[BioC] GOstats install error under Linux Debian

[Thomas Girke]

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