Ting-Yuan, John actually suggested the same. I guess it's time for another update! Seth, I encountered this problem while I was trying to modify the queryGEO function to download the full soft file and parse the sample information file. As I said in my previous email, it wasn't crucial for me and I could easily circumvent it, but just curious. Thanks, ...Tao --- Ting-Yuan Liu <tliu at="" fhcrc.org=""> wrote: > > Hi Tao, > > As John and Seth mentioned, this is a namespace issue. However, John's > code works on my machine. I notice that you are using R 2.1.1. Please > update your R to 2.2 and then use the following steps to update your > AnnBuilder as well: > > > source("http://bioconductor.org/biocLite.R") > > biocLite("AnnBuilder") > > Here is the sessionInfo on my machine: > > sessionInfo() > R version 2.2.0, 2005-10-31, i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > AnnBuilder annotate XML Biobase > "1.8.0" "1.8.0" "0.99-4" "1.8.0" > > > > HTH, > Ting-Yuan > ______________________________________ > Ting-Yuan Liu > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > Seattle, WA, USA > ______________________________________ > > On Mon, 19 Dec 2005, Shi, Tao wrote: > > > Hi John, > > > > Thanks for your speedy reply! > > > > It's still not working (see below). This is not crucial for me, but I'm just curious why R > can't recognize this function after I load the AnnBuilder package? > > > > ...Tao > > > > > 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 > > > geo <- GEO() > > > AnnBuilder::srcUrl(geo) > > Error: 'srcUrl' is not an exported object from 'namespace:AnnBuilder' > > > > > > > > > > John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > > >Do you know why srcUrl function is not working outside a function such as > > queryGEO? (see below) > > > > try: > > > > >geo <- GEO() > > >AnnBuilder::srcUrl(geo) > > > > > > > > > > > >Thanks, > > > > > >...Tao > > > > > >=================================================== > > >> 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 > > >> geo <- GEO() > > >> srcUrl(geo) > > >Error: couldn't find function "srcUrl" > > > > > >> R.version > > > _ > > >platform i386-pc-mingw32 > > >arch i386 > > >os mingw32 > > >system i386, mingw32 > > >status > > >major 2 > > >minor 1.1 > > >year 2005 > > >month 06 > > >day 20 > > >language R > > > > > >> package.version("AnnBuilder") > > >[1] "1.5.31" > > >> > > > > > > > > >__________________________________________________ > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > >_______________________________________________ > > >Bioconductor mailing list > > >Bioconductor at stat.math.ethz.ch > > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > Jianhua Zhang > > Department of Medical Oncology > > Dana-Farber Cancer Institute > > 44 Binney Street > > Boston, MA 02115-6084 > > > > > > > > > > __________________________________________________ > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >