Entering edit mode
Yong Jiang
▴
30
@yong-jiang-1558
Last seen 10.2 years ago
Hi,
i followed the manual of AnnBuilder
(http://bioconductor.org/repository/devel/vignette/ABPrimer.pdf) and
also the script showed in the AnnBuilder package. no sucess. here is
the
error msg and output.
> 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: XML
Loading required package: annotate
> read.table(file.path(.path.package("AnnBuilder"), "data",
"thgu95a"),sep = "\t", head
er = 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 <- c(EG =
"ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz",UG = "ftp://
ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz",GP =
"http://www.genome.ucsc.edu/golden
Path/14nov2002/database/", GO =
"http://archive.godatabase.org/latest/go_200512-termdb-
data.gz", KEGG = "ftp://ftp.genome.ad.jp/pub/kegg/pathways")
> mySrcUrls <- getOption("AnnBuilderSourceUrls")
> mySrcUrls
NULL
> mySrcUrls <- c(EG =
"ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz",UG = "ftp://
ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz",GP =
"http://www.genome.ucsc.edu/golden
Path/14nov2002/database/", GO =
"http://archive.godatabase.org/latest/go_200512-termdb-
data.gz", KEGG = "ftp://ftp.genome.ad.jp/pub/kegg/pathways")
> mySrcUrls
EG
"ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz"
UG
"ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz"
GP
"http://www.genome.ucsc.edu/goldenPath/14nov2002/database/"
GO
"http://archive.godatabase.org/latest/go_200512-termdb-data.gz"
KEGG
"ftp://ftp.genome.ad.jp/pub/kegg/pathways"
> 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",
"srcb"),sep
= "\t", header
= FALSE, as.is = TRUE)
V1 V2
1 32468_f_at NA
2 32469_at NA
3 32481_at 7051
4 33825_at NA
5 35730_at NA
6 36512_at 1084
7 38912_at NA
8 38936_at NA
9 39368_at 89
> myOtherSrc <- c(srcone =
file.path(.path.package("AnnBuilder"),"data",
"srca"), srctwo = file.path(.path.package("AnnBuilder"),"data",
"srcb"))
> myDir <- tempdir()
> if (.Platform$OS.type != "windows" && interactive()) {
+ + ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
myBaseType,
+ + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
Error: syntax error
> + organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE,
Error: syntax error
> + author = list(author = "myname", maintainer = "myname at
myemail.com"),
Error: syntax error
> + fromWeb = TRUE)
Error: syntax error
> if (.Platform$OS.type != "windows" && interactive()) {
+ ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
myBaseType,
+ otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
+ organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE,
+ author = list(author = "myname", maintainer = "myname at
myemail.com"),
+ fromWeb = TRUE)
+ }
Error in gsub(pattern, replacement, x, ignore.case, extended, fixed) :
invalid regular expression '*.*/(*.*)'
R version 2.1.1, getBioC version 0.8, AnnBuilder_1.5.31.
any suggestion ?
thanks in advance.
yong