[BioC] Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db'; RS-DBI driver -database locked

[Hervé Pagès]

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.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/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]]
>
>
>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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