[BioC] AnnBuilder URL error.

[Ting-Yuan Liu]

Hi Johan,

This problem has been solved for several weeks.  If you install the 
development version of AnnBuilder, you won't run into this kind of error.  
You can find the development version of AnnBuilder here:
http://www.bioconductor.org/packages/bioc/devel/src/contrib/html/

When you post any question next time, please remember to post the result 
of sessionInfo() as well.  It will be helpful for people to determine the 
problems with this information.  

HTH,
Ting-Yuan

On Mon, 3 Oct 2005, Johan Lindberg wrote:

> Hi all. I know there has been a lot debated about AnnBuilders URL:s and I
> tried to find some thread on the list that would help me. If this has
> already been answered I apologize and please direct me to that thread.
>  
> As you probably know the unigeneLink in "sourceURLs.txt" is wrong. 
>  
> It is today "UG ftp://ftp.ncbi.nih.gov/repository/UniGene "
>  
> If I use that I get the following error message:
>  
> mySrcUrls <- getSrcUrl("all", organism = "Homo Sapiens")
> ABPkgBuilder(baseName="C:/R/rw2011/temp/GBbatch1to5.txt", srcUrls=mySrcUrls,
> baseMapType = "gb",pkgName="Hum30kbatch1to5",
> pkgPath="C:\R\rw2011\temp\humbatch1to5", organism = "Homo Sapiens", version
> = "1.1.0", author = list(author = "Johan Lindberg", maintainer =
> "johanl at biotech.kth.se"), fromWeb = TRUE)
>  
> Error in loadFromUrl(srcUrls[i]) : URL
> ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz is incorrect or the
> target site is not responding!
>  
> Which is explained if of go into ftp://ftp.ncbi.nih.gov/repository/UniGene/
> where they have put the human stuff into
> ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/ so if I change the
> link to
>  
>  
> > mySrcUrls[2] <-
> "ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz"
>  
> > ABPkgBuilder(baseName="C:/R/rw2011/temp/GBbatch1to5.txt",
> srcUrls=mySrcUrls, baseMapType = "gb",pkgName="Hum30kbatch1to5",
> pkgPath="C:\R\rw2011\temp\humbatch1to5", organism = "Homo Sapiens", version
> = "1.1.0", author = list(author = "Johan Lindberg", maintainer =
> "johanl at biotech.kth.se"), fromWeb = TRUE)
> Error in readURL(infoUrl) : Can't read from url:
> ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info
>  
> Then the file Hs.data.gz will be downloaded correctly but not the Hs.info.
>  
> As you understand the Hs.info is in
> ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.info
>  
> and not ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info
>  
> How do I solve this? Perhaps someone can direct me where I can change the
> URL in order to get it to work.
>  
> Thank you for your help.
>  
> Best Regards
>  
> // Johan Lindberg
>  
>  
> 
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