Question: GDCdownload error on CentOS 6.10 server
0
gravatar for t.kuilman
6 months ago by
t.kuilman140
Netherlands
t.kuilman140 wrote:

I am trying to download data from TCGA using the TCGAbiolinks package. I have used the pet example from the TCGAbiolinks Bioconductor-mirror, which works just fine on my Macbook, but throws an error on my server (CentOS 6.10):

> library(TCGAbiolinks)
> query <- GDCquery(project = "TARGET-AML",
+                    data.category = "Transcriptome Profiling",
+                    data.type = "miRNA Expression Quantification",
+                    workflow.type = "BCGSC miRNA Profiling",
+                    barcode = c("TARGET-20-PARUDL-03A-01R","TARGET-20-PASRRB-03A-01R"))
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TARGET-AML
--------------------
oo Filtering results
--------------------
ooo By data.type
ooo By workflow.type
ooo By barcode
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
>  # data will be saved in:
>  # example_data_dir/TARGET-AML/harmonized/Transcriptome_Profiling/miRNA_Expression_Quantification
>  GDCdownload(query, method = "client", directory = "~/tmp/")
Downloading data for project TARGET-AML
**Error in if (grepl("^https?://", url)) { : argument is of length zero**

I have tried to look in the source code where things go awry, but was not able to trace the error. Does anyone have an idea what goes wrong (or can anyone help me trace back the error)?

My sessionInfo() is below.

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.10 (Final)

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] TCGAbiolinks_2.10.5

loaded via a namespace (and not attached):
  [1] backports_1.1.4               circlize_0.4.6               
  [3] AnnotationHub_2.14.5          aroma.light_3.12.0           
  [5] plyr_1.8.4                    selectr_0.4-1                
  [7] ConsensusClusterPlus_1.46.0   lazyeval_0.2.2               
  [9] splines_3.5.2                 BiocParallel_1.16.6          
 [11] GenomeInfoDb_1.18.2           ggplot2_3.1.1                
 [13] sva_3.30.1                    digest_0.6.18                
 [15] foreach_1.4.4                 htmltools_0.3.6              
 [17] magrittr_1.5                  memoise_1.1.0                
 [19] cluster_2.0.8                 doParallel_1.0.14            
 [21] limma_3.38.3                  ComplexHeatmap_1.20.0        
 [23] Biostrings_2.50.2             readr_1.3.1                  
 [25] annotate_1.60.1               matrixStats_0.54.0           
 [27] sesameData_1.0.0              R.utils_2.8.0                
 [29] prettyunits_1.0.2             colorspace_1.4-1             
 [31] blob_1.1.1                    rvest_0.3.3                  
 [33] ggrepel_0.8.0                 xfun_0.6                     
 [35] dplyr_0.8.0.1                 crayon_1.3.4                 
 [37] RCurl_1.95-4.12               jsonlite_1.6                 
 [39] genefilter_1.64.0             survival_2.44-1.1            
 [41] zoo_1.8-5                     iterators_1.0.10             
 [43] glue_1.3.1                    survminer_0.4.3              
 [45] gtable_0.3.0                  sesame_1.0.0                 
 [47] zlibbioc_1.28.0               XVector_0.22.0               
 [49] GetoptLong_0.1.7              DelayedArray_0.8.0           
 [51] wheatmap_0.1.0                shape_1.4.4                  
 [53] BiocGenerics_0.28.0           scales_1.0.0                 
 [55] DESeq_1.34.1                  DBI_1.0.0                    
 [57] edgeR_3.24.3                  ggthemes_4.1.1               
 [59] Rcpp_1.0.1                    xtable_1.8-3                 
 [61] progress_1.2.0                cmprsk_2.2-7                 
 [63] bit_1.1-14                    matlab_1.0.2                 
 [65] preprocessCore_1.44.0         km.ci_0.5-2                  
 [67] stats4_3.5.2                  httr_1.4.0                   
 [69] RColorBrewer_1.1-2            pkgconfig_2.0.2              
 [71] XML_3.98-1.19                 R.methodsS3_1.7.1            
 [73] locfit_1.5-9.1                DNAcopy_1.56.0               
 [75] tidyselect_0.2.5              rlang_0.3.4                  
 [77] later_0.8.0                   AnnotationDbi_1.44.0         
 [79] munsell_0.5.0                 tools_3.5.2                  
 [81] downloader_0.4                generics_0.0.2               
 [83] RSQLite_2.1.1                 ExperimentHub_1.8.0          
 [85] broom_0.5.2                   stringr_1.4.0                
 [87] yaml_2.2.0                    knitr_1.22                   
 [89] bit64_0.9-7                   survMisc_0.5.5               
 [91] purrr_0.3.2                   randomForest_4.6-14          
 [93] EDASeq_2.16.3                 nlme_3.1-139                 
 [95] mime_0.6                      R.oo_1.22.0                  
 [97] xml2_1.2.0                    biomaRt_2.38.0               
 [99] compiler_3.5.2                curl_3.3                     
[101] interactiveDisplayBase_1.20.0 tibble_2.1.1                 
[103] geneplotter_1.60.0            stringi_1.4.3                
[105] GenomicFeatures_1.34.8        lattice_0.20-38              
[107] Matrix_1.2-17                 KMsurv_0.1-5                 
[109] pillar_1.3.1                  BiocManager_1.30.4           
[111] GlobalOptions_0.1.0           data.table_1.12.2            
[113] bitops_1.0-6                  httpuv_1.5.1                 
[115] rtracklayer_1.42.2            GenomicRanges_1.34.0         
[117] R6_2.4.0                      latticeExtra_0.6-28          
[119] hwriter_1.3.2                 promises_1.0.1               
[121] ShortRead_1.40.0              gridExtra_2.3                
[123] IRanges_2.16.0                codetools_0.2-16             
[125] assertthat_0.2.1              SummarizedExperiment_1.12.0  
[127] rjson_0.2.20                  GenomicAlignments_1.18.1     
[129] Rsamtools_1.34.1              S4Vectors_0.20.1             
[131] GenomeInfoDbData_1.2.0        mgcv_1.8-28                  
[133] parallel_3.5.2                hms_0.4.2                    
[135] grid_3.5.2                    tidyr_0.8.3                  
[137] ggpubr_0.2                    Biobase_2.42.0               
[139] shiny_1.3.1
tcgabiolinks • 125 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by t.kuilman140
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