hi all, I'm building a custom annotation service, and have encountered the following problems. Upon Reading the SQLForge.pdf vignette, i decided that i would not choose to use these functions popHUMANCHIPDB populateDB but instead build my own SQLite Database following the Database Schema Version 1.0 described in AnnotationDbi/inst/DBschemas/schemas_1.0/HUMANCHIP_DB.sql The SQLite Database was initiated by the following R code *library(AnnotationDbi) library(RSQLite) filename<-'myCustomChip.sqlite' drv<-dbDriver('SQLite') db<-dbConnect(drv,dbname=filename) ##Create SQLite Database create.sql <- readLines('HUMANCHIP_DB.sql') create.sql <- paste(collapse="\n", create.sql) create.sql <- strsplit(create.sql, ";")[[1]] create.sql <- create.sql[-length(create.sql)] database <- sapply(create.sql, function(x) sqliteQuickSQL(db, x))* Subsequently, the following tables were populated according to the rules stated Genes Probes Alias Ensembl Chromosomes Chromosomes_Locations Cytogenetic_Locations Gene_Info Refseq Unigene MetaData Tables were populated as follows. Other tables, go, ec, etc were left empty *metadata<-rbind(c("DBSCHEMA", "HUMANCHIP_DB"), c("ORGANISM", "Homo sapiens"), c("SPECIES", "Human"), c("DBSCHEMAVERSON", "1.0"), c("MANUFACTURER","AFFYMETRIX"), c("CHIPNAME","HG-U133_Plus_2"), c("MANUFACTURERURL","http://www.affymetrix.com")) q11<- paste(sep="", 'INSERT INTO "metadata" VALUES("', metadata[,1], '", "', metadata[,2], '");') database<- sapply(q11, function(x) sqliteQuickSQL(db,x)) map.counts<-rbind(c("GENES", nrow(idtable)), c("PROBES", nrow(finalprobes)), c("ALIAS", nrow(alias)), c("ENSEMBL", nrow(ensembl)), c("CHROMOSOMES", nrow(chromosomes)), c("CHROMOSOME_LOCATIONS", nrow(chromosome_location)), c("CYTOGENETIC_LOCATIONS", nrow(cytoband)), c("GENE_INFO", nrow(gene_info)), c("REFSEQ", nrow(refseq)), c("UNIGENE", nrow(unigene))) q12<- paste(sep="", 'INSERT INTO "map_counts" VALUES("', map.counts[,1], '",' , map.counts[,2], ');') * *database<- sapply(q12, function(x) sqliteQuickSQL(db,x)) * *map.metadata<-rbind(c("GENES", "XXXX", "TST612", "26 MAY 2010"), c("PROBES", "XXXX", "TST612", "26 MAY 2010"), c("ALIAS", "XXXX", "TST612", "26 MAY 2010"), c("ENSEMBL", "XXXX", "TST612", "26 MAY 2010"), c("CHROMOSOMES", "XXXX", "TST612", "26 MAY 2010"), c("CHROMOSOME_LOCATIONS", "XXXX", "TST612", "26 MAY 2010"), c("CYTOGENETIC_LOCATIONS", "XXXX", "TST612", "26 MAY 2010"), c("GENE_INFO", "XXXX", "TST612", "26 MAY 2010"), c("REFSEQ", "XXXX", "TST612", "26 MAY 2010"), c("UNIGENE", "XXXX", "TST612", "26 MAY 2010"))* * q13<- paste(sep="", 'INSERT INTO "map_metadata" VALUES("', map.metadata[,1], '", "', map.metadata[,2], '","', map.metadata[,3], '","', map.metadata[,4], '");') database <- sapply(q13, function(x) sqliteQuickSQL(db,x))* Upon completion of populating the SQLite Database, i then proceeded to build my custom annotationDBI.db package. *seed <- new("AnnDbPkgSeed", Package = "myCustomChip.db", Version = "1.0-0", PkgTemplate = "HUMANCHIP.DB", AnnObjPrefix = "myCustomChip", Title = "MyCustom Annotation for HG-U133PLUS2", Author = "Annotation Services", Maintainer = "Julian Lee <julianlhe@gmail.com>", organism = "Homo sapiens", species = "Human", biocViews = "AnnotationData, FunctionalAnnotation", DBschema = "HUMANCHIP_DB", ) system("rm -rf myCustomChip.db") makeAnnDbPkg(seed, filename, dest.dir=getwd(),no.man=F)* and got the following errors *Error in cpSubsCon(src[k], destname) : trying to replace @ACCNUMSOURCE@ by an NA* I'm trying to figure out where @ACCNUMSOURCE@ is used, and i can't quite find it. There's some mention of it in the man *.Rd pages, but can't quite get to it. Much help in getting to the bottom of this would help. Thank you very much Julian Lee *> sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US [4] LC_COLLATE=en_US LC_MONETARY=C LC_MESSAGES=en_US [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RSQLite_0.8-4 DBI_0.2-5 AnnotationDbi_1.8.2 [4] Biobase_2.6.1 loaded via a namespace (and not attached): [1] tools_2.10.1 * *Acknowledgements for some scripts to get me started* Computational Biology Group Department of Medical Genetics <http: www.unil.ch="" dgm="">, University of Lausanne <http: www.unil.ch=""/> http://www2.unil.ch/cbg/index.php?title=Building_BioConductor_Annotati on_Packages [[alternative HTML version deleted]]