[BioC] I have trouble running the AnnBuilder Vignette

[John Zhang]

The files were certainly not created since the code did not get to run under 
Windows. You have to remove "if(.Platform$OS.type != "windows" && 
interactive()){" when you rn ABPkgBuilder(...). Since human interference is 
required to finish the vignette, I have to put the checking there to make the 
vignette pass the building process under Windows. 


>Date: Wed, 10 Nov 2004 15:22:23 -0500 (EST)
>From: Richard Friedman <friedman at cancercenter.columbia.edu>
>To: bioconductor at stat.math.ethz.ch
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>Subject: [BioC] I have trouble running the AnnBuilder Vignette
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>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
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084