[BioC] help aobut AnnBuilder

[Ting-Yuan Liu]

Hi Yong,

I agree that some information in this vignette is out-of-dated because the 
public resources change frequently.  We will improve this vignette in the 
next release.  

Meanwhile, please remove the argument "srcUrls" while you are using 
ABPkgBuilder.  This should solve your problem IF you are using the latest 
version of R and AnnBuilder.  

The R and AnnBuilder you are using right now it also out-of-dated.  The 
latest stable versions of R and AnnBuilder are 2.2.1 and 1.8.0, 
respectively.  Please update them if you have a chance.  

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Thu, 5 Jan 2006, Yong Jiang wrote:

> Hi, 
> i followed the manual of AnnBuilder
> (http://bioconductor.org/repository/devel/vignette/ABPrimer.pdf) and
> also the script showed in the AnnBuilder package. no sucess. here is the
> error msg and output.
> 
> > 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
> > read.table(file.path(.path.package("AnnBuilder"), "data",
> "thgu95a"),sep = "\t", head
> er = 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(EG =
> "ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz",UG = "ftp://
> ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz",GP =
> "http://www.genome.ucsc.edu/golden
> Path/14nov2002/database/", GO =
> "http://archive.godatabase.org/latest/go_200512-termdb-
> data.gz", KEGG = "ftp://ftp.genome.ad.jp/pub/kegg/pathways")
> > mySrcUrls <- getOption("AnnBuilderSourceUrls")
> > mySrcUrls
> NULL
> > mySrcUrls <- c(EG =
> "ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz",UG = "ftp://
> ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz",GP =
> "http://www.genome.ucsc.edu/golden
> Path/14nov2002/database/", GO =
> "http://archive.godatabase.org/latest/go_200512-termdb-
> data.gz", KEGG = "ftp://ftp.genome.ad.jp/pub/kegg/pathways")
> > mySrcUrls
>                                                              EG
>            "ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz"
>                                                              UG
>          "ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz"
>                                                              GP
>     "http://www.genome.ucsc.edu/goldenPath/14nov2002/database/"
>                                                              GO
> "http://archive.godatabase.org/latest/go_200512-termdb-data.gz"
>                                                            KEGG
>                      "ftp://ftp.genome.ad.jp/pub/kegg/pathways"
> > 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 <- tempdir()
> > if (.Platform$OS.type != "windows" && interactive()) {
> + + ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> myBaseType,
> + + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
> Error: syntax error
> > + organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE,
> Error: syntax error
> > + author = list(author = "myname", maintainer = "myname at myemail.com"),
> Error: syntax error
> > + fromWeb = TRUE)
> Error: syntax error
> > if (.Platform$OS.type != "windows" && interactive()) {
> + ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> myBaseType,
> + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
> + organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE,
> + author = list(author = "myname", maintainer = "myname at myemail.com"),
> + fromWeb = TRUE)
> + }
> Error in gsub(pattern, replacement, x, ignore.case, extended, fixed) :
>         invalid regular expression '*.*/(*.*)'
> 
>  
> R version  2.1.1, getBioC version 0.8,   AnnBuilder_1.5.31. 
> 
> any suggestion ?
> 
> thanks in advance.
> 
> yong
> 
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