[BioC] AnnBuilder URL error.

[John Zhang]

>described by Margaret Gardiner.
>Running the first AnnBuilder vignette (Windows OS, R 2.0.1, BioC 1.5, Active 
>PERL, Environment variables and PATH modified),
>I obtain:
>
>Error in readURL(infoUrl) : Can't read from url:
>ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info

The URL is valid. 

UniGene was down when you were trying to read the file? 
Were you behind a fire wall that prevented you from accessing the URL?

>
>Could someone help me?
>
>Here is the code:
>
>>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
>Warning message:
>'addPDF2Vig' is deprecated.
>Use 'addVigs2WinMenu' instead.
>See help("Deprecated")
>>
>>read.table(file.path(.path.package("AnnBuilder"), "data", "thgu95a"), sep = 
>>"\t", header = FALSE, as.is = TRUE)
>          V1       V2
>1 32468_f_at   D90278
>2   32469_at   L00693
>3   32481_at AL031663
>4   33825_at   X68733
>5   35730_at   X03350
>6   36512_at   L32179
>7   38912_at   D90042
>8   38936_at   M16652
>9   39368_at AL031668
>>myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a")
>>myBaseType <- "gb"
>>
>>
>>mySrcUrls <- c(LL = 
>>"http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz",
>+ UG = "http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz",
>+ GO = "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml")
>>
>>
>>read.table(file.path(.path.package("AnnBuilder"), "data", "srca"),
>+ sep = "\t", header = FALSE, as.is = TRUE)
>          V1   V2
>1 32468_f_at   NA
>2   32469_at    2
>3   32481_at   NA
>4   33825_at    9
>5   35730_at 1576
>6   36512_at   NA
>7   38912_at   10
>8   38936_at   NA
>9   39368_at   NA
>>read.table(file.path(.path.package("AnnBuilder"), "data", "srcb"),
>+ sep = "\t", header = FALSE, as.is = TRUE)
>          V1   V2
>1 32468_f_at   NA
>2   32469_at   NA
>3   32481_at 7051
>4   33825_at   NA
>5   35730_at   NA
>6   36512_at 1084
>7   38912_at   NA
>8   38936_at   NA
>9   39368_at   89
>>myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"),
>+ "data", "srca"), srctwo = file.path(.path.package("AnnBuilder"),
>+ "data", "srcb"))
>>
>>
>>myDir <- "H:/DATI/pkg"
>>
>>ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = 
>>myBaseType,
>+ otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
>+ organism = "human", version = "1.1.0", makeXML = TRUE,
>+ author = list(author = "myname", maintainer = "myname at myemail.com"),
>+ fromWeb = TRUE)
>Error in readURL(infoUrl) : Can't read from url: 
>ftp://ftp.ncbi.nih.gov/repository/UniGene/.info
>>
>
>Thanks a lot.
>
>Giulio Di Giovanni.
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084