BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Error with GDCdownload using client method #565

Open james-e-barrett opened 1 year ago

james-e-barrett commented 1 year ago

Running

query <- GDCquery(project = "TCGA-ACC",
                  data.category =  "Copy number variation",
                  legacy = TRUE,
                  file.type = "hg19.seg",
                  barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01", "TCGA-OR-A5LJ-10A-01D-A29K-01"))

GDCdownload(query, method = "client")

I get the following error:

Downloading data for project TCGA-ACC
trying URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
Error in download.file(url, ...) : 
  cannot open URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
In addition: Warning message:
In download.file(url, ...) :
  URL '/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip': status was 'URL using bad/illegal format or missing URL'
> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] TCGAbiolinks_2.24.3         BiocManager_1.30.19        
 [3] SummarizedExperiment_1.28.0 Biobase_2.58.0             
 [5] GenomicRanges_1.50.1        GenomeInfoDb_1.34.3        
 [7] IRanges_2.32.0              MatrixGenerics_1.10.0      
 [9] matrixStats_0.63.0          dplyr_1.0.10               
[11] here_1.0.1                  readr_2.1.3                
[13] kableExtra_1.3.4            scales_1.2.1               
[15] reshape2_1.4.4              ggplot2_3.4.0              
[17] S4Vectors_0.36.0            BiocGenerics_0.44.0        

loaded via a namespace (and not attached):
 [1] nlme_3.1-162                bitops_1.0-7               
 [3] bit64_4.0.5                 filelock_1.0.2             
 [5] progress_1.2.2              webshot_0.5.4              
 [7] httr_1.4.4                  rprojroot_2.0.3            
 [9] tools_4.2.2                 utf8_1.2.2                 
[11] R6_2.5.1                    DBI_1.1.3                  
[13] mgcv_1.8-41                 colorspace_2.0-3           
[15] withr_2.5.0                 prettyunits_1.1.1          
[17] tidyselect_1.2.0            curl_4.3.3                 
[19] bit_4.0.5                   compiler_4.2.2             
[21] cli_3.4.1                   rvest_1.0.3                
[23] formatR_1.12                xml2_1.3.3                 
[25] DelayedArray_0.24.0         labeling_0.4.2             
[27] rappdirs_0.3.3              systemfonts_1.0.4          
[29] stringr_1.5.0               digest_0.6.30              
[31] R.utils_2.12.2              rmarkdown_2.18             
[33] svglite_2.1.0               XVector_0.38.0             
[35] pkgconfig_2.0.3             htmltools_0.5.3            
[37] dbplyr_2.2.1                fastmap_1.1.0              
[39] rlang_1.0.6                 readxl_1.4.1               
[41] rstudioapi_0.14             RSQLite_2.2.19             
[43] farver_2.1.1                generics_0.1.3             
[45] jsonlite_1.8.3              vroom_1.6.0                
[47] R.oo_1.25.0                 RCurl_1.98-1.9             
[49] magrittr_2.0.3              GenomeInfoDbData_1.2.9     
[51] Matrix_1.5-3                Rcpp_1.0.9                 
[53] munsell_0.5.0               fansi_1.0.3                
[55] R.methodsS3_1.8.2           lifecycle_1.0.3            
[57] stringi_1.7.8               yaml_2.3.6                 
[59] zlibbioc_1.44.0             BiocFileCache_2.6.0        
[61] plyr_1.8.8                  grid_4.2.2                 
[63] blob_1.2.3                  parallel_4.2.2             
[65] crayon_1.5.2                lattice_0.20-45            
[67] Biostrings_2.66.0           splines_4.2.2              
[69] hms_1.1.2                   KEGGREST_1.38.0            
[71] knitr_1.41                  pillar_1.8.1               
[73] TCGAbiolinksGUI.data_1.16.0 biomaRt_2.54.0             
[75] XML_3.99-0.12               glue_1.6.2                 
[77] evaluate_0.18               downloader_0.4             
[79] data.table_1.14.6           lambda.r_1.2.4             
[81] selectr_0.4-2               png_0.1-8                  
[83] vctrs_0.5.2                 tzdb_0.3.0                 
[85] cellranger_1.1.0            tidyr_1.3.0                
[87] purrr_1.0.1                 gtable_0.3.1               
[89] assertthat_0.2.1            cachem_1.0.6               
[91] xfun_0.35                   viridisLite_0.4.1          
[93] tibble_3.1.8                AnnotationDbi_1.60.0       
[95] memoise_2.0.1               ellipsis_0.3.2  

Thank you for your help.