Hi, Chuen, The purpose of the GenBank-environment (i.e. ACCNUM) is to record the probset to GenBank Accession mapping provided by users via the base mapping file. It will contain nothing but NAs when the base mapping type is "ll". ABPkgBuilder currently doesn't extract GenBank Accessions based on Entrez Gene ID. This is due to design choices rather than technical changes as I understood. The missing of GO-environments is a real problem. The perl complaints right after loading GO in your outputs is abnormal. Not sure whether it relates to the GO problem. I know ABPkgBuilder only utilizes the perl scripts when it maps probset IDs to Entrez Gene IDs. Everything is pure R when it gets to GO annotations. You have already given the mappings as input, and you got most of the annotations (PATH, CHR, etc), so it seems the perl problem is not the cause of the GO problem. Sorry that I don't have more useful information :( best nianhua

Hi Chuen, I have not been successful in replicating your bug. But I HAVE been successful in building the package that you were trying to make. I will mail it to you in a personal email. Here is the code as I ran it in linux (using the same packages that you used). library(AnnBuilder) mysrcUrls<-getSrcUrl("all","Homo sapiens") ABPkgBuilder(baseName="/home/mcarlson/tmp/Chuen_Tan/baseName3.txt", srcUrls=mysrcUrls,baseMapType="ll",pkgName="chip89",pkgPath="/home/mca rlson/tmp/Chuen_ Tan",organism="Homo sapiens", version="1.1.0",author=list(author="Chuen Seng",maintainer="<chuenseng.tan at="" ki.se="">"),fromWeb = TRUE) In the meantime, you might want to make double sure that your environment is set up correctly. There is a lot of information out there about how to build R packages in windows. Perhaps this FAQ might be helpful? http://c*r*an.*r*-p*r*oject.o*r*g/bin/*windows*/base/*r*w-FAQ.html#*Pa ckage*s <http: cran.r-project.org="" bin="" windows="" base="" rw-="" faq.html#packages=""> Good Luck, Marc > Hi, Chuen, > > The purpose of the GenBank-environment (i.e. ACCNUM) is to record the probset > to GenBank Accession mapping provided by users via the base mapping file. It > will contain nothing but NAs when the base mapping type is "ll". ABPkgBuilder > currently doesn't extract GenBank Accessions based on Entrez Gene ID. This is > due to design choices rather than technical changes as I understood. > > The missing of GO-environments is a real problem. The perl complaints right > after loading GO in your outputs is abnormal. Not sure whether it relates to > the GO problem. I know ABPkgBuilder only utilizes the perl scripts when it > maps probset IDs to Entrez Gene IDs. Everything is pure R when it gets to GO > annotations. You have already given the mappings as input, and you got most of > the annotations (PATH, CHR, etc), so it seems the perl problem is not the > cause of the GO problem. Sorry that I don't have more useful information :( > > best > > nianhua > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -------------------------------------------------------------------- ---- > > > >