Error: failed to load resource name: EH762 title: LGG_Mutation-20160128 reason: 1 resources failed to download

[lwaldron]

I got this error when attempting:

muts <- curatedTCGAData(assays = "Mutation", dry.run = FALSE)

Using RELEASE_3_12 (AnVIL/Terra). Tail of output below.

Working on: LGG_Mutation-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
downloading 1 resources
retrieving 1 resource
  |===========================================================================================================| 100%

download failed
  web resource path: ‘https://experimenthub.bioconductor.org/fetch/762’
  local file path: ‘~/.cache/ExperimentHub/126b4e6c5b_762’
  reason: Internal Server Error (HTTP 500).bfcadd() failed; resource removed
  rid: BFC17
  fpath: ‘https://experimenthub.bioconductor.org/fetch/762’
  reason: download faileddownload failed
  hub path: ‘https://experimenthub.bioconductor.org/fetch/762’
  cache resource: ‘EH762 : 762’
  reason: bfcadd() failed; see warnings()Error: failed to load resource
  name: EH762
  title: LGG_Mutation-20160128
  reason: 1 resources failed to download
> 

```r
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C              LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               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] curatedTCGAData_1.12.1      MultiAssayExperiment_1.16.0 SummarizedExperiment_1.20.0 Biobase_2.50.0             
 [5] MatrixGenerics_1.2.1        matrixStats_0.58.0          PublicDataResources_0.2.1   RaggedExperiment_1.14.2    
 [9] GenomicRanges_1.42.0        GenomeInfoDb_1.26.7         IRanges_2.24.1              S4Vectors_0.28.1           
[13] BiocGenerics_0.36.1         BiocManager_1.30.12        

loaded via a namespace (and not attached):
  [1] fgsea_1.16.0                  colorspace_2.0-0              ellipsis_0.3.1               
  [4] lsa_0.73.2                    XVector_0.30.0                rstudioapi_0.13              
  [7] SnowballC_0.7.0               bit64_4.0.5                   DT_0.17                      
 [10] AnnotationDbi_1.52.0          interactiveDisplayBase_1.28.0 fansi_0.4.2                  
 [13] xml2_1.3.2                    cachem_1.0.4                  knitr_1.33                   
 [16] jsonlite_1.7.2                magicaxis_2.2.1               dbplyr_2.1.0                 
 [19] cluster_2.1.1                 shinydashboard_0.7.1          shiny_1.6.0                  
 [22] mapproj_1.2.7                 readr_1.4.0                   compiler_4.0.3               
 [25] httr_1.4.2                    assertthat_0.2.1              Matrix_1.3-2                 
 [28] fastmap_1.1.0                 limma_3.46.0                  cli_2.4.0                    
 [31] later_1.1.0.1                 visNetwork_2.0.9              htmltools_0.5.1.1            
 [34] tools_4.0.3                   igraph_1.2.6                  CoreGx_1.2.0                 
 [37] gtable_0.3.0                  glue_1.4.2                    GenomeInfoDbData_1.2.4       
 [40] RANN_2.6.1                    reshape2_1.4.4                dplyr_1.0.4                  
 [43] maps_3.3.0                    rappdirs_0.3.3                tinytex_0.31                 
 [46] fastmatch_1.1-0               Rcpp_1.0.6                    slam_0.1-48                  
 [49] vctrs_0.3.7                   PharmacoGx_2.2.4              ExperimentHub_1.16.1         
 [52] xfun_0.22                     stringr_1.4.0                 mime_0.10                    
 [55] lifecycle_1.0.0               gtools_3.8.2                  AnnotationHub_2.22.1         
 [58] zlibbioc_1.36.0               MASS_7.3-53.1                 scales_1.1.1                 
 [61] hms_1.0.0                     promises_1.2.0.1              relations_0.6-9              
 [64] RColorBrewer_1.1-2            sets_1.0-18                   curl_4.3                     
 [67] yaml_2.2.1                    memoise_2.0.0                 gridExtra_2.3                
 [70] ggplot2_3.3.3                 downloader_0.4                RSQLite_2.2.7                
 [73] stringi_1.5.3                 BiocVersion_3.12.0            NISTunits_1.0.1              
 [76] GenomicDataCommons_1.14.0     plotrix_3.8-1                 caTools_1.18.2               
 [79] BiocParallel_1.24.1           rlang_0.4.10                  pkgconfig_2.0.3              
 [82] bitops_1.0-7                  pracma_2.3.3                  evaluate_0.14                
 [85] lattice_0.20-41               purrr_0.3.4                   htmlwidgets_1.5.3            
