I used rtracklayer to change the coordinates of a GRanges object from those of human genome hg38 to hg19. I think that everything worked fine, but I got a warning about an unclosed connection. The code is pasted below How should I change things so I don't get this warning?

Thanks.

Eric

> fl <- '/fh/fast/bedalov_a/user/efoss/gene_databases/UCSC/liftover_files/hg38ToHg19.over.chain'
> 
> chainhg38tohg19 <- import(con = fl)
> 
> hg38gr <- GRanges(seqnames = Rle(hg38df[,1]), 
+                   ranges = IRanges(start = hg38df[,2], width = 1), 
+                   strand = Rle(strand(rep('*', nrow(hg38df)))), 
+                   seqlengths = lngths)
> 
> values(hg38gr) <- hg38df[,3:17]
> 
> hg19gr <- liftOver(x = hg38gr, chain = chainhg38tohg19)
Warning message:
In for (i in 2:nargs) { :
  closing unused connection 3 (/fh/fast/bedalov_a/user/efoss/gene_databases/UCSC/liftover_files/hg38ToHg19.over.chain)
>
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.6 LTS

Matrix products: default
BLAS/LAPACK: /app/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib/libopenblas_prescottp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=C               LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] rtracklayer_1.42.2   GenomicRanges_1.34.0 GenomeInfoDb_1.18.2  IRanges_2.16.0       S4Vectors_0.20.1    
[6] BiocGenerics_0.29.2 

loaded via a namespace (and not attached):
 [1] rstudioapi_0.10             XVector_0.22.0              zlibbioc_1.28.0            
 [4] GenomicAlignments_1.18.1    BiocParallel_1.16.6         lattice_0.20-38            
 [7] tools_3.6.0                 SummarizedExperiment_1.12.0 grid_3.6.0                 
[10] Biobase_2.42.0              sessioninfo_1.1.1           cli_1.1.0                  
[13] withr_2.1.2                 matrixStats_0.54.0          assertthat_0.2.1           
[16] yaml_2.2.0                  crayon_1.3.4                Matrix_1.2-17              
[19] GenomeInfoDbData_1.2.0      bitops_1.0-6                RCurl_1.95-4.12            
[22] DelayedArray_0.8.0          compiler_3.6.0              Biostrings_2.50.2          
[25] Rsamtools_1.34.1            XML_3.98-1.19              
>