[BioC] GenomeGraphs alternate input

[Amanda Miotto]

When trying to alter GenomeGraphs so that it queries a local mysql database 
instead of ensembl_mart, I get the following error. Why? What is chunk 4? and 
is it due to ens not being classed correctly?

Thankyou.

sudo R --verbose CMD build MyGenomeGraphs
......

 * DONE (GenomeGraphs)
* creating vignettes ... ERROR
Loading required package: biomaRt
Loading required package: RCurl
Loading required package: grid
Loading required package: DBI

Error: processing vignette 'GenomeGraphs.Rnw' failed with diagnostics:
 chunk 4 
Error in ens[i, 5] - ens[i, 4] : non-numeric argument to binary operator
Execution halted


The additional code I included was in GenomeGraphs-classes.R
---------------------------------------------------------------------------------------

#############################################################################################################################
setMethod("initialize", "Gene", function(.Object, ...){
    .Object <- callNextMethod()
library(RMySQL)
con <- dbConnect(MySQL(),host="", user="", dbname="", password="")
q1<-("select * from alldata where " )
q3<-("=")
p4<-("'")
.Object at ens<-dbGetQuery(con, paste(q1,.Object at type,q3,p4,.Object at id,p4, 
sep=""))

dbDisconnect(con)


#    .Object at ens <- 
getBM(c("ensembl_gene_id","structure_transcript_stable_id","structure_exon_stable_id",
 
#                          "structure_exon_chrom_start","structure_exon_chrom_end","structure_exon_rank",
  
#                         "structure_transcript_chrom_strand", "structure_biotype"),
   #                      filters = .Object at type, values=.Object at id, 
mart=.Object at biomart)
###########################################################################################################################

-----------------------------------------------------------------------------------------
#############################################################################################################################
    if (!is.null(.Object at biomart)) {
library(RMySQL)
con <- dbConnect(MySQL(),host="", user="", dbname="", password="")
q1<-("select * from alldata where structure_transcript_chrom_strand =" )
q3<-("and exon_chrom_start<")
q4<-("and exon_chrom_end>")
q5<-("and structure_strand=")
p4<-("'")

.Object at ens<-dbGetQuery(con, 
paste(q1,.Object at chromosome,q3,.Object at start,q4,.Object at end,q5,p4,strand,p4, 
sep=""))

dbDisconnect(con)

#        .Object at ens <- 
getBM(c("ensembl_gene_id","structure_transcript_stable_id",
 
#                              "structure_exon_stable_id","structure_exon_chrom_start","structure_exon_chrom_end",
  
#                             "structure_exon_rank", "structure_transcript_chrom_strand","structure_biotype"),
   #                          
filters=c("chromosome_name", "start", "end", "strand"),
    #                         
values=list(.Object at chromosome,.Object at start, .Object at end, strand),
     #                        mart=.Object at biomart)
    }
    
############################################################################################################################
------------------------------------------------------------------------------------------------

#########################################################################################################################
library(RMySQL)
con <- dbConnect(MySQL(),host="", user="", dbname="", password="")
q1<-("select * from alldata where " )
q3<-("='")
p4<-("'")
.Object at ens<-dbGetQuery(con, paste(q1,.Object at type,q3,.Object at id,p4, sep=""))

dbDisconnect(con)


#  .Object at ens <- 
getBM(c("ensembl_gene_id","structure_transcript_stable_id","structure_exon_stable_id",
 
#                        "structure_exon_chrom_start","structure_exon_chrom_end","structure_exon_rank",
  
#                       "structure_transcript_chrom_strand","structure_biotype"),
   #                    filters = .Object at type, 
values=.Object at id,mart=.Object at biomart)
##########################################################################################################################