[BioC] AnnBuilder URL error.
Ting-Yuan Liu
tliu at fhcrc.org
Tue Oct 4 19:58:46 CEST 2005
Hi Johan,
I also post our conversation to the list because the mailing list is
archived regularly and other users can search the archive to get some
useful information.
Again, you have to change all "Homo Sapiens" to "Homo sapiens", including
the one you used in ABPkgBuilder.
I believe "Homo sapiens" is the correct and exact organism name for human
(according to NCBI). Please be careful about the spelling.
HTH,
Ting-Yuan
On Tue, 4 Oct 2005, Johan Lindberg wrote:
> Hi again. I either I am missing the point but it does not work. Look at the
> code further down.
>
> ##################################################################
> mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens")
> 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
> ##################################################################
>
> This generates an error when the Hs.info file is downloaded. That is, using
> Homo sapiens with a small s generates an error. BUT using Homo Sapiens with
> a capital S also generates an error.
>
> ##################################################################>
> mySrcUrls <- getSrcUrl("all", organism = "Homo Sapiens")
> 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 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!
> ##################################################################
>
> This means that both a small s and a capital S in Homo Sapiens/sapiens
> generates an error. Could you please tell me where in the code I could
> change the link to
> ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_Sapiens/Hs.info
> to
> ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.info
>
> ###################################################################
> 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"
> ###################################################################
>
>
> // Johan
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Ting-Yuan Liu
> Sent: Tuesday, October 04, 2005 9:05 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] AnnBuilder URL error.
>
>
> 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
> > >
> >
> >
>
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