[BioC] I have trouble running the AnnBuilder Vignette

[Richard Friedman]

Dear Bioconductor Users,

	I am trying to learn to use AnnBuilder in Bioconductor 1.5.0
under R2.0 under Windows XP Professional. Here is a transcript
of my session:
###################################################################
> library(XML)
> 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: 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 <- getSrcUrl("all", organism = "Homo sapiens")
> mySrcUrls

LL

"ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz"

GP

"http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/"

UG

"ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz"

GO
"http://www.godatabase.org/dev/database/archive/2004-09-01/go_200409-termdb.xml.gz"

KEGG

"ftp://ftp.genome.ad.jp/pub/kegg/pathways"

YG

"http://www.yeastgenome.org/DownloadContents.shtml"

HG

"ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp"
>
> myDir <- tempdir()
> if(.Platform$OS.type != "windows" && interactive()){
+         ABPkgBuilder(baseName = thgu95a, srcUrls = mySrcUrls,
baseMapType = g,
+              pkgName = "myPkg",
+              pkgPath = myDir, organism = "Homo sapiens", version =
"1.1.0",
+              makeXML = TRUE, author = list(author = "RichardFriedman",
maintainer =
+                              "friedman at cancercenter.columbia.edu"),
fromWeb = TRUE)
+ }
> ls()
[1] "last.warning" "myBase"       "myBaseType"   "myDir"
"mySrcUrls"    "sourceURLs"
> if(.Platform$OS.type != "windows"  && interactive()){
+         list.files(file.path(myDir, "myPkg"))
+         list.files(file.path(myDir, "myPkg", "data"))
+         list.files(file.path(myDir, "myPkg", "man"))
+         list.files(file.path(myDir, "myPkg", "R"))
+     }
>
>
> list.files(file.path(myDir, "myPkg"))
Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg is
not a readable directory
character(0)
> list.files(file.path(myDir, "myPkg", "data"))
Warning: list.files:
C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg/data is not a readable
directory
character(0)
##############################################################################

Apparently the package was not created.
Am I correct in this?
If the package was created, how can I access it?
If the package was not created, how can I create it?

Thanks and best wieshes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"That was written by Felix Mendelsohn?
Did he start Mendelsohn's Pizza?"
-Rose Friedman, age 8