[BioC] GOstats install error under Linux Debian
Herve Pages
hpages at fhcrc.org
Wed Oct 10 03:27:05 CEST 2007
Thomas Girke wrote:
> Hi Herve and Marc,
>
> Thanks for your quick response. Below is the addition system info:
>
> GO.db doesn't load in R. When I try it then it hangs for several minutes and prints out the
> following error message:
>
> ###############################################
>> 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
> 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/namespace load failed for 'GO.db'
> ###############################################
>
>
> Since GO.db doesn't load in R, there is no sessionInfo() for it, but the shell command
> cat /usr/local/lib/R/site-library/GO.db/DESCRIPTION
> returns the following message:
>
> ###############################################
> Package: GO.db
> Title: A set of annotation maps describing the entire Gene Ontology
> Description: A set of annotation maps describing the entire Gene
> Ontology assembled using data from GO
> Version: 2.0.0
> Author: Marc Carlson, Seth Falcon, Herve Pages, Nianhua Li
> Maintainer: Biocore Data Team <biocannotation at lists.fhcrc.org>
> Depends: R (>= 2.6.0), methods, AnnotationDbi (>= 1.0.1)
> Imports: methods, AnnotationDbi
> License: The Artistic License, Version 2.0
> biocViews: AnnotationData, FunctionalAnnotation
> Packaged: Thu Oct 4 18:45:14 2007; hpages
> Built: R 2.6.0; ; 2007-10-09 15:39:00; unix
> ###############################################
>
> My permissions for GO.sqlite are:
> ls -l /usr/local/lib/R/site-library/GO.db/extdata/GO.sqlite
>
> -rw-r--r-- 1 tgirke Users 38252544 Oct 9 15:39 /usr/local/lib/R/site-library/GO.db/extdata/GO.sqlite
>
> When I try to open it with the following command then sqlite3 just hangs until I kill it:
> sqlite3 /usr/local/lib/R/site-library/GO.db/extdata/GO.sqlite
Mmmh, it looks like the DB is locked by another process. I have no idea why this
would happen, unless one process is actually trying to modify the DB (this is not
a normal situation though). Do you have another R session opened?
Anyway, we definitely want people to be able to open several concurrent
connections to the same DB. An we also want different users to be able to
share a system-wide DB when it's installed under some shared location like
/usr/local/lib/R/site-library/
I'm hoping that having the GO.sqlite file read-only will do the trick. I've
put a new GO.db source package here:
http://bioconductor.org/packages/misc/GO.db_2.0.1.tar.gz
The GO.sqlite file in this tarball is read-only. Can you install it and let us know
if this solves your problem? (download the tarball and use 'R CMD INSTALL' on it,
quit all your R sessions before you do this). If it does, then we'll need to fix
all our .db packages. Thanks!
H.
>
>
> Thanks,
>
> Thomas
>
>
> On Tue 10/09/07 16:56, Herve Pages wrote:
>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
More information about the Bioconductor
mailing list