[BioC] help aobut AnnBuilder

[Yong Jiang]

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