 [88] bit_4.0.4                     tidyselect_1.1.0              plyr_1.8.6                   
 [91] magrittr_2.0.1                R6_2.5.0                      gplots_3.1.1                 
 [94] generics_0.1.0                DelayedArray_0.16.3           DBI_1.1.1                    
 [97] sm_2.2-5.6                    withr_2.4.2                   pillar_1.6.0                 
[100] RCurl_1.98-1.3                tibble_3.1.1                  crayon_1.4.1                 
[103] KernSmooth_2.23-18            utf8_1.2.1                    BiocFileCache_1.14.0         
[106] rmarkdown_2.6                 grid_4.0.3                    data.table_1.14.0            
[109] marray_1.68.0                 blob_1.2.1                    piano_2.6.0                  
[112] digest_0.6.27                 xtable_1.8-4                  httpuv_1.5.5                 
[115] munsell_0.5.0                 celestial_1.4.6               tcltk_4.0.3                  
[118] shinyjs_2.0.0                
>

[LiNk-NY]

Hi Levi, @lwaldron

It looks like it might be a connection issue: Internal Server Error (HTTP 500).bfcadd() failed; resource removed

On my local computer, I've tried this and I get:

>  curatedTCGAData(assays = "Mutation", dry.run = FALSE)
[ ... ]
A MultiAssayExperiment object of 32 listed
 experiments with user-defined names and respective classes.
 Containing an ExperimentList class object of length 32:
 [1] ACC_Mutation-20160128: RaggedExperiment with 20166 rows and 90 columns
 [2] BLCA_Mutation-20160128: RaggedExperiment with 39312 rows and 130 columns
 [3] BRCA_Mutation-20160128: RaggedExperiment with 90490 rows and 993 columns
 [4] CESC_Mutation-20160128: RaggedExperiment with 46547 rows and 194 columns
 [5] CHOL_Mutation-20160128: RaggedExperiment with 6755 rows and 35 columns
 [6] COAD_Mutation-20160128: RaggedExperiment with 62530 rows and 154 columns
 [7] DLBC_Mutation-20160128: RaggedExperiment with 16918 rows and 48 columns
 [8] ESCA_Mutation-20160128: RaggedExperiment with 58602 rows and 185 columns
 [9] GBM_Mutation-20160128: RaggedExperiment with 22073 rows and 290 columns
 [10] HNSC_Mutation-20160128: RaggedExperiment with 51799 rows and 279 columns
 [11] KICH_Mutation-20160128: RaggedExperiment with 7559 rows and 66 columns
 [12] KIRC_Mutation-20160128: RaggedExperiment with 26369 rows and 437 columns
 [13] KIRP_Mutation-20160128: RaggedExperiment with 15585 rows and 161 columns
 [14] LAML_Mutation-20160128: RaggedExperiment with 2585 rows and 197 columns
 [15] LGG_Mutation-20160128: RaggedExperiment with 9885 rows and 286 columns
 [16] LIHC_Mutation-20160128: RaggedExperiment with 27892 rows and 198 columns
 [17] LUAD_Mutation-20160128: RaggedExperiment with 72541 rows and 230 columns
 [18] LUSC_Mutation-20160128: RaggedExperiment with 65305 rows and 178 columns
 [19] OV_Mutation-20160128: RaggedExperiment with 20219 rows and 316 columns
 [20] PAAD_Mutation-20160128: RaggedExperiment with 30357 rows and 150 columns
 [21] PCPG_Mutation-20160128: RaggedExperiment with 4662 rows and 184 columns
 [22] PRAD_Mutation-20160128: RaggedExperiment with 12348 rows and 332 columns
 [23] READ_Mutation-20160128: RaggedExperiment with 22075 rows and 69 columns
 [24] SARC_Mutation-20160128: RaggedExperiment with 20376 rows and 247 columns
 [25] SKCM_Mutation-20160128: RaggedExperiment with 290322 rows and 345 columns
 [26] STAD_Mutation-20160128: RaggedExperiment with 148520 rows and 289 columns
 [27] TGCT_Mutation-20160128: RaggedExperiment with 14672 rows and 138 columns
 [28] THCA_Mutation-20160128: RaggedExperiment with 7458 rows and 405 columns
 [29] THYM_Mutation-20160128: RaggedExperiment with 3064 rows and 123 columns
 [30] UCEC_Mutation-20160128: RaggedExperiment with 184861 rows and 248 columns
 [31] UCS_Mutation-20160128: RaggedExperiment with 11339 rows and 57 columns
 [32] UVM_Mutation-20160128: RaggedExperiment with 2174 rows and 80 columns
Functionality:
 experiments() - obtain the ExperimentList instance
 colData() - the primary/phenotype DataFrame
 sampleMap() - the sample coordination DataFrame
 `$`, `[`, `[[` - extract colData columns, subset, or experiment
 *Format() - convert into a long or wide DataFrame
 assays() - convert ExperimentList to a SimpleList of matrices
 exportClass() - save all data to files
> packageVersion("curatedTCGAData")
[1] '1.12.1'
> BiocManager::valid()
[1] TRUE

You could try clearing the cache for that particular resource in case it became corrupt during the download.

-Marcel

sessionInfo

