I have been working on the following code. But I keep facing the error mentioned below.

Code should be placed in three backticks as shown below

> #overview
> ## ----loadKnitr, echo=FALSE----------------------------------------------------
> library("knitr")
> # opts_chunk$set(eval = FALSE)
> opts_chunk$set(fig.width = 6, fig.height = 6)
> library(pander)
> panderOptions("digits", 3)
> 
> ## ----install, eval=FALSE------------------------------------------------------
> #  ## try http:// if https:// URLs are not supported
> #  if (!requireNamespace("BiocManager", quietly=TRUE))
> #      install.packages("BiocManager")
> #  BiocManager::install("ramwas")
> 
> ## ----loadIt, eval=FALSE-------------------------------------------------------
> #  library(ramwas) # Loads the package
> #  browseVignettes("ramwas") # Opens vignettes
> #  help(package = "ramwas") # Lists package functions
> 
> ## ----loadPackages, echo=FALSE, warning=FALSE, message=FALSE-------------------
> suppressPackageStartupMessages(library(ramwas))
> # dr = "D:/temp"
> 
> ## ----generateData, warning=FALSE, message=FALSE-------------------------------
> library(ramwas)
> dr = paste0(tempdir(), "/simulated_project")
> ramwas0createArtificialData(
+   dir = dr,
+   nsamples = 20,
+   nreads = 100e3,
+   ncpgs = 25e3,
+   threads = 2)
Wed Feb 22 17:10:46 2023, Start ramwas0createArtificialData() call
Wed Feb 22 17:10:46 2023, Generating 25000 CpG locations
Wed Feb 22 17:10:46 2023, Saving CpG locations in: /tmp/7666325.1.all.q/Rtmpuh8vir/simulated_project/Simulated_chromosome.rds
Wed Feb 22 17:10:46 2023, Generating fragment size distribution
Wed Feb 22 17:10:46 2023, Generating covariates
Wed Feb 22 17:10:46 2023, Savings covariates in: /tmp/7666325.1.all.q/Rtmpuh8vir/simulated_project/covariates.txt
Wed Feb 22 17:10:46 2023, Savings BAM list in: /tmp/7666325.1.all.q/Rtmpuh8vir/simulated_project/bam_list.txt
Wed Feb 22 17:10:46 2023, Start generating BAM files in: /tmp/7666325.1.all.q/Rtmpuh8vir/simulated_project/bams
Wed Feb 22 17:11:09 2023, Done generating BAM files in: /tmp/7666325.1.all.q/Rtmpuh8vir/simulated_project/bams
> cat("Project directory:", dr)
Project directory: /tmp/7666325.1.all.q/Rtmpuh8vir/simulated_project> 
> ## ----parameters---------------------------------------------------------------
> param = ramwasParameters(
+   dirproject = dr,
+   dirbam = "bams",
+   filebamlist = "bam_list.txt",
+   filecpgset = "Simulated_chromosome.rds",
+   cputhreads = 2,
+   scoretag = "MAPQ",
+   minscore = 4,
+   minfragmentsize = 50,
+   maxfragmentsize = 250,
+   minavgcpgcoverage = 0.3,
+   minnonzerosamples = 0.3,
+   filecovariates = "covariates.txt",
+   modelcovariates = NULL,
+   modeloutcome = "age",
+   modelPCs = 0,
+   toppvthreshold = 1e-5,
+   bihost = "grch37.ensembl.org",
+   bimart = "ENSEMBL_MART_ENSEMBL",
+   bidataset = "hsapiens_gene_ensembl",
+   biattributes = c("hgnc_symbol","entrezgene","strand"),
+   bifilters = list(with_hgnc_trans_name = TRUE),
+   biflank = 0,
+   cvnfolds = 5,
+   mmalpha = 0,
+   mmncpgs = c(5, 10, 50, 100, 500, 1000, 2000)
+ )
> 
> ## ----scan-bams, warning=FALSE, message=FALSE----------------------------------
 > sessionInfo( )

This is the error that comes up even after I have set the maxfragmentsize above.

> ramwas1scanBams(param)
Error in ramwas1scanBams(param) : Parameter not set: maxfragmentsize
Execution halted

I am not sure what I can do to correct this error. I also need to have the ramwas1scanBams step create the qc files and rbam files. That does not happen either. Can I please get some help with these errors?