Thomas Girke wrote: > Hi Herve and Marc, > > Thanks for your quick response. Below is the addition system info: > > GO.db doesn't load in R. When I try it then it hangs for several minutes and prints out the > following error message: > > ############################################### >> library(GO.db) > Loading required package: AnnotationDbi > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: DBI > Loading required package: RSQLite > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: database is locked) > Error : .onLoad failed in 'loadNamespace' for 'GO.db' > Error: package/namespace load failed for 'GO.db' > ############################################### > > > Since GO.db doesn't load in R, there is no sessionInfo() for it, but the shell command > cat /usr/local/lib/R/site-library/GO.db/DESCRIPTION > returns the following message: > > ############################################### > Package: GO.db > Title: A set of annotation maps describing the entire Gene Ontology > Description: A set of annotation maps describing the entire Gene > Ontology assembled using data from GO > Version: 2.0.0 > Author: Marc Carlson, Seth Falcon, Herve Pages, Nianhua Li > Maintainer: Biocore Data Team <biocannotation at="" lists.fhcrc.org=""> > Depends: R (>= 2.6.0), methods, AnnotationDbi (>= 1.0.1) > Imports: methods, AnnotationDbi > License: The Artistic License, Version 2.0 > biocViews: AnnotationData, FunctionalAnnotation > Packaged: Thu Oct 4 18:45:14 2007; hpages > Built: R 2.6.0; ; 2007-10-09 15:39:00; unix > ############################################### > > My permissions for GO.sqlite are: > ls -l /usr/local/lib/R/site-library/GO.db/extdata/GO.sqlite > > -rw-r--r-- 1 tgirke Users 38252544 Oct 9 15:39 /usr/local/lib/R /site-library/GO.db/extdata/GO.sqlite > > When I try to open it with the following command then sqlite3 just hangs until I kill it: > sqlite3 /usr/local/lib/R/site-library/GO.db/extdata/GO.sqlite Mmmh, it looks like the DB is locked by another process. I have no idea why this would happen, unless one process is actually trying to modify the DB (this is not a normal situation though). Do you have another R session opened? Anyway, we definitely want people to be able to open several concurrent connections to the same DB. An we also want different users to be able to share a system-wide DB when it's installed under some shared location like /usr/local/lib/R/site-library/ I'm hoping that having the GO.sqlite file read-only will do the trick. I've put a new GO.db source package here: http://bioconductor.org/packages/misc/GO.db_2.0.1.tar.gz The GO.sqlite file in this tarball is read-only. Can you install it and let us know if this solves your problem? (download the tarball and use 'R CMD INSTALL' on it, quit all your R sessions before you do this). If it does, then we'll need to fix all our .db packages. Thanks! H. > > > Thanks, > > Thomas > > > On Tue 10/09/07 16:56, Herve Pages wrote: >> Hi Thomas, >> >> The problem seems to be with your GO.db package and it seems that you >> have it installed under /usr/local/lib/R/site-library >> Can you load it? >> Which version are you using? (sessionInfo() if you were able to load it >> or 'cat /usr/local/lib/R/site-library/GO.db/DESCRIPTION' from the shell >> if not). >> What are the permissions of the embedded DB? >> ls -l /usr/local/lib/R/site-library/GO.db/extdata/GO.sqlite >> Can you open it with >> sqlite3 /usr/local/lib/R/site-library/GO.db/extdata/GO.sqlite >> >> Thanks! >> H. >> >> >> Thomas Girke wrote: >>> I am experiencing problems with the installation of the new GOstats package under Debian "etch" Linux. >>> The installation of all the standard biocLite() BioC 2.1 packages worked fine under R 2.6.0. >>> >>> The manual installation of GOstats and all its dependency packages didn't solve the problem either. >>> >>> The session info and error messages are printed below. >>> >>> Thanks in advance for any suggestions to solve this problem. >>> >>> Best, >>> >>> Thomas >>> >>> ################# >>> ## sessionInfo ## >>> ################# >>>> sessionInfo() >>> R version 2.6.0 (2007-10-03) >>> x86_64-pc-linux-gnu >>> >>> locale: >>> C >>> >>> attached base packages: >>> [1] tools stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] AnnotationDbi_1.0.4 RSQLite_0.6-3 DBI_0.2-3 Biobase_1.16.0 GO_2.0.0 >>> >>> loaded via a namespace (and not attached): >>> [1] rcompgen_0.1-15 >>> >>> >>> #################### >>> ## Error Messages ## >>> #################### >>>> source("http://bioconductor.org/biocLite.R") >>>> biocLite("GOstats") >>> Running biocinstall version 2.1.7 with R version 2.6.0 (under development) >>> Your version of R requires version 2.1 of Bioconductor. >>> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : >>> argument 'lib' is missing: using '/usr/local/lib/R/site-library' >>> trying URL 'http://bioconductor.org/packages/2.1/bioc/src/contrib/ GOstats_2.4.0.tar.gz' >>> Content type 'application/x-gzip' length 2187872 bytes (2.1 Mb) >>> opened URL >>> ================================================== >>> downloaded 2.1 Mb >>> >>> * Installing *source* package 'GOstats' ... >>> ** R >>> ** data >>> ** inst >>> ** preparing package for lazy loading >>> Loading required package: graph >>> Loading required package: GO.db >>> Loading required package: AnnotationDbi >>> Loading required package: Biobase >>> Loading required package: tools >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>> Loading required package: DBI >>> Loading required package: RSQLite >>> Error in sqliteExecStatement(con, statement, bind.data) : >>> RS-DBI driver: (error in statement: database is locked) >>> Error : .onLoad failed in 'loadNamespace' for 'GO.db' >>> Error: package 'GO.db' could not be loaded >>> Execution halted >>> ERROR: lazy loading failed for package 'GOstats' >>> ** Removing '/usr/local/lib/R/site-library/GOstats' >>> >>> The downloaded packages are in >>> /tmp/Rtmp7w5IVh/downloaded_packages >>> Warning message: >>> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : >>> installation of package 'GOstats' had non-zero exit status >>> >>> >>> >>> >>> >>> >> >