[BioC] AnnBuilder URL error.

[Ting-Yuan Liu]

Hi Johan,

Try "Homo sapiens" instead of "Homo Sapiens":

> 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
> mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens")
> mySrcUrls["UG"]
                                                                 UG
"ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz"
> sessionInfo()
R version 2.2.0, 2005-10-03, x86_64-unknown-linux-gnu

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

other attached packages:
AnnBuilder   annotate        XML    Biobase
  "1.6.31"    "1.6.3"   "0.97-0"    "1.6.7"
>

I will modify the documentation in order to clarify this.  

HTH,
Ting-Yuan

On Tue, 4 Oct 2005, Johan Lindberg wrote:

> 
> Ok, thanks Ting-Yuan. 
> I have now downloaded the devel version 1.6.31 of AnnBuilder but there is
> still a bug in the link. 
> 
> ######################################
> mySrcUrls <- getSrcUrl("all", organism = "Homo Sapiens")
> mySrcUrls[2]
> 
> UG 
> "ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_Sapiens/Hs.data.gz"
> ######################################
> 
> This link is wrong since it has a capital S in sapiens but when you look at
> UniGene the s in Sapiens is not capital. When I change it as before in 
> 
> ######################################
> mySrcUrls[2]
> <-"ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz"
> 
> ABPkgBuilder(baseName="C:/R/rw2011/emp/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/Homo_Sapiens/Hs.info
> ######################################
> 
> Then I get an error in Hs.info instead since the capital S is still there 
> How can I change this? 
> Thank you for your help.
> 
> ######################################
> > sessionInfo()
> R version 2.1.1, 2005-06-20, i386-pc-mingw32 
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"  "base"     
> 
> other attached packages:
>         GO AnnBuilder        XML   annotate    Biobase 
>    "1.8.2"   "1.6.31"   "0.97-7"   "1.5.16"   "1.5.12"
> ######################################
> 
> Best regards
> 
> // Johan
> 
> 
> 
> 
> -----Original Message-----
> From: Ting-Yuan Liu [mailto:tliu at fhcrc.org] 
> Sent: Tuesday, October 04, 2005 5:43 AM
> To: Johan Lindberg
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] AnnBuilder URL error.
> 
> 
> 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
> >  
> >  
> > 
> > 	[[alternative HTML version deleted]]
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
>