```r R version 4.0.5 Patched (2021-04-30 r80280) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.10 Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] RaggedExperiment_1.14.2 curatedTCGAData_1.12.1 [3] MultiAssayExperiment_1.16.0 SummarizedExperiment_1.20.0 [5] Biobase_2.50.0 GenomicRanges_1.42.0 [7] GenomeInfoDb_1.26.7 IRanges_2.24.1 [9] S4Vectors_0.28.1 BiocGenerics_0.36.1 [11] MatrixGenerics_1.2.1 matrixStats_0.58.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.6 lattice_0.20-44 [3] assertthat_0.2.1 digest_0.6.27 [5] utf8_1.2.1 mime_0.10 [7] BiocFileCache_1.14.0 R6_2.5.0 [9] RSQLite_2.2.7 httr_1.4.2 [11] pillar_1.6.0 zlibbioc_1.36.0 [13] rlang_0.4.11 curl_4.3.1 [15] blob_1.2.1 Matrix_1.3-3 [17] AnnotationHub_2.22.1 RCurl_1.98-1.3 [19] bit_4.0.4 shiny_1.6.0 [21] DelayedArray_0.16.3 compiler_4.0.5 [23] httpuv_1.6.1 pkgconfig_2.0.3 [25] htmltools_0.5.1.1 tidyselect_1.1.1 [27] tibble_3.1.1 GenomeInfoDbData_1.2.4 [29] interactiveDisplayBase_1.28.0 fansi_0.4.2 [31] withr_2.4.2 crayon_1.4.1 [33] dplyr_1.0.6 dbplyr_2.1.1 [35] later_1.2.0 bitops_1.0-7 [37] rappdirs_0.3.3 grid_4.0.5 [39] xtable_1.8-4 lifecycle_1.0.0 [41] DBI_1.1.1 magrittr_2.0.1 [43] cachem_1.0.4 XVector_0.30.0 [45] promises_1.2.0.1 ellipsis_0.3.2 [47] generics_0.1.0 vctrs_0.3.8 [49] tools_4.0.5 bit64_4.0.5 [51] glue_1.4.2 purrr_0.3.4 [53] BiocVersion_3.12.0 fastmap_1.1.0 [55] yaml_2.2.1 AnnotationDbi_1.52.0 [57] ExperimentHub_1.16.1 BiocManager_1.30.15 [59] memoise_2.0.0 ```

[lwaldron]

Oops, thanks @LiNk-NY !