Hi Rebecca,
It looks like you need to reinstall DB_File perl module. According to the
README of this module, the problem is caused by having two versions of Berkely
DB on your system:
Incompatible versions of db.h and libdb
---------------------------------------
BerkeleyDB seems to have built correctly, but you get an error like this
when you run the test harness:
$ make test
PERL_DL_NONLAZY=1 /home/paul/perl/install/bin/perl5.00560 -Iblib/arch
-Iblib/lib -I/home/paul/perl/install/5.005_60/lib/5.00560/i586-linux
-I/home/paul/perl/install/5.005_60/lib/5.00560 -e 'use Test::Harness
qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/db-btree..........
DB_File was build with libdb version 2.3.7
but you are attempting to run it with libdb version 2.7.5
BEGIN failed--compilation aborted at t/db-btree.t line 21.
...
Another variation on the theme of having two versions of Berkeley DB on
your system.
Solution: Setting the LIB & INCLUDE variables in config.in to point to the
correct directories can sometimes be enough to fix this
problem. If that doesn't work the easiest way to fix the
problem is to either delete or temporarily rename the copies
of db.h and libdb.a that you don't want BerkeleyDB to use.
If you are running Linux, please read the Linux Notes section
below.
Hope this is useful.
Please write if you need further assistance.
Cheers,
Junjun
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of Rebecca Ewing
> Sent: Friday, January 09, 2009 6:23 AM
> To: [email protected]
> Subject: [mart-dev] Biomart installation
>
> Hi
>
> I am trying to install Biomart. When running perl
> bin/configure.pl -r conf/registryURLPointer.xml I get the
> following error message:
>
> DB_File needs compatible versions of libdb & db.h
> you have db.h version 4.3.27 and libdb version 4.3.29
> Compilation failed in require at CGI/Session/Driver/db_file.pm line 8.
> BEGIN failed--compilation aborted at
> CGI/Session/Driver/db_file.pm line 8.
> Compilation failed in require at
> /var/tmp/apache/conf/biomart-perl/bin/../lib/BioMart/Web.pm line 47.
> BEGIN failed--compilation aborted at
> /var/tmp/apache/conf/biomart-perl/bin/../lib/BioMart/Web.pm line 47.
> Compilation failed in require at (eval 15) line 3.
> ...propagated at /software/perl-5.8.8/lib/5.8.8/base.pm line 85.
> BEGIN failed--compilation aborted at
> /var/tmp/apache/conf/biomart-perl/bin/../lib/BioMart/Web/Templ
ateBuilder.pm
> line 53.
> Compilation failed in require at
> /var/tmp/apache/conf/biomart-perl/bin/configureBioMart.pl line 39.
> BEGIN failed--compilation aborted at
> /var/tmp/apache/conf/biomart-perl/bin/configureBioMart.pl line 39.
>
> Please would you be able to tell me how to fix this?
>
> Thanks
>
> Rebecca
>
>
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> The Wellcome Trust Sanger Institute is operated by Genome
> Research Limited, a charity registered in England with
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>
