[R-sig-DB] PostgreSQL
Tom Dye
t@d @end|ng |rom t@dye@com
Thu Sep 8 08:35:43 CEST 2005
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
>
> [[alternative HTML version deleted]]
>
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Thomas S. Dye, Ph.D.
T. S. Dye & Colleagues, Archaeologists, Inc.
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