[BioC] AnnBuilder URL

[Ting-Yuan Liu]

Hi Toni,

First, your R is version 2.1.0 which is out-of-dated.  Please update it to 
the latest version, 2.2.0.

Second, one suggestion I gave to Anja regarding to the post on Dec 7 is 
removing the argument "srcUrls=mySrcUrls" because AnnBuilder will do this 
for you automatically.  

Third, you have a typo in the argument "author".  It should be

author=list(authors="Toni Juli", maintainer="Toni 
Juli <ajulia[AT]vhebron.net>")

See the typo?  (There could be more than one author for a package.) If 
this is a typo somewhere in the examples/vignettes, please let me know 
and I will fix them in the next release.  

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, Toni Julià wrote:

> Hi,
>  
> Ive been trying to create an annotation package using AnnBuilder but an
> error keeps appearing:
>  
> Warning message:
> Built for UCSC is not valid! in: getUCSCBuilt(organism) 
> Error in loadFromUrl(srcUrls[i]) : URL
> ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz is
> incorrect or the target site is not responding!
>  
> On Wed, 7 Dec 2005, Anja Schiel also posted the same problem using mouse
> annotation. At that time the unavailability of the Unigene site was the
> problem but in this case the URL can be directly accessed with no problem.
> My ABPkgBuilder function and system info are:
>  
> mySrcUrls <- getSrcUrl("all", "Homo sapiens")
>  
> ABPkgBuilder(baseName = myBase,  baseMapType = myBaseType, srcUrls =
> mySrcUrls, pkgName = "Human.annot" , pkgPath = mydir, organism ="Homo
> sapiens", version = "1.1.0", author = list(author= "Toni Juli", maintainer
> = "ajulia[AT]vhebron.net"), fromWeb=T)  
>  
>  
> sessionInfo()
> R version 2.1.0, 2005-04-18, i386-pc-mingw32 
>  
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"    
> [7] "datasets"  "base"     
>  
> other attached packages:
>         GO AnnBuilder   annotate        XML    Biobase 
>    "1.8.2"    "1.8.0"   "1.5.16"   "0.97-8"   "1.5.12"
>  
>  
> What could be going wrong?
>  
> Thanks for your help!
>  
>  
> Toni
>  
>  
>  
>  
> Antonio Juli 
> Unitat de Recerca de Reumatologia (URR)
> Hospital Universitari Vall d'Hebron 
> Pg Vall d'Hebron, 119-129
> 08035, Barcelona, SPAIN
> Tel: + 34 93 274 6200
> e-mail: ajulia at vhebron.net
>  
> 
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> 
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