GDCquery failes due to getURL error

[ReharrC]

The following call fails:

> query.exp <- GDCquery(project = "TCGA-COAD", data.category = "Transcriptome rofiling",data.type = "Gene Expression Quantification", workflow.type = "HTSeq - FPKM-UQ", sample.type = c("Solid Tissue Normal")) 

Error:  Error in getURL(url, fromJSON, timeout(600), simplifyDataFrame = TRUE): 'getURL()' failed:
  URL: https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=2493&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-COAD%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22HTSeq%20-%20FPKM-UQ%22]%7D%7D]%7D&format=JSON

and sessionInfo() gives:

R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] DT_0.4               dplyr_0.7.5          TCGAbiolinks_2.8.0  
[4] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            selectr_0.4-1              
  [3] rjson_0.2.19                hwriter_1.3.2              
  [5] circlize_0.4.3              XVector_0.20.0             
  [7] GenomicRanges_1.32.3        GlobalOptions_0.0.13       
  [9] ggpubr_0.1.6                matlab_1.0.2               
 [11] ggrepel_0.8.0               bit64_0.9-7                
 [13] AnnotationDbi_1.42.1        xml2_1.2.0                 
 [15] codetools_0.2-15            splines_3.5.0              
 [17] R.methodsS3_1.7.1           mnormt_1.5-5               
 [19] doParallel_1.0.11           DESeq_1.32.0               
 [21] geneplotter_1.58.0          knitr_1.20                 
 [23] jsonlite_1.5                Rsamtools_1.32.0           
 [25] km.ci_0.5-2                 broom_0.4.4                
 [27] annotate_1.58.0             cluster_2.0.7-1            
 [29] R.oo_1.22.0                 readr_1.1.1                
 [31] compiler_3.5.0              httr_1.3.1                 
 [33] assertthat_0.2.0            Matrix_1.2-14              
 [35] lazyeval_0.2.1              limma_3.36.1               
 [37] htmltools_0.3.6             prettyunits_1.0.2          
 [39] tools_3.5.0                 bindrcpp_0.2.2             
 [41] gtable_0.2.0                glue_1.2.0                 
 [43] GenomeInfoDbData_1.1.0      reshape2_1.4.3             
 [45] ggthemes_3.5.0              ShortRead_1.38.0           
 [47] Rcpp_0.12.17                Biobase_2.40.0             
 [49] Biostrings_2.48.0           nlme_3.1-137               
 [51] rtracklayer_1.40.3          iterators_1.0.9            
 [53] psych_1.8.4                 stringr_1.3.1              
 [55] rvest_0.3.2                 XML_3.98-1.11              
 [57] edgeR_3.22.2                zoo_1.8-1                  
 [59] zlibbioc_1.26.0             scales_0.5.0               
 [61] aroma.light_3.10.0          hms_0.4.2                  
 [63] parallel_3.5.0              SummarizedExperiment_1.10.1
 [65] RColorBrewer_1.1-2          curl_3.2                   
 [67] ComplexHeatmap_1.18.0       memoise_1.1.0              
 [69] gridExtra_2.3               KMsurv_0.1-5               
 [71] ggplot2_2.2.1               downloader_0.4             
 [73] biomaRt_2.36.1              latticeExtra_0.6-28        
 [75] stringi_1.1.7               RSQLite_2.1.1              
 [77] genefilter_1.62.0           S4Vectors_0.18.2           
 [79] foreach_1.4.4               GenomicFeatures_1.32.0     
 [81] BiocGenerics_0.26.0         BiocParallel_1.14.1        
 [83] shape_1.4.4                 GenomeInfoDb_1.16.0        
 [85] rlang_0.2.1                 pkgconfig_2.0.1            
 [87] matrixStats_0.53.1          bitops_1.0-6               
 [89] lattice_0.20-35             purrr_0.2.5                
 [91] bindr_0.1.1                 htmlwidgets_1.2            
 [93] cmprsk_2.2-7                GenomicAlignments_1.16.0   
 [95] bit_1.1-14                  tidyselect_0.2.4           
 [97] plyr_1.8.4                  magrittr_1.5               
 [99] R6_2.2.2                    IRanges_2.14.10            
[101] DelayedArray_0.6.0          DBI_1.0.0                  
[103] mgcv_1.8-23                 pillar_1.2.3               
[105] foreign_0.8-70              survival_2.41-3            
[107] RCurl_1.95-4.10             tibble_1.4.2               
[109] EDASeq_2.14.0               survMisc_0.5.4             
[111] GetoptLong_0.1.6            progress_1.1.2             
[113] locfit_1.5-9.1              grid_3.5.0                 
[115] sva_3.28.0                  data.table_1.11.4          
[117] blob_1.1.1                  ConsensusClusterPlus_1.44.0
[119] digest_0.6.15               xtable_1.8-2               
[121] tidyr_0.8.1                 R.utils_2.6.0              
[123] stats4_3.5.0                munsell_0.4.3              
[125] survminer_0.4.2   

[stephwen]

same error, with R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

and TCGAbiolinks_2.8.0:

> query <- GDCquery(project = CancerProject,
+                   data.category = "Transcriptome Profiling",
+                   data.type = "Gene Expression Quantification", 
+                   workflow.type = "HTSeq - Counts")

--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-UCEC
Error:  Error in getURL(url, fromJSON, timeout(600), simplifyDataFrame = TRUE): 'getURL()' failed:
  URL: https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=2919&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-UCEC%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22HTSeq%20-%20Counts%22]%7D%7D]%7D&format=JSON
  error: SSLRead() return error -9806

We will retry to access GDC!
Error in is.response(x) : 'getURL()' failed:
  URL: https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=2919&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-UCEC%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22HTSeq%20-%20Counts%22]%7D%7D]%7D&format=JSON
  error: SSLRead() return error -9806

[Melkiades]

Did you update the package? We are in version 2.9.1 and you both have 2.8.0. I think @tiagochst solved the change of API some days ago. Try always to be updated with the github repo:

devtools::install_github('BioinformaticsFMRP/TCGAbiolinks')

Note from the package DESCRIPTION file:

Package: TCGAbiolinks Type: Package Title: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data Version: 2.9.1

[stephwen]

I tried to install the very last version, but it failed.

I just installed the version from June 4th ( 53a64014f38bd03e4a15145aa88c810bbd12a63a ) and it seems to work!

ReharrC , try this:

devtools::install_github("BioinformaticsFMRP/TCGAbiolinks",ref = "53a64014f38bd03e4a15145aa88c810bbd12a63a")

[ReharrC]

I tried this one here: devtools::install_github(repo ="BioinformaticsFMRP/TCGAbiolinks") IT WORKED, thanks!

[sz-kazemi]

This command worked for me, too. Many thanks! devtools::install_github(repo ="BioinformaticsFMRP/TCGAbiolinks")