Hello, I am running AnnBuilder 1.8.o and GO 1.10.0 in R 2.2.0 and when trying to built an annotation always end up with this error: ABPkgBuilder(baseName=ASBase, srcUrls =ASSrcUrls, baseMapType = ASBaseType, pk gName="Sigma Oligo 071205", pkgPath=ASDir, organism="Mus musculus", version="1.1 .0", author = list(author = "Anja E. Schiel", maintainer ="Anja E. Schiel<a.e.sc hiel="" at="" lumc.nl="">")) Attaching package: 'GO' The following object(s) are masked from package:AnnBuilder : GO Warning message: Built for UCSC is not valid! in: getUCSCBuilt(organism) Error in loadFromUrl(srcUrls[i]) : URL ftp://ftp.ncbi.nih.gov/repository/UniGene /Mus_musculus/Mm.data.gz is incorrect or the target site is not responding! If I try to go directly to the Url it won't work either. My list after > getSrcUrl("ALL", organism"Mus musculus") looks like this. GP "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/ database/" UG "ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz" GO "http://www.godatabase.org/dev/database/archive/latest/go_200512-termd b.rdf-xml.gz" KEGG "ftp://ftp.genome.ad.jp/pub/kegg/pathways" YG "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/" HG "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" EG "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA" IPI "ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/" I can clearly not connect to the ncbi Url, but have I done something wrong or has this something to do with a change in the database? I searched the archive but didn't find an answer. Thanks for you support! Anja

Hi Anja, If you try again the NCBI link, it should work now. I just try it and it works fine. I think that's because the NCBI ftp site was unavailable temporarily, for some reason, when you were using AnnBuilder. Let me know if you still cannot use it correctly. One more suggestion: Please do not use any "space" in the package name. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ We should live by the second, as each second is a critical period to pass through. ---Master Cheng Yen On Wed, 7 Dec 2005, Anja Schiel wrote: > Hello, > I am running AnnBuilder 1.8.o and GO 1.10.0 in R 2.2.0 and when trying > to built an annotation always end up with this error: > > > ABPkgBuilder(baseName=ASBase, srcUrls =ASSrcUrls, baseMapType = > ASBaseType, pk gName="Sigma Oligo 071205", pkgPath=ASDir, organism="Mus > musculus", version="1.1 .0", author = list(author = "Anja E. Schiel", > maintainer ="Anja E. Schiel<a.e.sc hiel="" at="" lumc.nl="">")) > > Attaching package: 'GO' > > > The following object(s) are masked from package:AnnBuilder : > > GO > > Warning message: > Built for UCSC is not valid! in: getUCSCBuilt(organism) > Error in loadFromUrl(srcUrls[i]) : URL > ftp://ftp.ncbi.nih.gov/repository/UniGene /Mus_musculus/Mm.data.gz is > incorrect or the target site is not responding! > > If I try to go directly to the Url it won't work either. > My list after > getSrcUrl("ALL", organism"Mus musculus") looks like > this. > > > > GP > > "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculu s/database/" > > UG > > "ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz" > > GO > "http://www.godatabase.org/dev/database/archive/latest/go_200512-ter mdb.rdf-xml.gz" > > KEGG > > "ftp://ftp.genome.ad.jp/pub/kegg/pathways" > > YG > > "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/" > > HG > > "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" > > EG > > "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA" > > IPI > > "ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/" > > > I can clearly not connect to the ncbi Url, but have I done something > wrong or has this something to do with a change in the database? > I searched the archive but didn't find an answer. > > Thanks for you support! > > Anja > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >