[BioC] oligo package locked database question

[thchung at tgen.org]

Hi, All;

The sessionInfo() was like this:

R version 2.5.1 (2007-06-27) 
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=en_US.UTF-8;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] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"    
[7] "datasets"  "methods"   "base"     

other attached packages:
                oligo                affyio               Biobase 
            "1.0.2-6"               "1.4.1"              "1.14.0" 
BufferedMatrixMethods        BufferedMatrix               RSQLite 
              "1.0.0"               "1.0.1"               "0.5-4" 
                  DBI 
              "0.2-3" 

I've used three different methods to install the annotation package: getBioC, biocLite, and R CMD INSTALL. But all failed. One catch: I've been trying to install it in a server into one of my local folder called "~/Library/R64" using either getBioC("pd.mapping50k.hind240", lib="~/Library/R64") or biocLite("pd.mapping50k.hind240", lib="~/Library/R64") or R CMD INSTALL -l ~/Library/R64 pd.mapping50k.hind240_0.2.8.tar.gz.

-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org]
Sent: Mon 8/6/2007 10:18 PM
To: Tae-Hoon Chung
Cc: Bioconductor list list
Subject: Re: [BioC] oligo package locked database question
 
Hi Tae-Hoon,

It's a bit hard to say what might be the problem.  Can you send us the
sessionInfo() output?  In particular, can you make sure that DBI and
RSQLite are up to date?

I just tried installing pd.mapping50k.hind240 using R 2.6.0 (devel)
and BioC devel packages and it worked fine...

> biocLite("pd.mapping50k.hind240")
[snip]
> library("pd.mapping50k.hind240")
[snip]
> sessionInfo()
R version 2.6.0 Under development (unstable) (--) 
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] splines   tools     stats     graphics  grDevices datasets  utils    
[8] methods   base     

other attached packages:
[1] pd.mapping50k.hind240_0.3.2 oligo_1.1.5                
[3] preprocessCore_0.99.8       BufferedMatrixMethods_1.1.2
[5] BufferedMatrix_1.1.3        affyio_1.5.6               
[7] Biobase_1.15.19             RSQLite_0.6-3              
[9] DBI_0.2-3                  

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/