It looks like this is just a bug in cummeRbund (rather, it just hasn't been updated to match the current version of ggplot2). You might post this to the bioconductor email list and CC the package maintainer. The fix is actually really simple (it's just changing one line).

For what it's worth, a slightly modified version of that function is below. It'll probably work (but please do notify the package maintainer in any case). Note that I've changed the case of the function name to not mask the original.

expressionbarplot<-function(object,logMode=FALSE,pseudocount=1.0,showErrorbars=TRUE,showStatus=TRUE,replicates=FALSE,...){
        quant_types<-c("OK","FAIL","LOWDATA","HIDATA","TOOSHORT")
        quant_types<-factor(quant_types,levels=quant_types)
        quant_colors<-c("black","red","blue","orange","green")
        names(quant_colors)<-quant_types

        dat<-fpkm(object)
        if(replicates){
                repDat<-repFpkm(object)
                colnames(repDat)[1]<-"tracking_id"
        }
        #TODO: Test dat to ensure that there are >0 rows to plot.  If not, trap error and move on...

        colnames(dat)[1]<-"tracking_id"

        if(logMode)
        {
            dat$fpkm <- dat$fpkm + pseudocount
            dat$conf_hi <- dat$conf_hi + pseudocount
            dat$conf_lo <- dat$conf_lo + pseudocount

                if(replicates){
                        repDat$fpkm<-repDat$fpkm + pseudocount
                }
    }

    p<-ggplot(dat,aes(x=sample_name,y=fpkm,fill=sample_name))

        p <- p + geom_bar(stat="identity")

        if(replicates){
                p <- p + geom_point(aes(x=sample_name,y=fpkm),size=3,shape=18,colour="black",data=repDat)
        }

        if (showErrorbars)
        {
            p <- p +
                    geom_errorbar(aes(ymin=conf_lo,ymax=conf_hi,group=1),width=0.5)
        }

        if (logMode)
        {
            p <- p + scale_y_log10()
    }

    p <- p + facet_wrap('tracking_id') +
          labs(title=object@annotation$gene_short_name)+theme(axis.text.x=element_text(hjust=0,angle=-90))

    if (logMode)
    {
        p <- p + ylab(paste("FPKM +",pseudocount))
    } else {
        p <- p + ylab("FPKM")
    }

        if (showStatus){
                if(logMode){
                        p<-p+geom_text(aes(x=sample_name,y=1,label=quant_status,color=quant_status),vjust=1.5,size=3)

                }else{
                        p<-p+geom_text(aes(x=sample_name,y=0,label=quant_status,color=quant_status),vjust=1.5,size=3)
                }
        }

        p <- p + theme(legend.position="none")

        #Default cummeRbund colorscheme
        p<-p + scale_fill_hue(l=50,h.start=200)

        #Recolor quant flags
        p<- p+ scale_colour_manual(name='quant_status',values=quant_colors)

        p
}