library(ChAMP)
library(GEOquery)
gset <- getGEO('GSE46306', destdir=".",
               AnnotGPL = F,
               getGPL = F)
exprSet = exprs(gset[[1]])
pdata = pData(gset[[1]])
write.csv(pdata,file="G:/geo/pdata.csv")
#filter bad probe
myImpute <- champ.impute(exprSet,pdata)
myfilter <- champ.filter(beta=exprSet,pd=pdata)                                  
exprSet=myfilter$beta
myNorm <- champ.norm(exprSet,method="PBC")        
save(myNorm,file="myNorm.rda")   

QC.GUI(myNorm,arraytype="450K",pheno=pdata$'disease status:ch1')                
#dendrogram plot: Listening on http://127.0.0.1:4177
Warning: Error in if: missing value where TRUE/FALSE needed

Here, I check the pheno file(pdata), and find pdata includes NA. My solution is to save the pdata file in csv format(above code:write.csv(pdata,file="G:/geo/pdata.csv")), modify the na value and read again.

library(ChAMP)
load("exprSet.rda")
rt=read.csv("G:/geo/pdata.csv")   
> class(rt)
[1] "data.frame"
> head(rt)
           X                 title geo_accession                status submission_date last_update_date
1 GSM1128470 NT2_2008216.1_1R01C01    GSM1128470 Public on Jan 06 2014     Apr 23 2013      Jan 06 2014

rownames(rt)<-rt[,1] #The first column as the row name
rt<-rt[,-1]          #
pdata=rt
> class(pdata)
[1] "data.frame"
> head(pdata)
                           title geo_accession                status submission_date last_update_date
GSM1128470 NT2_2008216.1_1R01C01    GSM1128470 Public on Jan 06 2014     Apr 23 2013      Jan 06 2014

myImpute <- champ.impute(exprSet,pdata)
myfilter <- champ.filter(beta=exprSet,pd=pdata)                                   
exprSet=myfilter$beta

myNorm <- champ.norm(exprSet,method="PBC")
[>>>>> ChAMP.NORM END <<<<<<]
[===========================]
[You may want to process champ.SVD() next.]

Warning message:
In dir.create(resultsDir) : '.\CHAMP_Normalization' already exists
> QC.GUI(myNorm,arraytype="450K",pheno=pdata$'disease status:ch1')                  

Listening on http://127.0.0.1:4177
Warning: Error in data.frame: arguments imply differing number of rows: 44, 0
  101: stop
  100: data.frame
   99: innermdsplot
   96: func
   83: origRenderFunc
   82: output$mdsPlot
    2: runApp
    1: QC.GUI

Error in data.frame: arguments imply differing number of rows: 44, 0