[BioC] srcUrl function in AnnBuilder

[Shi, Tao]

Ting-Yuan,

John actually suggested the same.  I guess it's time for another update!


Seth,

I encountered this problem while I was trying to modify the queryGEO function to download the full
soft file and parse the sample information file.  As I said in my previous email, it wasn't
crucial for me and I could easily circumvent it, but just curious.

Thanks,

...Tao




--- Ting-Yuan Liu <tliu at fhcrc.org> wrote:

> 
> 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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> > 
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>