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Question: GOstats install error under Linux Debian
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gravatar for Thomas Girke
11.2 years ago by
Thomas Girke1.7k
United States
Thomas Girke1.7k 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/GOst ats_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 -- Thomas Girke Assistant Professor of Bioinformatics Director, IIGB Bioinformatic Facility Center for Plant Cell Biology (CEPCEB) Institute for Integrative Genome Biology (IIGB) Department of Botany and Plant Sciences 1008 Noel T. Keen Hall University of California Riverside, CA 92521 E-mail: thomas.girke at ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-827-2469 Fax: 951-827-4437
ADD COMMENTlink modified 11.2 years ago by Marc Carlson7.2k • written 11.2 years ago by Thomas Girke1.7k
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gravatar for Hervé Pagès
11.2 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k 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/GO stats_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 > > > > > >
ADD COMMENTlink written 11.2 years ago by Hervé Pagès ♦♦ 13k
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 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 > > > > > > > > > > > > > > -- Thomas Girke Assistant Professor of Bioinformatics Director, IIGB Bioinformatic Facility Center for Plant Cell Biology (CEPCEB) Institute for Integrative Genome Biology (IIGB) Department of Botany and Plant Sciences 1008 Noel T. Keen Hall University of California Riverside, CA 92521 E-mail: thomas.girke at ucr.edu Website: http://faculty.ucr.edu/~tgirke Ph: 951-827-2469 Fax: 951-827-4437
ADD REPLYlink written 11.2 years ago by Thomas Girke1.7k
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 >>> >>> >>> >>> >>> >>> >> >
ADD REPLYlink written 11.2 years ago by Hervé Pagès ♦♦ 13k
0
gravatar for Marc Carlson
11.2 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
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/GO stats_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 > > Hi Thomas, Do you think you could give us your sessionInfo() after you have loaded GO.db? So for me: library("GO.db") sessionInfo() Gives me: > 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 > sessionInfo() R version 2.6.0 alpha (2007-09-13 r42838) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GO.db_2.0.0 AnnotationDbi_1.0.4 RSQLite_0.6-3 [4] DBI_0.2-3 Biobase_1.16.0 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 Specifically, I am wondering what version of GO.db you have installed? Marc
ADD COMMENTlink written 11.2 years ago by Marc Carlson7.2k
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