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.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
>
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>
>   
>
>
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