Your code, expected output and some example input data would be helpful in understanding the problem.

I am also getting same error as above:

Loading binned counts file
Checking every sampleID has an outcome
No outcomes for Sample Sample1
No outcomes for Sample Sample2
No outcomes for Sample Sample3
No outcomes for Sample Sample4
Error in `[.data.frame`(sampleIDs.with.outcomes, , "Gender") : 
  undefined columns selected

My code is

source("https://bioconductor.org/biocLite.R")
biocLite("SummarizedExperiment")
library(SummarizedExperiment)
makeBinnedCountsFile(bam.file.list = c("Sample1.bam","Sample2.bam","Sample3.bam","Sample4.bam"),
  sampleIDs = c("Sample1","Sample2","Sample3","Sample4"),  
  binned.counts.fname = "Rapidr-output",
  k = 20000)                  
library(RAPIDR)
rapidr.dir <- system.file(package = "RAPIDR")
data(outcomes)
data(gcContent)
T21.pos <- which(finalref$Dx == "T21")
chr.lens <- sapply(gcContent, length)
chr.names <- names(chr.lens)
header <- c("SampleID")
for (i in 1:length(chr.lens)) {
  header <- c(header, rep(chr.names[i], chr.lens[i]))  
}  
nbins <- sum(chr.lens)
ncols <- nbins + 1
binned.counts <- matrix(nrow = nrow(finalref), ncol = ncols)
for (i in 1:nrow(binned.counts)) {
  binned.counts[i,] <- rpois(ncols, lambda = 100)  
  if (i %in% T21.pos) {  
    binned.counts[i, 139087:141493] <- rpois(chr.lens[21], lambda = 115)    
  }
}    
binned.counts[,1] <- finalref$sampleID
colnames(binned.counts) <- header
t <- tempfile()
write.table(binned.counts, file = t, col.names = TRUE, row.names = FALSE, quote = FALSE, sep = ",")
"Rapidr-output" <- t
message(t)  
gcContent.fname <- paste(rapidr.dir, "C:/Users/Pooja/Documents/R/win-library/3.4/RAPIDR/data/gcContent.rda", sep = "")
head(outcomes)
ref.set <- createReferenceSetFromCounts("Rapidr-output",
                                        outcomes,                                        
                                        gcCorrect = FALSE,                                        
                                        PCA = FALSE,                                        
                                        filterBin = FALSE,                                        
                                        gcContentFile = gcContent.fname)  


**My input is**
outcomes
     sampleID.Gender.Dx
1 sample1,Female,Normal
2 sample2,Female,Normal
3   sample3,Male,Normal
4   sample4,Male,Normal

My session info is :

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252    LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C                   LC_TIME=English_India.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SummarizedExperiment_1.8.1        DelayedArray_0.4.1                matrixStats_0.53.1               
 [4] Biobase_2.38.0                    BiocInstaller_1.28.0              BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [7] BSgenome_1.46.0                   rtracklayer_1.38.3                Biostrings_2.46.0                
[10] XVector_0.18.0                    GenomicRanges_1.30.3              GenomeInfoDb_1.14.0              
[13] IRanges_2.12.0                    S4Vectors_0.16.0                  BiocGenerics_0.24.0              
[16] RAPIDR_0.1.1                      NIPTeR_1.0.2                     

loaded via a namespace (and not attached):
 [1] zlibbioc_1.24.0          GenomicAlignments_1.14.2 BiocParallel_1.12.0      lattice_0.20-35         
 [5] tools_3.4.1              grid_3.4.1               data.table_1.11.2        Matrix_1.2-10           
 [9] GenomeInfoDbData_1.0.0   PropCIs_0.3-0            sets_1.0-18              bitops_1.0-6            
[13] RCurl_1.95-4.10          compiler_3.4.1           Rsamtools_1.30.0         XML_3.98-1.11