Hi all, hope you might help me. I'm not very computer savvy, yet I try to create an org.db as it didn't look too hard. And in fact, 3 days ago I was able to do it, but then I tried to do another one and I got this error: .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name. I thought it might be because I mistakingly did not have unique column names, but I couldn't find a problem with it. Then I went back to the authors' examples:
> setwd("~/test/") > library(AnnotationForge) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Attaching package: ‘IRanges’ The following object is masked from ‘package:grDevices’: windows > > finchFile <- system.file("extdata","finch_info.txt", + package="AnnotationForge") > finch <- read.table(finchFile,sep="\t") > > fSym <- finch[,c(2,3,9)] > fSym <- fSym[fSym[,2]!="-",] > fSym <- fSym[fSym[,3]!="-",] > colnames(fSym) <- c("GID","SYMBOL","GENENAME") > > fChr <- finch[,c(2,7)] > fChr <- fChr[fChr[,2]!="-",] > colnames(fChr) <- c("GID","CHROMOSOME") > > finchGOFile <- system.file("extdata","GO_finch.txt", + package="AnnotationForge") > fGO <- read.table(finchGOFile,sep="\t") > fGO <- fGO[fGO[,2]!="",] > fGO <- fGO[fGO[,3]!="",] > colnames(fGO) <- c("GID","GO","EVIDENCE") > > makeOrgPackage(gene_info=fSym, chromosome=fChr, go=fGO, + version="0.1", + maintainer="Some One <email@example.com>", + author="Some One <firstname.lastname@example.org>", + outputDir = ".", + tax_id="59729", + genus="Taeniopygia", + species="guttata", + goTable="go") Populating genes table: genes table filled Populating gene_info table: gene_info table filled Populating chromosome table: chromosome table filled Populating go table: go table filled table metadata filled 'select()' returned many:1 mapping between keys and columns Dropping GO IDs that are too new for the current GO.db Populating go table: go table filled Populating go_bp table: go_bp table filled Populating go_cc table: go_cc table filled Populating go_mf table: go_mf table filled 'select()' returned many:1 mapping between keys and columns Populating go_bp_all table: go_bp_all table filled Populating go_cc_all table: go_cc_all table filled Populating go_mf_all table: go_mf_all table filled Populating go_all table: go_all table filled Creating package in ./org.Tguttata.eg.db Now deleting temporary database file  "./org.Tguttata.eg.db" There were 50 or more warnings (use warnings() to see the first 50) > install.packages("./org.Tguttata.eg.db", repos=NULL, type="source") * installing *source* package 'org.Tguttata.eg.db' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'org.Tguttata.eg.db' finding HTML links ... done org.Tguttata.egBASE html org.Tguttata.egORGANISM html org.Tguttata.eg_dbconn html ** building package indices ** testing if installed package can be loaded from temporary location *** arch - i386 *** arch - x64 ** testing if installed package can be loaded from final location *** arch - i386 *** arch - x64 ** testing if installed package keeps a record of temporary installation path * DONE (org.Tguttata.eg.db) > library(org.Tguttata.eg.db) > keytypes(org.Tguttata.eg.db)  "CHROMOSOME" "EVIDENCE" "EVIDENCEALL" "GENENAME" "GID" "GO" "GOALL" "ONTOLOGY"  "ONTOLOGYALL" "SYMBOL" > keys(org.Tguttata.eg.db,"GO") Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name.
if anyone can help, I will ver much appreciate it.