[R-sig-DB] PostgreSQL

[Tom Dye]

Aloha all,

Thank you all so much for your help with installing RdbiPgSQL.  The 
problem turned out to be the one Jim McLoughlin describes below.  R wasn't 
picking up the environment variables PG_LIB_DIR and PG_INCLUDE_DIR.  I set 
these with:

Sys.putenv("PG_LIB_DIR"="/usr/local/pgsql/lib")
Sys.putenv("PG_INCLUDE_DIR"="/usr/local/pgsql/include"),

then gave R permission to run system commands as root, and the source 
install from BioConductor ran without a hitch.

I very much appreciate your time and effort.  It has been a pleasure 
interacting with you all.

Tom

  On Wed, 7 Sep 2005, Jim McLoughlin wrote:

> On Sep 6, 2005, at 12:53 AM, Tom Dye wrote:
>
>> 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:
>>
>> 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.
>
> I have not installed this on my mac in a while, but my guess is that
> while these variables are set in you environment, they are not
> available in R for some reason.
>
> You could check whether they are set in the session by looking at
> Sys.getenv()
>
> If they are not there, I would try setting them directly in your R
> session before installing.  I think you would do that with:
>
> Sys.setenv("PG_LIB_DIR"="/usr/local/pgsql/lib")
> Sys.setenv("PG_INCLUDE_DIR"="/usr/local/pgsql/include")
>
> But I could be off on whether the variable names need to be quoted.
>
> Jim
>
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>
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Thomas S. Dye, Ph.D. 
T. S. Dye & Colleagues, Archaeologists, Inc. 
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