[BioC] GOstats install error under Linux Debian

[Marc Carlson]

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
>
>   

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_TELEPHONE=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