Hi there, I am unable to load "hgu133a2.db", "hgu133a.db", "hgu133b.db", "hgu133plus2.db" packages from Bioconductor. When I give biocLite("hgu133a2.db"), it does download and install the required package. However, while testing itself to launch the package, it gives the following error messages and remove the installed packages: Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: sqliteExecStatement(con, statement, bind.data) error: RS-DBI driver: (error in statement: database is locked) ERROR: loading failed This is similar to the one reported at http://permalink.gmane.org/gmane.science.biology.informatics.conductor /28843 . I have tried to load several times after rebooting, but the errors persist. Could you help me to sort this out? Thanks. Regards, Mani > pkgs <- c("hgu133a2.db", "hgu133a.db", "hgu133b.db", "hgu133plus2.db") > biocLite(pkgs) Using R version 2.11.1, biocinstall version 2.6.7. Installing Bioconductor version 2.6 packages: [1] "hgu133a2.db" "hgu133a.db" "hgu133b.db" "hgu133plus2.db" Please wait... also installing the dependency ‘org.Hs.eg.db’ trying URL ' http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib/o rg.Hs.eg.db_2.4.1.tar.gz ' Content type 'application/x-gzip' length 39900148 bytes (38.1 Mb) opened URL ================================================== downloaded 38.1 Mb trying URL ' http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib/h gu133a2.db_2.4.1.tar.gz ' Content type 'application/x-gzip' length 901523 bytes (880 Kb) opened URL ================================================== downloaded 880 Kb trying URL ' http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib/h gu133a.db_2.4.1.tar.gz ' Content type 'application/x-gzip' length 904178 bytes (882 Kb) opened URL ================================================== downloaded 882 Kb trying URL ' http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib/h gu133b.db_2.4.1.tar.gz ' Content type 'application/x-gzip' length 834521 bytes (814 Kb) opened URL ================================================== downloaded 814 Kb trying URL ' http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib/h gu133plus2.db_2.4.1.tar.gz ' Content type 'application/x-gzip' length 2117771 bytes (2.0 Mb) opened URL ================================================== downloaded 2.0 Mb * installing *source* package ‘org.Hs.eg.db’ ... ** R ** inst ** preparing package for lazy loading Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: sqliteExecStatement(con, statement, bind.data) error: RS-DBI driver: (error in statement: database is locked) ERROR: loading failed * removing ‘/R/R-2.11.1/library/org.Hs.eg.db’ ERROR: dependencies ‘org.Hs.eg.db’ are not available for package ‘hgu133a2.db’ * removing ‘/R/R-2.11.1/library/hgu133a2.db’ ERROR: dependencies ‘org.Hs.eg.db’ are not available for package ‘hgu133a.db’ * removing ‘/R/R-2.11.1/library/hgu133a.db’ ERROR: dependencies ‘org.Hs.eg.db’ are not available for package ‘hgu133b.db’ * removing ‘/R/R-2.11.1/library/hgu133b.db’ ERROR: dependencies ‘org.Hs.eg.db’ are not available for package ‘hgu133plus2.db’ * removing ‘/R/R-2.11.1/library/hgu133plus2.db’ The downloaded packages are in ‘/tmp/RtmpjGYvZn/downloaded_packages’ Updating HTML index of packages in '.Library' Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'org.Hs.eg.db' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'hgu133a2.db' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'hgu133a.db' had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'hgu133b.db' had non-zero exit status 5: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'hgu133plus2.db' had non-zero exit status [[alternative HTML version deleted]]

Hi Manikhandan, I am unable to reproduce this problem. Can you please give us your sessionInfo() as described in the posting guide? http://www.bioconductor.org/docs/postingGuide.html I can tell you that none of the human chip packages will work without the org.Hs.eg.db package installed so getting this installed is going to be critical to your success. Marc On 06/29/2010 08:53 AM, Manikhandan V A wrote: > Hi there, > > I am unable to load "hgu133a2.db", "hgu133a.db", "hgu133b.db", > "hgu133plus2.db" > packages from Bioconductor. When I give biocLite("hgu133a2.db"), it does > download and install the required package. However, while testing itself to > launch the package, it gives the following error messages and remove the > installed packages: > > Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: > call: sqliteExecStatement(con, statement, bind.data) > error: RS-DBI driver: (error in statement: database is locked) > ERROR: loading failed > > > This is similar to the one reported at > http://permalink.gmane.org/gmane.science.biology.informatics.conduct or/28843 > . > > I have tried to load several times after rebooting, but the errors persist. > > Could you help me to sort this out? > Thanks. > Regards, > Mani > > > > >> pkgs <- c("hgu133a2.db", "hgu133a.db", "hgu133b.db", "hgu133plus2.db") >> biocLite(pkgs) >> > Using R version 2.11.1, biocinstall version 2.6.7. > Installing Bioconductor version 2.6 packages: > [1] "hgu133a2.db" "hgu133a.db" "hgu133b.db" "hgu133plus2.db" > Please wait... > > also installing the dependency 'org.Hs.eg.db' > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /org.Hs.eg.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 39900148 bytes (38.1 Mb) > opened URL > ================================================== > downloaded 38.1 Mb > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /hgu133a2.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 901523 bytes (880 Kb) > opened URL > ================================================== > downloaded 880 Kb > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /hgu133a.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 904178 bytes (882 Kb) > opened URL > ================================================== > downloaded 882 Kb > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /hgu133b.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 834521 bytes (814 Kb) > opened URL > ================================================== > downloaded 814 Kb > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /hgu133plus2.