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Question: RdbiPgSQL installation trouble
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gravatar for Tena Sakai
7.1 years ago by
Tena Sakai40
Tena Sakai40 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? Thank you in advance. Regards, Tena Sakai tsakai@gallo.ucsf.edu Below is the entire session of what happens. =========================================== [root@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/contri b/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@dasher Scripts]# [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.1 years ago by Martin Morgan ♦♦ 20k • written 7.1 years ago by Tena Sakai40
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gravatar for Martin Morgan
7.1 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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/cont rib/RdbiPgSQL_1.22.0.tar.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
ADD COMMENTlink written 7.1 years ago by Martin Morgan ♦♦ 20k
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 >
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