







Dear Bioconductor Users,

 

I am trying to use AnnBuilder under
R2.4.1 windows XP professional. Here is a
transcript of my session:

 

>
library(AnnBuilder)

 

Loading required
package: Biobase

 

Loading required
package: tools

 



 

Welcome to
Bioconductor

 



 

    Vignettes contain
introductory material. To view, type

 

    'openVignette()' or
start with 'help(Biobase)'. For details

 

    on reading vignettes,
see the openVignette help page.

 



 

Loading required
package: XML

 

Loading required
package: annotate

 

Loading required
package: RSQLite

 

Loading required
package: DBI

 

>
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<-getOption("AnnBuilderSourceUrls")

 

> mySrcUrls

 

$EG

 

[1]
"ftp://ftp.ncbi.nlm.nih.gov/gene/DATA"

 



 

$GEO

 

[1] "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?"

 



 

$GO

 

[1]
"http://www.godatabase.org/dev/database/archive/latest"

 



 

$GP

 

[1]
"ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes"

 



 

$HG

 

[1]
"ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp"

 



 

$KEGG

 

[1] " ftp://ftp.genome.ad.jp/pub/kegg/pathways"

 



 

$LL

 

[1]
"ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz"

 



 

$UG

 

[1]
"ftp://ftp.ncbi.nih.gov/repository/UniGene"

 



 

$YG

 

[1]
"ftp://genome-ftp.stanford.edu/pub/yeast/data_download/"

 



 

$AT

 

[1]
"ftp://ftp.arabidopsis.org/home/tair/"

 



 

$IPI

 

[1]
"ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/"

 



 

$CMAP

 

[1]
"ftp://ftp1.nci.nih.gov/pub/CMAP/"

 



 

$YEAST

 

[1]
"ftp://ftp.yeastgenome.org/pub/yeast/sequence_similarity/domains/"

 



 

$KEGGGENOME

 

[1]
"ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/genome"

 



 

$PFAM

 

[1]
"ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz"

 



 

>
mySrcUrls<-c(LL="http://www.bioconductor.org/datafiles/wwwsourcers/Tll_tmpl.gz",

 

+
UG="http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz",

 

+
GO="http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml")

 

>
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","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

 

>
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,

 

+ organism="Homo
sapiens",version="1.1.0",author=list(authors="myname",

 

+
maintainer=myname@myemail.com),fromWeb=TRUE)

 

+ }

 

>
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"))

 

+ }

 

> myDir

 

[1]
"C:\\DOCUME~1\\owner_2\\LOCALS~1\\Temp\\RtmpVWomrb"

 

>
list.files(file.path(myDir,"myPkg"))

 

character(0)

 

Warning message:

 

list.files:
'C:\DOCUME~1\owner_2\LOCALS~1\Temp\RtmpVWomrb/myPkg' is not a readable
directory

 



 

Where is the package?If the package was
not created,how can I create it?


 

It would be great, if someone could help
me! Thanks in Advance.


 

Best Wishes,
Qing


 


	[[alternative HTML version deleted]]

