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

Hi Yong, I agree that some information in this vignette is out-of-dated because the public resources change frequently. We will improve this vignette in the next release. Meanwhile, please remove the argument "srcUrls" while you are using ABPkgBuilder. This should solve your problem IF you are using the latest version of R and AnnBuilder. The R and AnnBuilder you are using right now it also out-of-dated. The latest stable versions of R and AnnBuilder are 2.2.1 and 1.8.0, respectively. Please update them if you have a chance. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Thu, 5 Jan 2006, Yong Jiang wrote: > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >