[BioC] RdbiPgSQL installation trouble

[Martin Morgan]

On 09/30/2010 08:54 PM, Tena Sakai wrote:
> Greetings,
> 
> I am having a problem installing RdbiPgSQL on Centos 5.5 machine,
> running on Dell hardware.  The version of R I am using is 2.11.1 and
> Postgres  version is 8.4.4.
> 
> I have set the following environment variables:
>   PGHOST=dasher
>   PG_LIB_DIR=/usr/local/pgsql/lib
>   PG_INCLUDE_DIR=//usr/local/pgsql/include
> and ran two commands below from R:
>   source("http://bioconductor.org/biocLite.R")
>   biocLite("RdbiPgSQL")
> 
> What happens is:
>   Error in dyn.load(file, DLLpath = DLLpath, ...) :
>     unable to load shared library '/usr/local/lib64/R/library/RdbiPgSQL/libs/RdbiPgSQL.so':
>     libpq.so.5: cannot open shared object file: No such file or directory
>   ERROR: loading failed
> 
> Would someone please give me some idea how to get this corrected?

Hi Tena --

This is likely a system configuration issue, e.g., a Windows PATH
environment variable is not set correctly, or the Linux ldconfig program
or LD_LIBRARY_PATH environment variable is incorrect. Set these so that
libpq.so.5 is available to R, e.g.,, /sbin/ldconfig -p |grep libpq
returns something sensible.

This package

  http://cran.fhcrc.org/web/packages/RPostgreSQL/index.html

is more recent and actively maintained, if you're looking for a Postgres
client.

Martin

> 
> Thank you in advance.
> 
> Regards,
> 
> Tena Sakai
> tsakai at gallo.ucsf.edu
> 
> Below is the entire session of what happens.
> ===========================================
> 
> 
>   [root at dasher Scripts]# R
> 
>   R version 2.11.1 (2010-05-31)
>   Copyright (C) 2010 The R Foundation for Statistical Computing
>   ISBN 3-900051-07-0
> 
>   R is free software and comes with ABSOLUTELY NO WARRANTY.
>   You are welcome to redistribute it under certain conditions.
>   Type 'license()' or 'licence()' for distribution details.
> 
>     Natural language support but running in an English locale
> 
>   R is a collaborative project with many contributors.
>   Type 'contributors()' for more information and
>   'citation()' on how to cite R or R packages in publications.
> 
>   Type 'demo()' for some demos, 'help()' for on-line help, or
>   'help.start()' for an HTML browser interface to help.
>   Type 'q()' to quit R.
> 
>   > Sys.getenv('PGHOST')
>     PGHOST
>   "dasher"
>   >
>   > Sys.getenv('PG_LIB_DIR')
>               PG_LIB_DIR
>   "/usr/local/pgsql/lib"
>   >
>   > Sys.getenv('PG_INCLUDE_DIR')
>                PG_INCLUDE_DIR
>   "//usr/local/pgsql/include"
>   >
>   > source("http://bioconductor.org/biocLite.R")
>   BioC_mirror = http://www.bioconductor.org
>   Change using chooseBioCmirror().
>   >
>   > biocLite("RdbiPgSQL")
>   Using R version 2.11.1, biocinstall version 2.6.8.
>   Installing Bioconductor version 2.6 packages:
>   [1] "RdbiPgSQL"
>   Please wait...
> 
>   trying URL 'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/RdbiPgSQL_1.22.0.tar.gz'
>   Content type 'application/x-gzip' length 28079 bytes (27 Kb)
>   opened URL
>   ==================================================
>   downloaded 27 Kb
> 
>   * installing *source* package âRdbiPgSQLâ ...
>   creating cache ./config.cache
>   updating cache ./config.cache
>   creating ./config.status
>   creating src/Makevars
>   ** libs
>   gcc -std=gnu99 -I/usr/local/lib64/R/include -I//usr/local/pgsql/include -I/usr/local/include    -fpic  -g -O2 -c PgSQL.c -o PgSQL.o
>   gcc -std=gnu99 -I/usr/local/lib64/R/include -I//usr/local/pgsql/include -I/usr/local/include    -fpic  -g -O2 -c PgSQLInit.c -o PgSQLInit.o
>   gcc -std=gnu99 -shared -L/usr/local/lib64 -o RdbiPgSQL.so PgSQL.o PgSQLInit.o -L/usr/local/pgsql/lib -lpq
>   installing to /usr/local/lib64/R/library/RdbiPgSQL/libs
>   ** R
>   ** preparing package for lazy loading
>   ** help
>   *** installing help indices
>   ** building package indices ...
>   ** testing if installed package can be loaded
>   Error in dyn.load(file, DLLpath = DLLpath, ...) :
>     unable to load shared library '/usr/local/lib64/R/library/RdbiPgSQL/libs/RdbiPgSQL.so':
>     libpq.so.5: cannot open shared object file: No such file or directory
>   ERROR: loading failed
>   * removing â/usr/local/lib64/R/library/RdbiPgSQLâ
> 
>   The downloaded packages are in
>           â/tmp/Rtmpr9mGSM/downloaded_packagesâ
>   Updating HTML index of packages in '.Library'
>   Warning message:
>   In install.packages(pkgs = pkgs, repos = repos, ...) :
>     installation of package 'RdbiPgSQL' had non-zero exit status
>   >
>   > q()
>   Save workspace image? [y/n/c]: n
>   [root at dasher Scripts]#
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
> 
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