[BioC] AnnBuilder downloadSourceData()

Ting-Yuan Liu tliu at fhcrc.org
Wed Oct 12 09:09:47 CEST 2005

Hi Denise,

First of all, could you please report the output of sessionInfo()?  This 
information is critical for people to determine the possible sources of 

getPubDataXXX are in the file "downloadSourceData.R" which locates at the 
AnnBuilder/R subdirectory.  There is a file called 
"mirroringDataResources.rst" in AnnBuilder/inst/doc.  You can get more 
details about how to use downloadSourceData() in this document.  

BTW, here is my sessionInfo() output:
> sessionInfo()
R version 2.2.0, 2005-10-05, x86_64-unknown-linux-gnu

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
AnnBuilder   annotate        XML    Biobase
  "1.6.38"    "1.6.5"   "0.97-0"    "1.7.6"

Please remember to update your R/packages if you are using old R/packages.  
This might help to solve your question.


On Mon, 10 Oct 2005, Denise Mauldin wrote:

> Hey all,
> My AnnBuilder makeSourceData() function won't work because wget requires 
> the --passive-ftp in order to download from ftp.ncbi.nih.gov, however,  I 
> can't seem to find the getPubDataXXX functions anywhere in the the 
> AnnBuilder directory other than help files.
> Can anyone tell me where I can find the code for the getPubDataXXX 
> functions (getPubDataGo?)?  Is there a way in R to get it to print out the 
> location of the files that it's using?
> Thanks,
> Denise
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