Hey all, I'm having a problem with Annbuilder: > tempConfig <- tempfile() > writeSourceUrlConfig(tempConfig) > root = "http://sioux.fhcrc.org/MIRROR" > urlData = readSourceUrlConfig(tempConfig, root) > origUrls = getOption("AnnBuilderSourceUrls") > geoUrl = origUrls[["GEO"]] > urlData[["GEO"]] = geoUrl > options(AnnBuilderSourceUrls=urlData) > localMirror <- paste(root, "ftp.arabidopsis.org/home/tair/", sep="/") > > ABPkgBuilder(baseName="mpedbadm_genbank.txt", + baseMapType="gbNRef", + pkgName="MPEDB", + organism="Mus musculus", + otherSrc=c(UG="mpedbadm_unigene.txt"), + pkgPath="./", + version="0.1", + author=list(authors="Denise Mauldin", maintainer="Denise Mauldin <dmauldin at="" fhcrc.org="">")) Warning message: Built for UCSC is not valid! in: getUCSCBuilt(organism) Error in parseKEGGGenome() : Faild to obtain KEGG organism code >sessionInfo() R version 2.2.0, 2005-10-06, sparc-sun-solaris2.9 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: AnnBuilder annotate XML Biobase GO "1.8.0" "1.8.0" "0.97-8" "1.8.0" "1.10.0" ---- Warning issue with UCSC: If you browse to the MIRROR directory, it exists and has the Mus_musculus subdirectory. If I look at the code in 1.8.0 Annbuilder for getUCSCBuilt() it says: getUCSCBuilt <- function(organism){ url <- getSrcUrl(src = "GP", organism = organism) built <- NA ifis.na(built) || is.null(built) || built == ""){ warning("Built for UCSC is not valid!") return("N/A") } else { return(built) } } So it seems like this was changed to always be nothing and always throw this error? (The rest of the code has been commented out.) --- Error issue with KEGG However, it doesn't die on that error, it dies on the following KEGG error. This seems to be because even though I altered the URLs, it's using the original URLs (which shouldn't that work anyway?). I then altered my ABPkgBuilder call to include srcUrls = urlData (as that's how the ABPkgBuilder documentation now reads), but this throws a separate error: Error in validObject(.Object) : invalid class "GO" object: invalid object for slot "srcUrl" in class "GO": got class "list", should be or extend class "character" > mode(urlData[["GO"]]) [1] "character" > class(urlData[["GO"]]) [1] "character" > urlData[["GO"]] [1] "http://sioux.fhcrc.org/MIRROR archive.godatabase.org/latest" So this seems to be something in the code in one of the KEGG calls? Anyone have any ideas on what I'm doing wrong? Anyone have any ideas on what to do next? Thanks, Denise

The end of my previous message had an error. The urlData[["GO"]] is actually as follows and still gives the list error. > urlData[["GO"]] [1] "http://sioux.fhcrc.org/MIRROR/archive.godatabase.org/latest" > class(urlData[["GO"]]) [1] "character" > mode(urlData[["GO"]]) [1] "character" Thanks, Denise

Hi Denise, For the UCSC part: It is us to force the build of Golden Path (GP) to be NA in the BioC 1.7 release. Before the 1.7 release, the build of GP is the url of the GP source data. It will cause some problem when running the R CMD check on the annotation packages because there is an "_" in the url. Moreover, it doesn't make sense to put the url again in the built slot because the url is already in the documentation and the build slot is designed for the version (or date, etc) of source data. Before we can find a better information for the GP build slot, please ignore the warning message for a while. For the KEGG part: KEGG anonymous ftp site is too busy (more than 400 users) to be accessed on Monday, October 31, PST. I have the same problem on Monday, and I wrote an email to KEGG for the issue. KEGG fixed the problem on Monday night (PST). Please try again to see if you still have this kind of problem. Sincerely, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Mon, 31 Oct 2005, Denise Mauldin wrote: > > Hey all, > > I'm having a problem with Annbuilder: > > > tempConfig <- tempfile() > > writeSourceUrlConfig(tempConfig) > > root = "http://sioux.fhcrc.org/MIRROR" > > urlData = readSourceUrlConfig(tempConfig, root) > > origUrls = getOption("AnnBuilderSourceUrls") > > geoUrl = origUrls[["GEO"]] > > urlData[["GEO"]] = geoUrl > > options(AnnBuilderSourceUrls=urlData) > > localMirror <- paste(root, "ftp.arabidopsis.org/home/tair/", sep="/") > > > > ABPkgBuilder(baseName="mpedbadm_genbank.txt", > + baseMapType="gbNRef", > + pkgName="MPEDB", > + organism="Mus musculus", > + otherSrc=c(UG="mpedbadm_unigene.txt"), > + pkgPath="./", > + version="0.1", > + author=list(authors="Denise Mauldin", maintainer="Denise Mauldin <dmauldin at="" fhcrc.org="">")) > > Warning message: > Built for UCSC is not valid! in: getUCSCBuilt(organism) > Error in parseKEGGGenome() : Faild to obtain KEGG organism code > > >sessionInfo() > R version 2.2.0, 2005-10-06, sparc-sun-solaris2.9 > > attached base packages: [1] "tools" "methods" "stats" "graphics" > "grDevices" "utils" [7] "datasets" "base" > > other attached packages: > AnnBuilder annotate XML Biobase GO > "1.8.0" "1.8.0" "0.97-8" "1.8.0" "1.10.0" > > > ---- > Warning issue with UCSC: > > If you browse to the MIRROR directory, it exists and has the Mus_musculus > subdirectory. > > If I look at the code in 1.8.0 Annbuilder for getUCSCBuilt() it says: > > getUCSCBuilt <- function(organism){ > url <- getSrcUrl(src = "GP", organism = organism) > > built <- NA > > ifis.na(built) || is.null(built) || built == ""){ > warning("Built for UCSC is not valid!") > return("N/A") > } else { > return(built) > } > } > > So it seems like this was changed to always be nothing and always throw > this error? (The rest of the code has been commented out.) > > --- > Error issue with KEGG > > However, it doesn't die on that error, it dies on the following KEGG > error. This seems to be because even though I altered the URLs, it's > using the original URLs (which shouldn't that work anyway?). I then > altered my ABPkgBuilder call to include srcUrls = urlData (as that's how > the ABPkgBuilder documentation now reads), but this throws a separate > error: > > Error in validObject(.Object) : invalid class "GO" object: invalid object > for slot "srcUrl" in class "GO": got class "list", should be or extend > class "character" > > > mode(urlData[["GO"]]) > [1] "character" > > class(urlData[["GO"]]) > [1] "character" > > urlData[["GO"]] > [1] "http://sioux.fhcrc.org/MIRROR archive.godatabase.org/latest" > > So this seems to be something in the code in one of the KEGG calls? > > Anyone have any ideas on what I'm doing wrong? Anyone have any ideas on > what to do next? > > Thanks, > Denise > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >