# Loading a library
library(rtracklayer)

# assigning bed file location to variable
summits_file <- 'C:/Users/utente/Desktop/Tesi/Dati/peak_C1_H3K4me3_peaks.narrowPeak'

# import the BED data
twist.summits <- import(summits_file)

# what kind of object is this?
class(twist.summits)
twist.summits

> GRanges object with 226 ranges and 2 metadata columns:
        seqnames    ranges strand |                   name     score
           <Rle> <IRanges>  <Rle> |            <character> <numeric>
    [1]        I    801380      * | peak_C1_H3K4me3_peak_1   4.01076
    [2]        I    915512      * | peak_C1_H3K4me3_peak_2   3.18610
    [3]        I   2646543      * | peak_C1_H3K4me3_peak_3   3.94499
    [4]        I   2647293      * | peak_C1_H3K4me3_peak_4   4.32684
    [5]        I   2648461      * | peak_C1_H3K4me3_peak_5   8.31980

library(ChIPpeakAnno)
txdb <- TxDb.Celegans.UCSC.ce11.ensGene
annoData <- toGRanges(TxDb.Celegans.UCSC.ce11.ensGene, feature="gene")
annoData

### Get all the transcripts for each gene
allTx <- transcriptsBy(txdb, by='gene')

# examine the result
allTx
> GRangesList object of length 46904:
$WBGene00000001.1
GRanges object with 2 ranges and 2 metadata columns:
      seqnames          ranges strand |     tx_id      tx_name
         <Rle>       <IRanges>  <Rle> | <integer>  <character>
  [1]     chrI 5107833-5110183      + |      1083 Y110A7A.10.1
  [2]     chrI 5107843-5110164      + |      1084 Y110A7A.10.2
  -------
  seqinfo: 7 sequences (1 circular) from ce11 genome


BiocManager::install('biomaRt')
library(biomaRt)
ensamble<- biomaRt::useMart('ensembl', dataset = 'celegans_gene_ensembl') 
wormGenes <- biomaRt::getBM(attributes = c('external_gene_name','chromosome_name','start_position', 'end_position','gene_biotype','description'), mart= ensamble)


##################################################
## CODE BLOCK #3
##################################################

### Getting the foot print of all transcripts

# collapse all transcripts into a single range
genic.tx <- reduce(allTx)

# examine the result
genic.tx

# Then, let's get rid of the list format
genes <- unlist(genic.tx)

# examine the result
genes
> GRanges object with 46905 ranges and 0 metadata columns:
                   seqnames            ranges strand
                      <Rle>         <IRanges>  <Rle>
  WBGene00000001.1     chrI   5107833-5110183      +
  WBGene00000002.1    chrIV   9598986-9601695      -
  WBGene00000003.1     chrV   9244402-9246360      -


### Count how many peaks overlap each gene
overlap.genes <- suppressWarnings(countOverlaps(genes,twist.summits), classes = "warning")


head(overlap.genes)
> head(overlap.genes)
WBGene00000001.1 WBGene00000002.1 WBGene00000003.1 WBGene00000004.1 WBGene00000005.1 
               0                0                0                0                0 
WBGene00000006.1 
               0

This are my code but I don't understand why the overlap genes return zero

What I have to change?

When you suppressWarnings you won't get warnings that tell you that there are problems! The main warning you will be suppressing will look something like this:

## These are not identical things!
> gr1 <- GRanges(rep("I", 5), IRanges(c(2,8,23,45,78), width = 5))
> gr2 <- GRanges(rep("chrI", 5), IRanges(c(2,8,23,45,78), width = 5))
> countOverlaps(gr1, gr2)
[1] 0 0 0 0 0
Warning message:
In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

I mean, it does say you can suppress the warnings, but it's good to know why there isn't any overlap, no?