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_Annotation_Packages

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