I am creating an R package and trying to run devtools::check(). The generated NOTE appear as follows :

checking R code for possible problems ... NOTE myFunction: missing arguments not allowed in calls to ‘list’

How to know which argument is missing? What does that even mean? I have a large function with many variables.

Here is part of the function: It is basically creating an html-report for my bioinformatics analysis.

cAMARETTO_HTMLreport <- function(cAMARETTOresults,
                                cAMARETTOnetworkM,
                                cAMARETTOnetworkC,
                                PhenotypeTablesList = NULL,
                                output_address ="./",
                                HTMLsAMARETTOlist = NULL,
                                CopyAMARETTOReport = TRUE,
                                hyper_geo_reference = NULL,
                                hyper_geo_reference_gp = NULL,
                                hyper_geo_reference_cp = NULL,
                                driverGSEA = TRUE,
                                NrCores=2){

    ##################################### Bioconductor Considerations :
    Run_Names <- AMARETTOres <- Weights <- Color<- Type<- GeneNames<-NULL
    GeneName <- Community <- TypeColored <- Community_key<-NULL
    Community_type<- ModuleNr<-NULL
    ModuleName <- Run <- Genes <- q.value<-NULL
    #####################################

    RunInfoList<-InitialCheckInputs(cAMARETTOresults=cAMARETTOresults,
                                    output_address,
                                    HTMLsAMARETTOlist=cAMARETTOresults,
                                    CopyAMARETTOReport,
                                    hyper_geo_reference,
                                    hyper_geo_reference_gp,
                                    hyper_geo_reference_cp)
    RunInfo<-RunInfoList$RunInfo
    RunInfo2<-RunInfoList$RunInfo2
    full_path<-RunInfoList$full_path
    HTMLsAMARETTOlist<-RunInfoList$HTMLsAMARETTOlist
    #====================================================================
    # Extract main dataframes
    com_gene_df<-suppressWarnings(
        ComRunModGenInfo(cAMARETTOresults,cAMARETTOnetworkM,
                        cAMARETTOnetworkC))
    comm_info <-suppressWarnings(
        cAMARETTO_InformationTable(cAMARETTOnetworkM,cAMARETTOnetworkC))
    #====================================================================
    Runs_AMARETTOs_info<-com_gene_df%>%
        dplyr::select(Run_Names,AMARETTOres)%>%
        dplyr::distinct()%>%
        dplyr::mutate(Run_Names = RunHyperLink(Run_Names,AMARETTOres,
                    HTMLsAMARETTOlist,CopyAMARETTOReport))%>%
                        filter(AMARETTOres==1)%>%select(Run_Names)
    #====================================================================
    ComModulesLink<-CommunityModuleTableCreate(cAMARETTOresults,
                                                cAMARETTOnetworkM, 
                                                cAMARETTOnetworkC,
                                                HTMLsAMARETTOlist,
                                                CopyAMARETTOReport)
    #====================================================================
 ...
}

If this is a question about Bioconductor package development then please ask on the bioc-devel mailing list. If it's about general R usage try the r-help or R-pkg-devel mailing list or StackOverflow.

I'd guess the check is complaining about something like list(foo,,bar) or list(foo,) where there is an implied argument but it is not present; note that this generates an error in R

list(1,)

so probably indicates an opportunity for a unit test / example that covers this part of the code.