[BioC] Can't load the arabidopsis.db annotation package created in AnnotationDbi

[Groot, Philip de]

Oops,
 
Sorry, I should have known! Here you have it:
 
> library(ath1attair.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
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: no such table: chrlengths)
Error : .onLoad failed in 'loadNamespace' for 'ath1attair.db'
Error: package/namespace load failed for 'ath1attair.db'
> sessionInfo()
R version 2.8.0 (2008-10-20) 
x86_64-unknown-linux-gnu 
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     
other attached packages:
[1] RSQLite_0.7-0       DBI_0.2-4           AnnotationDbi_1.4.0
[4] Biobase_2.2.0      
> 

What I think that is going on is that no chrlength information is available and hence the generation of this table is skipped. However, on library load it is still checked whether this table is available...
 
Regards,
 
Philip

________________________________

Van: seandavi at gmail.com namens Sean Davis
Verzonden: ma 3-11-2008 17:16
Aan: Groot, Philip de
CC: bioconductor at stat.math.ethz.ch
Onderwerp: Re: [BioC] Can't load the arabidopsis.db annotation package created in AnnotationDbi




On Mon, Nov 3, 2008 at 11:10 AM, Groot, Philip de <philip.degroot at wur.nl> wrote:


	Hello all,
	
	I created an arabidopsis library based on the MBNI custom CDF version 10 (TAIR), see http://nugo-r.bioinformatics.nl/NuGO_R.html. In BioC 2.2 all works very well. However, when trying to load the package in R-2.8.0/BioC 2.3, I get the following error message:
	
	> library(ath1attair.db)
	Loading required package: DBI
	Error in sqliteExecStatement(con, statement, bind.data) :
	 RS-DBI driver: (error in statement: no such table: chrlengths)
	Error : .onLoad failed in 'loadNamespace' for 'ath1attair.db'
	Error: package/namespace load failed for 'ath1attair.db'
	
	
	Rebuilding the library with the "makeARABIDOPSISCHIP_DB" function did not solve the problem. The library installs without error message, but fails to load.
	
	The error message is obvious (no chrlengths table), but how can I solve this problem?
	


Hi, Philip.  I think you will need to include your sessionInfo() so that folks can see versions of AnnotationDbi, RSQLite, etc.

Sean