not
> a source page.
>
> thanks for all the help, Steve
>
> Jason Stajich wrote:
> >
> > Steve - can you download the DB_File module from CPAN
> > ftp://ftp.cpan.org/CPAN/modules/by-module/DB_File/DB_File-1.76.tar.gz
> > and run make test on it.  You should be getting problems with some of the
> > tests - this reconfirms that the problem is in DB_File, maybe there is
> > info in the README about this.
> >
> > I've had to write to the author - Paul Marquesss - already about solaris
> > 2.8 problems with libdb and DB_File so it is possible you are dealing with
> > a software bug - although one would think it would have been caught by RPM
> > maintainers, hah...
> >
> > -Jason
> >
> > On Mon, 16 Apr 2001, Steve Lane wrote:
> >
> > > Ewan Birney wrote:
> > > >
> > > > Steve - could you just go
> > > >
> > > > perl -I . t/Index.t
> > > >
> > > > and show us stdout/stderr from this.
> > >
> > > $ perl -I . t/Index.t
> > > 1..10
> > > File /usr/home/sml/Projects/bioperl/bioperl-live/t/multifa.seq already
> > > indexed. Skipping...
> > > File /usr/home/sml/Projects/bioperl/bioperl-live/t/seqs.fas already
> > > indexed. Skipping...
> > > File /usr/home/sml/Projects/bioperl/bioperl-live/t/multi_1.fa already
> > > indexed. Skipping...
> > > not ok 1
> > > # Failed test 1 in t/Index.t at line 34
> > > ok 2
> > > ok 3
> > > File /usr/home/sml/Projects/bioperl/bioperl-live/t/swisspfam.data
> > > already indexed. Skipping...
> > > not ok 4
> > > # Failed test 4 in t/Index.t at line 77
> > > File /usr/home/sml/Projects/bioperl/bioperl-live/t/test.embl already
> > > indexed. Skipping...
> > > not ok 5
> > > # Failed test 5 in t/Index.t at line 84
> > > ok 6
> > > File /usr/home/sml/Projects/bioperl/bioperl-live/t/roa1.swiss already
> > > indexed. Skipping...
> > > not ok 7
> > > # Failed test 7 in t/Index.t at line 92
> > > ok 8
> > > File /usr/home/sml/Projects/bioperl/bioperl-live/t/roa1.genbank already
> > > indexed. Skipping...
> > > not ok 9
> > > # Failed test 9 in t/Index.t at line 101
> > > ok 10
> > >
> > > the failures are: -e "Wibbl[1-5]" tests.
> > >
> > > > Also - have you installed Berekely DB on this (DBM::File)?
> > >
> > > i haven't installed DBM::File; in fact i've never heard of that.
> > >
> > > i don't think i've installed Berkeley DB.  i think that's the
> > > 'db' package?  here's the RPMs with db in them on my machine:
> > >
> > > # rpm -qa | grep db | sort
> > > db1-1.85-4
> > > db1-devel-1.85-4
> > > db2-2.4.14-4
> > > db3-3.1.17-5
> > > gdb-5.0-7
> > > gdbm-1.8.0-5
> > > gdbm-devel-1.8.0-5
> > > pwdb-0.61.1-1
> > > xxgdb-1.12-16
> > >
> > > i think the below is the Berkeley DB RPM:
> > >
> > > # ls -l /usr/local/src/db-2.7.7-1.i386.rpm
> > > -rw-rw----    1 sml      sml       1341765 Apr 15 17:13
> > > /usr/local/src/db-2.7.7-1.i386.rpm
> > >
> > > i did try to install this, but it failed on dependencies,
> > > even with --force.
> > >
> > > thanks, Steve
> > > --
> > > Steve Lane <sml@zfx.com>
> > >
> >
> > Jason Stajich
> > jason@chg.mc.duke.edu
> > Center for Human Genetics
> > Duke University Medical Center
> > http://www.chg.duke.edu/
>
> --
> Steve Lane <sml@zfx.com>
>

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/