Error in set(x, j = name, value = value) : Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code.

Code should be placed in three backticks as shown below

library(ASpli)
library(GenomicFeatures)
library(writexl)

#ASpli
AS_aspli <- function(GTF_File,
                     Bam_Files,
                     folderpath,
                     condition_names,
                     project_name)
{
  ASpliStarttime <- Sys.time()
  Dexseq_path <- dir.create(file.path(folderpath,project_name,"ASpli"))
  txdb <- makeTxDbFromGFF(GTF_File)
  features<-binGenome(txdb)
  targets<-data.frame(row.names=paste0('Sample',c(1:length(Bam_Files))),
                      bam=Bam_Files, 
                      f1=condition_names,
                      stringsAsFactors=FALSE)
  gbcounts<-gbCounts(features=features,
                     targets=targets, 
                     minReadLength=1,
                     maxISize=10000)
  asd<-jCounts(counts=gbcounts,
               features=features,
               minReadLength=1)
  gb<-gbDUreport(gbcounts,contrast=c(-1,1))
  jdur<-jDUreport(asd,contrast=c(-1,1))
  sr<-splicingReport(gb,jdur,counts=gbcounts)
  is<-integrateSignals(sr,asd)
  pvalues <- data.frame(is@signals$bin,is@signals$b.fdr)
  ASpliendtime <- Sys.time()
  totaltimeASpli <- ASpliendtime - ASpliStarttime
  totaltimeASpli

  rdata_file_path <- file.path(folderpath,project_name,"ASpli", "ASpli.RData")
  saveRDS(is, file = rdata_file_path)

  rdata_file_path <- file.path(folderpath,project_name,"ASpli", "ASplitime.RData")
  saveRDS(totaltimeASpli, file = rdata_file_path)

  rdata_file_path <- file.path(folderpath,project_name,"ASpli", "ASpli.xlsx")
  write_xlsx(pvalues, rdata_file_path)
}


GTF_File = "Datasets/Drosophila/dmel-all-r5.1.gff"
Bam_Files = c("Datasets/Drosophila/RNAi_1_SRR031721_Aligned.sortedByCoord.out.bam","Datasets/Drosophila/RNAi_3_SRR031725_Aligned.sortedByCoord.out.bam","Datasets/Drosophila/RNAi_4_SRR031726_Aligned.sortedByCoord.out.bam","Datasets/Drosophila/Untreated_1_SRR031713_Aligned.sortedByCoord.out.bam","Datasets/Drosophila/Untreated_3_SRR031714_Aligned.sortedByCoord.out.bam","Datasets/Drosophila/Untreated_4_SRR031717_Aligned.sortedByCoord.out.bam","Datasets/Drosophila/Untreated-6_SRR031729_Aligned.sortedByCoord.out.bam")
singleEnd_T_or_F = T
folderpath = "AS_DEXSeq_Aspli_rmats/"
condition_names = c("RNAi","RNAi","RNAi","untreated","untreated","untreated","untreated")
Drosophila_splicing= "Drosophila_splicing"
AS_aspli(GTF_File, 
                     Bam_Files, 
                     folderpath,
                     condition_names,
                     Drosophila_splicing)


sessionInfo( )
Genome binning completed
Summarizing Sample1
ETA: 5 min
Summarizing Sample2
ETA: 5 min
Summarizing Sample3
ETA: 4 min
Summarizing Sample4
ETA: 3 min
Summarizing Sample5
ETA: 2 min
Summarizing Sample6
ETA: 1 min
Summarizing Sample7
ETA: 0 min
Junctions PJU completed
Junctions PIR completed
Junctions IR PIR completed
Junctions AltSS PSI completed
Junctions ES PSI completed
Filtering genes:
  Filtering by reads.
  Filtering using RNAi,untreated conditions
  Filtering any condition with mean minimum value 10
  Filtering by read density.
  Filtering using RNAi,untreated conditions
  Filtering any condition with mean minimum value 0.05
Filtering genes done
Genes differential expression:
  Contrast:-1RNAi  1untreated  
  Running GLM LRT
Genes differential expression done
Genes DE completed
Bins DE completed
Running junctionsPJU test
Running junctionsPIR test
Running irPIR test
Running esPSI test
Running altPSI test
Error in set(x, j = name, value = value) : 
  Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code.
In addition: Warning messages:
1: In dir.create(file.path(folderpath, project_name, "ASpli")) :
  cannot create dir 'AS_DEXSeq_Aspli_rmats//Drosophila_splicing/ASpli', reason 'No such file or directory'
2: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  some CDS phases are missing or not between 0 and 2
3: In makeTxDbFromGRanges(gr, metadata = metadata) :
  The following transcripts were dropped because their exon ranks could not be inferred (either because the
  exons are not on the same chromosome/strand or because they are not separated by introns): FBtr0084079,
  FBtr0084080, FBtr0084081, FBtr0084082, FBtr0084083, FBtr0084084, FBtr0084085
4: In .splicingReport(bdu, jdu, counts) :
  Not every chromosome is present in both bins and locales:
2L 2R 3L 3R 4 X
2L 2R 3L 3R X