[BioC] GOstats install error under Linux Debian
Thomas Girke
thomas.girke at ucr.edu
Wed Oct 10 02:35:46 CEST 2007
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
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