Entering edit mode
Richard Friedman
★
2.0k
@richard-friedman-513
Last seen 9.6 years ago
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-t
ermdb.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$OS.type != "windows" && interactive()){
+ ABPkgBuilder(baseName = thgu95a, srcUrls = mySrcUrls,
baseMapType = g,
+ pkgName = "myPkg",
+ pkgPath = myDir, organism = "Homo sapiens", version =
"1.1.0",
+ makeXML = TRUE, author = list(author =
"RichardFriedman",
maintainer =
+ "friedman@cancercenter.columbia.edu"),
fromWeb = TRUE)
+ }
> ls()
[1] "last.warning" "myBase" "myBaseType" "myDir"
"mySrcUrls" "sourceURLs"
> if(.Platform$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@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/
"That was written by Felix Mendelsohn?
Did he start Mendelsohn's Pizza?"
-Rose Friedman, age 8
