[maker-devel] error with pg_putline in gmod_bulk_load_gff3

[Carson Holt]

Two things.

First look at this step by step tutorial on installing Chado from the GMOD Summer School 2009 ( http://gmod.org/wiki/Chado_Tutorial ).

Second.  Depending on how you have installed things you may have duplicates of some modules, so the wrong version might be used even though a newer version is installed somewhere else, but just in case try installing the newest versions of DBI and DBI::db first.  Then try gmod_bulk_load_gff3.pl again.  If it still doesn't work, it can be difficult to find all the old modules and clean them up, but there is a way to create a library in a directory you choose that will be searched for libraries first, so it will override any old versions.

Open the cpan shell -->  perl -MCPAN -e shell

You should now be asked to configure cpan; however, if cpan has already been configured, you will need to re-enter configuration by typing ->  o conf init

In the configuration, when asked if you want to send any special arguments to make add the following (edit DESTDIR to point to the location you want the libraries):

DESTDIR=$HOME/my_perl/ INSTALLDIRS=perl INSTALLMAN1DIR=none INSTALLMAN3DIR=none INSTALLARCHLIB=lib/ INSTALLPRIVLIB=lib/ INSTALLBIN=bin/

Now install everything you want to install with cpan (reinstall all required modules for Chado).

Finally edit your ~/.bash_profile (or /etc/profile to make changes global) to have the environmental variable PERL5LIB point to the same location as DESTDIR from the line above, but with the extra subdirectory lib/.

Example:
export PERL5LIB=$HOME/my_perl/lib/

After restarting your shell, perl will search the newly installed libraries first.

Thanks,
Carson



On 12/1/09 10:58 AM, "Shane Brubaker" <SBrubaker at Aurorabiofuels.com> wrote:

Hi, do you guys think you could help me with this?  I tried the gmod mailing list buy haven't gotten any reply yet.  Thanks :)


I installed DBD::Pg 1.32 on my system, thinking that I needed it.  I am now getting an error when running gmod_bulk_load_gff3.pl which says:
 "Can't locate object method pg_putline via package DBI::db " in GMOD/DB/Adapter.pm

It occurs to me that maybe DBD:Pg was already installed anyway, when I installed Gmod. I don't necessarily want to uninstall it and mess everything up.

I also tried using -inserts to avoid doing the copy from stdin, but I get an awful lot of errors and things definitely don't look right.

What should I do?


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