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@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@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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