Problem for downloading TCGA cancer data by TCGAbiolinks
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modarzi ▴ 10
Last seen 19 months ago

Hi, I would like to download TCGA data from GDC by TCGAbiolinks package.I wrote below code for that pupose:

query <- GDCquery(project = "TCGA-SARC",sample.type = "Primary solid Tumor",
                data.category = "Transcriptome Profiling",
                data.type = "Gene Expression Quantification",workflow.type = "HTSeq - Counts")

when I run below code:

 data <- GDCprepare(query)

I see below message in console:

Downloading data for project TCGA-SARC
GDCdownload will download 259 files. A total of 64.930633 MB
Downloading as: Thu_Dec_12_14_39_40_2019.tar.gz
Downloading: 65 MB

After a while and downloading 65 MB, I didn't see 'data' as R object. I see some message same as below:

ff8fba5e-f6e2-4db6-87cf-11958b27bc37/2b66a8a5-1e0a-4a4a-beb7-b2273b2ffb05.htseq.counts.gz: Can't create '\\\\?\\F:\\ff8fba5e-f6e2-4db6-87cf-11958b27bc37\\2b66a8a5-1e0a-4a4a-beb7-b2273b2ffb05.htseq.counts.gz'
tar.exe: Error exit delayed from previous errors.

I setwd() in my F driver. now in 'F' driver I see just 2 files:



when I get properties of 'ThuDec121439402019.tar.gz' file I see size: 61.6 MB (64,643,687 bytes).

Now I don't know what is my problem and what should I do by this process? I appreciate it if anybody shares his/her comment with me.

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] SummarizedExperiment_1.16.0 DelayedArray_0.12.0         matrixStats_0.55.0          Biobase_2.46.0             
 [5] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0         IRanges_2.20.0              S4Vectors_0.24.0           
 [9] BiocGenerics_0.32.0         TCGAbiolinks_2.14.0         sva_3.34.0                  BiocParallel_1.20.0        
[13] genefilter_1.68.0           mgcv_1.8-30                 nlme_3.1-141                stringr_1.4.0              
[17] dplyr_0.8.3                 Hmisc_4.2-0                 ggplot2_3.2.1               Formula_1.2-3              
[21] survival_2.44-1.1           lattice_0.20-38             impute_1.60.0               cluster_2.1.0              
[25] class_7.3-15                MASS_7.3-51.4               sqldf_0.4-11                RSQLite_2.1.2              
[29] gsubfn_0.7                  proto_1.0.0                 WGCNA_1.68                  fastcluster_1.1.25         
[33] dynamicTreeCut_1.63-1      

loaded via a namespace (and not attached):
  [1] backports_1.1.5             circlize_0.4.8              aroma.light_3.16.0          BiocFileCache_1.10.0       
  [5] plyr_1.8.4                  selectr_0.4-1               ConsensusClusterPlus_1.50.0 lazyeval_0.2.2             
  [9] splines_3.6.1               robust_0.4-18.1             digest_0.6.23               foreach_1.4.7              
 [13] htmltools_0.4.0             GO.db_3.10.0                magrittr_1.5                checkmate_1.9.4            
 [17] memoise_1.1.0               fit.models_0.5-14           doParallel_1.0.15           limma_3.42.0               
 [21] ComplexHeatmap_2.2.0        Biostrings_2.54.0           readr_1.3.1                 annotate_1.64.0            
 [25] R.utils_2.9.0               askpass_1.1                 prettyunits_1.0.2           colorspace_1.4-1           
 [29] rvest_0.3.4                 ggrepel_0.8.1               blob_1.2.0                  rappdirs_0.3.1             
 [33] rrcov_1.4-7                 xfun_0.10                   jsonlite_1.6                tcltk_3.6.1                
 [37] crayon_1.3.4                RCurl_1.95-4.12             zeallot_0.1.0               zoo_1.8-6                  
 [41] iterators_1.0.12            glue_1.3.1                  survminer_0.4.6             gtable_0.3.0               
 [45] zlibbioc_1.32.0             XVector_0.26.0              GetoptLong_0.1.7            shape_1.4.4                
 [49] DEoptimR_1.0-8              scales_1.0.0                DESeq_1.38.0                mvtnorm_1.0-11             
 [53] edgeR_3.28.0                DBI_1.0.0                   ggthemes_4.2.0              Rcpp_1.0.3                 
 [57] xtable_1.8-4                progress_1.2.2              htmlTable_1.13.2            clue_0.3-57                
 [61] matlab_1.0.2                foreign_0.8-72              bit_1.1-14                  km.ci_0.5-2                
 [65] preprocessCore_1.48.0       htmlwidgets_1.5.1           httr_1.4.1                  RColorBrewer_1.1-2         
 [69] acepack_1.4.1               pkgconfig_2.0.3             XML_3.98-1.20               R.methodsS3_1.7.1          
 [73] nnet_7.3-12                 dbplyr_1.4.2                locfit_1.5-9.1              tidyselect_0.2.5           
 [77] rlang_0.4.2                 AnnotationDbi_1.48.0        munsell_0.5.0               tools_3.6.1                
 [81] downloader_0.4              generics_0.0.2              broom_0.5.2                 knitr_1.25                 
 [85] bit64_0.9-7                 robustbase_0.93-5           survMisc_0.5.5              purrr_0.3.3                
 [89] EDASeq_2.20.0               R.oo_1.23.0                 xml2_1.2.2                  biomaRt_2.42.0             
 [93] compiler_3.6.1              rstudioapi_0.10             curl_4.2                    png_0.1-7                  
 [97] ggsignif_0.6.0              tibble_2.1.3                geneplotter_1.64.0          pcaPP_1.9-73               
[101] stringi_1.4.3               GenomicFeatures_1.38.0      Matrix_1.2-17               KMsurv_0.1-5               
[105] vctrs_0.2.0                 lifecycle_0.1.0             pillar_1.4.2                GlobalOptions_0.1.1        
[109] data.table_1.12.6           bitops_1.0-6                rtracklayer_1.46.0          hwriter_1.3.2              
[113] R6_2.4.0                    latticeExtra_0.6-28         ShortRead_1.44.0            gridExtra_2.3              
[117] codetools_0.2-16            assertthat_0.2.1            chron_2.3-54                openssl_1.4.1              
[121] rjson_0.2.20                withr_2.1.2                 GenomicAlignments_1.22.0    Rsamtools_2.2.0            
[125] GenomeInfoDbData_1.2.2      hms_0.5.2                   grid_3.6.1                  rpart_4.1-15               
[129] tidyr_1.0.0
TCGAbiolinks GDC TCGA • 306 views

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