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 2117771 bytes (2.0 Mb) > opened URL > ================================================== > downloaded 2.0 Mb > > * installing *source* package 'org.Hs.eg.db' ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > ** help > *** installing help indices > ** building package indices ... > ** testing if installed package can be loaded > Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: > call: sqliteExecStatement(con, statement, bind.data) > error: RS-DBI driver: (error in statement: database is locked) > ERROR: loading failed > * removing '/R/R-2.11.1/library/org.Hs.eg.db' > ERROR: dependencies 'org.Hs.eg.db' are not available for package > 'hgu133a2.db' > * removing '/R/R-2.11.1/library/hgu133a2.db' > ERROR: dependencies 'org.Hs.eg.db' are not available for package > 'hgu133a.db' > * removing '/R/R-2.11.1/library/hgu133a.db' > ERROR: dependencies 'org.Hs.eg.db' are not available for package > 'hgu133b.db' > * removing '/R/R-2.11.1/library/hgu133b.db' > ERROR: dependencies 'org.Hs.eg.db' are not available for package > 'hgu133plus2.db' > * removing '/R/R-2.11.1/library/hgu133plus2.db' > > The downloaded packages are in > '/tmp/RtmpjGYvZn/downloaded_packages' > Updating HTML index of packages in '.Library' > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'org.Hs.eg.db' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'hgu133a2.db' had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'hgu133a.db' had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'hgu133b.db' had non-zero exit status > 5: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'hgu133plus2.db' had non-zero exit status > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Hi Mani, Are you on a network mounted partition e.g. NFS or Samba share? On your Unix/Linux box, you can find out with something like: df path/to/your/library/directory where path/to/your/library/directory is given by: echo "`R CMD sh -c 'echo "$R_HOME"'`/library" If the line displayed by the 'df' command above starts with /dev/ then you are on a local filesystem. But if it starts with something like <hostname>:/some/path, then you are on a network mounted filesystem. According to this document http://www.sqlite.org/faq.html SQLite database files can have locking problems when put on NFS. Can you try to install R on a local filesystem and see if that solves your problem? If, for whatever reason, you can't re-install R, you can still control where to install packages with (from R): .libPaths("path/to/a/local/library/directory") # folder must exist # and be writable source("http://bioconductor.org/biocLite.R") biocLite("hgu133a2.db") library("hgu133a2.db") To have R remember permanently the location of this library, use environment variable R_LIBS. For example if you use sh or bash, you can put export R_LIBS="path/to/a/local/library/directory" in your ~/.profile, ~/.bash_profile or ~/.bashrc file (this is very system dependent). Cheers, H. On 06/29/2010 08:53 AM, Manikhandan V A wrote: > Hi there, > > I am unable to load "hgu133a2.db", "hgu133a.db", "hgu133b.db", > "hgu133plus2.db" > packages from Bioconductor. When I give biocLite("hgu133a2.db"), it does > download and install the required package. However, while testing itself to > launch the package, it gives the following error messages and remove the > installed packages: > > Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: > call: sqliteExecStatement(con, statement, bind.data) > error: RS-DBI driver: (error in statement: database is locked) > ERROR: loading failed > > > This is similar to the one reported at > http://permalink.gmane.org/gmane.science.biology.informatics.conduct or/28843 > . > > I have tried to load several times after rebooting, but the errors persist. > > Could you help me to sort this out? > Thanks. > Regards, > Mani > > > >> pkgs<- c("hgu133a2.db", "hgu133a.db", "hgu133b.db", "hgu133plus2.db") >> biocLite(pkgs) > Using R version 2.11.1, biocinstall version 2.6.7. > Installing Bioconductor version 2.6 packages: > [1] "hgu133a2.db" "hgu133a.db" "hgu133b.db" "hgu133plus2.db" > Please wait... > > also installing the dependency ?org.Hs.eg.db? > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /org.Hs.eg.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 39900148 bytes (38.1 Mb) > opened URL > ================================================== > downloaded 38.1 Mb > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /hgu133a2.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 901523 bytes (880 Kb) > opened URL > ================================================== > downloaded 880 Kb > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /hgu133a.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 904178 bytes (882 Kb) > opened URL > ================================================== > downloaded 882 Kb > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /hgu133b.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 834521 bytes (814 Kb) > opened URL > ================================================== > downloaded 814 Kb > > trying URL > ' > http://www.bioconductor.org/packages/2.6/data/annotation/src/contrib /hgu133plus2.db_2.4.1.tar.gz > ' > Content type 'application/x-gzip' length 2117771 bytes (2.0 Mb) > opened URL > ================================================== > downloaded 2.0 Mb > > * installing *source* package ?org.Hs.eg.db? ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > ** help > *** installing help indices > ** building package indices ... > ** testing if installed package can be loaded > Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: > call: sqliteExecStatement(con, statement, bind.data) > error: RS-DBI driver: (error in statement: database is locked) > ERROR: loading failed > * removing ?/R/R-2.11.1/library/org.Hs.eg.db? > ERROR: dependencies ?org.Hs.eg.db? are not available for package > ?hgu133a2.db? > * removing ?/R/R-2.11.1/library/hgu133a2.db? > ERROR: dependencies ?org.Hs.eg.db? are not available for package > ?hgu133a.db? > * removing ?/R/R-2.11.1/library/hgu133a.db? > ERROR: dependencies ?org.Hs.eg.db? are not available for package > ?hgu133b.db? > * removing ?/R/R-2.11.1/library/hgu133b.db? > ERROR: dependencies ?org.Hs.eg.db? are not available for package > ?hgu133plus2.db? > * removing ?/R/R-2.11.1/library/hgu133plus2.db? > > The downloaded packages are in > ?/tmp/RtmpjGYvZn/downloaded_packages? > Updating HTML index of packages in '.Library' > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'org.Hs.eg.db' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'hgu133a2.db' had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'hgu133a.db' had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'hgu133b.db' had non-zero exit status > 5: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'hgu133plus2.db' had non-zero exit status > > [[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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319