Dear there,

When I run the code below, I got an error about opening the URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/'.

gbm <- curatedTCGAData::curatedTCGAData("GBM",
        assays=c("GISTIC_Peaks", "CNVSNP", "RNASeq2GeneNorm"),
        dry.run=FALSE, version="2.1.1")

gbm <- TCGAutils::symbolsToRanges(gbm, unmapped=FALSE)

  403 genes were dropped because they have exons located on both strands of the same reference
  sequence or on more than one reference sequence, so cannot be represented by a single genomic
  range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use
  suppressMessages() to suppress this message.
Error in download.file(url, destfile, method, quiet = TRUE) : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/'
In addition: Warning message:
In download.file(url, destfile, method, quiet = TRUE) :
  URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/': Timeout of 60 seconds was reached


sessionInfo( )
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


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

other attached packages:
 [1] RaggedExperiment_1.30.0     curatedTCGAData_1.28.1      MultiAssayExperiment_1.32.0
 [4] SummarizedExperiment_1.36.0 Biobase_2.66.0              GenomicRanges_1.58.0       
 [7] GenomeInfoDb_1.42.1         IRanges_2.40.1              S4Vectors_0.44.0           
[10] BiocGenerics_0.52.0         MatrixGenerics_1.18.1       matrixStats_1.5.0          
[13] TCGAutils_1.26.0           

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1                        dplyr_1.1.4                            
 [3] blob_1.2.4                              filelock_1.0.3                         
 [5] Biostrings_2.74.1                       bitops_1.0-9                           
 [7] fastmap_1.2.0                           RCurl_1.98-1.16                        
 [9] BiocFileCache_2.14.0                    GenomicAlignments_1.42.0               
[11] XML_3.99-0.18                           mime_0.12                              
[13] lifecycle_1.0.4                         KEGGREST_1.46.0                        
[15] RSQLite_2.3.9                           magrittr_2.0.3                         
[17] compiler_4.4.2                          rlang_1.1.4                            
[19] tools_4.4.2                             yaml_2.3.10                            
[21] rtracklayer_1.66.0                      S4Arrays_1.6.0                         
[23] bit_4.5.0.1                             curl_6.1.0                             
[25] DelayedArray_0.32.0                     xml2_1.3.6                             
[27] abind_1.4-8                             BiocParallel_1.40.0                    
[29] withr_3.0.2                             purrr_1.0.2                            
[31] grid_4.4.2                              ExperimentHub_2.14.0                   
[33] cli_3.6.3                               crayon_1.5.3                           
[35] generics_0.1.3                          httr_1.4.7                             
[37] tzdb_0.4.0                              rjson_0.2.23                           
[39] GenomicDataCommons_1.30.0               DBI_1.2.3                              
[41] cachem_1.1.0                            stringr_1.5.1                          
[43] zlibbioc_1.52.0                         rvest_1.0.4                            
[45] parallel_4.4.2                          AnnotationDbi_1.68.0                   
[47] BiocManager_1.30.25                     XVector_0.46.0                         
[49] restfulr_0.0.15                         vctrs_0.6.5                            
[51] Matrix_1.7-1                            jsonlite_1.8.9                         
[53] hms_1.1.3                               bit64_4.5.2                            
[55] GenomicFeatures_1.58.0                  glue_1.8.0                             
[57] codetools_0.2-20                        stringi_1.8.4                          
[59] BiocVersion_3.20.0                      BiocIO_1.16.0                          
[61] UCSC.utils_1.2.0                        tibble_3.2.1                           
[63] pillar_1.10.1                           rappdirs_0.3.3                         
[65] GenomeInfoDbData_1.2.13                 R6_2.5.1                               
[67] dbplyr_2.5.0                            lattice_0.22-6                         
[69] readr_2.1.5                             AnnotationHub_3.14.0                   
[71] png_0.1-8                               Rsamtools_2.22.0                       
[73] memoise_2.0.1                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[75] SparseArray_1.6.0                       org.Hs.eg.db_3.20.0                    
[77] pkgconfig_2.0.3

That's a valid URI, so it is likely that you just need more time for the download. You can do options(timeout = 2000) or some similarly large number to stop R from timing out after 60 seconds.