[BioC] GOstats install error under Linux Debian

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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
> 
>  
> 
> 
> 
>