[BioC] srcUrl function in AnnBuilder

[Ting-Yuan Liu]

Hi Tao,

As John and Seth mentioned, this is a namespace issue.  However, John's 
code works on my machine.  I notice that you are using R 2.1.1.  Please 
update your R to 2.2 and then use the following steps to update your 
AnnBuilder as well:

> source("http://bioconductor.org/biocLite.R")
> biocLite("AnnBuilder")

Here is the sessionInfo on my machine:
> sessionInfo()
R version 2.2.0, 2005-10-31, i386-pc-mingw32 

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

other attached packages:
AnnBuilder   annotate        XML    Biobase 
   "1.8.0"    "1.8.0"   "0.99-4"    "1.8.0" 
> 

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Mon, 19 Dec 2005, Shi, Tao wrote:

> Hi John,
> 
> Thanks for your speedy reply!
> 
> It's still not working (see below).  This is not crucial for me, but I'm just curious why R can't recognize this function after I load the AnnBuilder package?
> 
> ...Tao
> 
> > library(AnnBuilder)
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor 
>          Vignettes contain introductory material.  To view, 
>          simply type: openVignette() 
>          For details on reading vignettes, see
>          the openVignette help page.
> Loading required package: XML
> Loading required package: annotate
> > geo <- GEO()
> > AnnBuilder::srcUrl(geo)
> Error: 'srcUrl' is not an exported object from 'namespace:AnnBuilder'
> 
> 
> 
> 
> John Zhang <jzhang at jimmy.harvard.edu> wrote: 
> >Do you know why srcUrl function is not working outside a function such as 
> queryGEO? (see below)
> 
> try:
> 
> >geo <- GEO()
> >AnnBuilder::srcUrl(geo)
> 
> 
> 
> >
> >Thanks,
> >
> >...Tao
> >
> >===================================================
> >> library(AnnBuilder)
> >Loading required package: Biobase
> >Loading required package: tools
> >Welcome to Bioconductor 
> >         Vignettes contain introductory material.  To view, 
> >         simply type: openVignette() 
> >         For details on reading vignettes, see
> >         the openVignette help page.
> >Loading required package: XML
> >Loading required package: annotate
> >> geo <- GEO()
> >> srcUrl(geo)
> >Error: couldn't find function "srcUrl"
> >
> >> R.version
> >         _              
> >platform i386-pc-mingw32
> >arch     i386           
> >os       mingw32        
> >system   i386, mingw32  
> >status                  
> >major    2              
> >minor    1.1            
> >year     2005           
> >month    06             
> >day      20             
> >language R              
> >
> >> package.version("AnnBuilder")
> >[1] "1.5.31"
> >> 
> > 
> >
> >__________________________________________________
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
> 
> 
> 
> 
> __________________________________________________
> 
> 
> 
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