[R-sig-DB] PostgreSQL

[Tom Dye]

Aloha Joe,

Rdbi installs just fine.

RdbiPgSQL is available as source, and even with
export PG_LIB_DIR=/usr/local/pgsql/lib/ and
export PG_INCLUDE_DIR=/usr/local/pgsql/include/
fails to install with the following messages:

trying URL 
'http://www.bioconductor.org/src/contrib/RdbiPgSQL_1.1.4.tar.gz'
Content type 'application/x-gzip' length 28046 bytes
opened URL
==================================================
downloaded 27Kb

* Installing *source* package 'RdbiPgSQL' ...
creating cache ./config.cache

The downloaded packages are in
 	/private/tmp/RtmpzKE7wz/downloaded_packages
checking for PQconnectdb in -lpq... no

I could not find your PostgreSQL client libraries!
Use --with-pgsql-libraries=PATH; if running R's INSTALL,
use --configure-args='--with-pgsql-libraries=PATH'; or
set PG_LIB_DIR in your environment to the library path,
and rerun the configure/install.

ERROR: configuration failed for package 'RdbiPgSQL'

I'm in way over my head here and will appreciate any help.

Tom

On Mon, 5 Sep 2005, Joe Conway wrote:
> (posting back to the list so others can join in and/or benefit)
>
> I think it also requires this:
> http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/Rdbi.html
>
> I'm afraid I don't have a Mac, and to be honest have not used RdbiPgSQL since 
> before it was moved to Bioconductor. My needs for R are very basic, and 
> usually I use my own connector, PL/R (see http://www.joeconway.com/plr/). 
> Slightly different approach, but might meet your needs.
>
> Anyway, I followed the instructions here:
> http://www.bioconductor.org/docs/install-howto.html
>
> Worked for me after I set two environment variables to point to my Postgres 
> headers and libs. I did something like:
>
>
> # export PG_LIB_DIR=/usr/local/pgsql-dev/lib
> # export PG_INCLUDE_DIR=/usr/local/pgsql-dev/include
> # R
>
> R : Copyright 2005, The R Foundation for Statistical Computing
> Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0
>
> <snip>
>
> [Previously saved workspace restored]
>
>> source("http://www.bioconductor.org/biocLite.R")
>> biocLite(c("Rdbi","RdbiPgSQL"))
>
> I haven't really tested it, but all indications are that they both installed 
> correctly.
>
> HTH,
>
> Joe
>

Thomas S. Dye, Ph.D. 
T. S. Dye & Colleagues, Archaeologists, Inc. 
735 Bishop Street, Suite 315
Honolulu, Hawai`i 96813 
Voice (808) 387-9352 
Fax (808) 529-0884
http://www.tsdye.com