[BioC] RdbiPgSQL installation trouble

[Tena Sakai]

Hi Martin,

Thank you for your reply.

I got it installed.  The trouble was due to postgres not
running at the time I was installing RdbiPgSQL.  There was
an error in postgresql.conf file in specification of
listen_address (and port number as well).  When I got
postgres running and retried the RdbiPgSQL installation
all went smoothly.

Thank you also for a tip about
  http://cran.fhcrc.org/web/packages/RPostgreSQL/index.html

I appreciate it.

Regards,

Tena Sakai
tsakai at gallo.ucsf.edu


On 10/1/10 6:30 AM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

> 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.t
>> ar.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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