Hi everyone,

while running code,

> makeBinnedCountsFile(bam.file.list = c("sample5.bam", "sample6.bam"),
+                       sampleIDs = c("", ""),
+                       binned.counts.fname = output.fname,
+                       k = 20000, mask)

I am getting error msg as: Binning counts in bam files
doing the binning
Error in assays(olap) : could not find function "assays"

The sessioninfo is:

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] RAPIDR_0.1.1                      GenomeInfoDbData_0.99.0          
 [3] matrixStats_0.52.2                Biobase_2.36.2                   
 [5] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.2                  
 [7] rtracklayer_1.36.6                Biostrings_2.44.2                
 [9] XVector_0.16.0                    GenomicRanges_1.28.6             
[11] GenomeInfoDb_1.12.3               IRanges_2.10.5                   
[13] S4Vectors_0.14.7                  BiocGenerics_0.22.1              
[15] BiocInstaller_1.26.1             

loaded via a namespace (and not attached):
 [1] zlibbioc_1.22.0            GenomicAlignments_1.12.2   BiocParallel_1.10.1       
 [4] lattice_0.20-35            tools_3.4.2                SummarizedExperiment_1.6.5
 [7] grid_3.4.2                 data.table_1.10.4-1        Matrix_1.2-11             
[10] PropCIs_0.2-5              bitops_1.0-6               RCurl_1.95-4.8            
[13] DelayedArray_0.3.21        compiler_3.4.2             Rsamtools_1.28.0          
[16] XML_3.98-1.9 

RAPIDR (I think that's the package defining makeBinnedCountsFile ?) is not a Bioconductor package, so you would rather contact maintainer("RAPIDR"). It looks like the package author did not formulate their NAMESPACE correctly; try evaluating

library(SummarizedExperiment)

before the code chunk above.

Yes. There are dependency problems among RAPIDR packages like S4vectors, SummarizedExperiment etc. If one's version is updated, then the other will be incompatible.