[maker-devel] Can't load DBI?

[Carson Holt]

I'm glad you were able to get everything to work.  It looks like you do in fact  have two versions of perl installed.  Another option for fixing your error would have been to edit the "#! /usr/bin/perl" line at the start of the maker and mpi_maker scripts to instead be the location of your other perl installation.  You can find out where the other version of perl is installed by typing "which perl" on the command line.

Thanks,
Carson

On 2/10/10 2:42 PM, "Matthew Conte" <mconte at umd.edu> wrote:

Hi Carson,

/usr/bin/perl -v
This is perl, v5.8.5 built for x86_64-linux-thread-multi

perl -v
This is perl, v5.8.7 built for x86_64-linux

which perl
/usr/local/bin/perl

It took me a bit, but I got DBI and DBD::SQLite installed using that perl 5.8.5 multi thread installation.  Maker seems to be running fine now.  I even got the MPI version running.

Thanks for sending me in the right direction.

-Matt

On Tue, Feb 9, 2010 at 3:13 PM, Carson Holt <carson.holt at genetics.utah.edu> wrote:
First type /usr/bin/perl -v rather than perl -v and see what you get.  There may be more than one version of perl installed.  Let me know. What you find.

If that is not the case, you can also delete the /maker/perl/lib/ directory and install DBI and DBD::SQLite manually via cpan and see if that makes a difference.

Thanks,
Carson



On 2/9/10 1:08 PM, "Matthew Conte" <mconte at umd.edu <http://mconte@umd.edu> > wrote:

Good afternoon,

I'm trying to get Maker running on a cluster of ours and I'm seeing the following error when I run maker after following all the install steps:

#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
#----------------------
FATAL: failed!!
#----------------------
Can't load '/a/f20-fs1/export/home/deepthought/mconte/maker/bin/../perl/lib/auto/DBI/DBI.so' for module DBI: /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../perl/lib/auto/DBI/DBI.so: undefined symbol: PL_sv_undef at /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm line 230.
 at /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../perl/lib/DBI.pm line 263

BEGIN failed--compilation aborted at /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../perl/lib/DBI.pm line 263.

Compilation failed in require at /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../lib/GFFDB.pm line 8.

BEGIN failed--compilation aborted at /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../lib/GFFDB.pm line 8.

Compilation failed in require at /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../lib/maker/auto_annotator.pm <http://auto_annotator.pm>  <http://auto_annotator.pm>  line 21.

BEGIN failed--compilation aborted at /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../lib/maker/auto_annotator.pm <http://auto_annotator.pm>  <http://auto_annotator.pm>  line 21.


Compilation failed in require at /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../lib/GI.pm line 39.

BEGIN failed--compilation aborted at /a/f20-fs1/export/home/deepthought/mconte/maker/bin/../lib/GI.pm line 39.

Compilation failed in require at /homes/mconte/maker/bin/maker line 61.

BEGIN failed--compilation aborted at /homes/mconte/maker/bin/maker line 61.


DBI and maker seem to have installed correctly during the perl Install.PL step.  I was wondering if anyone had encountered this issue before while I continue to figure out the problem.  The only thing that seems a little odd to me at this point is that I'm using perl 5.8.7 and it is mentioning /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/DynaLoader.pm . That DynaLoad.pm is identical to the one in the perl 5.8.7 install though.

Thanks,
Matt Conte




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