[BioC] Error using yeastPkgBuilder (AnnBuilder package)
melany black
melany.black at yahoo.fr
Sat Aug 18 12:48:47 CEST 2007
(sorry for the html in the previous mail)
Hi,
I'm trying to build an annotation package for yeast
chips using AnnBuilder.
I was successful, but at the end, I got an error.
Here's my code:
> library("AnnBuilder")
> read.table(file.path(.path.package("AnnBuilder"),
"data", "yeastsgd"),sep = "\t", header = FALSE, as.is
= TRUE)[1:5,]
V1 V2
1 A_75_00001 S000005688
2 A_75_00002 S000005689
3 A_75_00003 S000005690
4 A_75_00004 S000005691
5 A_75_00005 S000005692
> myBase <- file.path(.path.package("AnnBuilder"),
"data", "yeastsgd")
> myDir <- tempdir()
>
yeastPkgBuilder(pkgName="yeastAgilent",pkgPath=myDir,base=myBase,version
= "1.1.0",author = list(authors = "mel", maintainer
="mel.black at yahoo.fr"), fromWeb=TRUE)
package directory structure initialized
annotation data read complete
1:1 PROBE mappings complete
1:many PROBE mappings complete
CHRLOC complete
Error in l2e(dList, env) : require a list
Warning messages:
1: Organism Saccharomyces cerevisiae is not supported
by GoldenPath (GP). in: getUCSCUrl(organism)
2: no argument for max ; -Inf is returned in: max(i)
The following files were created in
"yeastAgilent\data" folder:
yeastAgilentALIAS.rda
yeastAgilentCHR.rda
yeastAgilentCHRLOC.rda
yeastAgilentDESCRIPTION.rda
yeastAgilentGENENAME.rda
yeastAgilentORF.rda
yeastAgilentPMID.rda
Hope someone could explain me where this error comes
from, and how to fix it.
> sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32
locale:
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
attached base packages:
[1] "tools" "stats" "graphics" "grDevices"
"utils" "datasets" "methods" "base"
other attached packages:
GO AnnBuilder annotate XML Biobase
"1.16.0" "1.14.0" "1.14.1" "1.9-0" "1.14.1"
Mel.
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