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/RdbiPgSQ L_1.22.0.t >> ar.gz' >> Content type 'application/x-gzip' length 28079 bytes (27 Kb) >> opened URL >> ================================================== >> downloaded 27 Kb >> >> * installing *source* package ?RdbiPgSQL? ... >> 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 ?/usr/local/lib64/R/library/RdbiPgSQL? >> >> The downloaded packages are in >> ?/tmp/Rtmpr9mGSM/downloaded_packages? >> 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]] >> >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >