TCGAbiolinks GDCprepare error
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Entering edit mode
Talip Zengin ▴ 10
@talip-zengin-14290
Last seen 13 months ago
Mugla, Turkiye

Hi, I am using TCGAbiolinks package for my pipeline. Today I got the error below. Could you please help me on fixing this error?

GeneExp_paired <- GDCprepare(query_exp, save = TRUE, save.filename = paste0(cancer, "_GeneExp_paired.rda"))

|=================================================================| 100%    1 MB
|======================================================================| 100%
    Starting to add information to samples
     => Add clinical information to samples
    Add FFPE information. More information at: 
    => https://cancergenome.nih.gov/cancersselected/biospeccriteria 
    => http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
     => Adding subtype information to samples
    luad subtype information from:doi:10.1038/nature13385
    Downloading genome information (try:0) Using: Human genes (GRCh38.p12)
    **Error: $ operator is invalid for atomic vectors**

Thanks in advance.

sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /truba/home/tzengin/R/lib64/R/lib/libRblas.so
LAPACK: /truba/home/tzengin/R/lib64/R/lib/libRlapack.so

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

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

other attached packages:
 [1] DT_0.5                      dplyr_0.8.0.1              
 [3] SummarizedExperiment_1.12.0 DelayedArray_0.8.0         
 [5] BiocParallel_1.16.6         matrixStats_0.54.0         
 [7] Biobase_2.42.0              GenomicRanges_1.34.0       
 [9] GenomeInfoDb_1.18.2         IRanges_2.16.0             
[11] S4Vectors_0.20.1            BiocGenerics_0.28.0        
[13] TCGAbiolinks_2.10.5        

loaded via a namespace (and not attached):
  [1] backports_1.1.3               circlize_0.4.5               
  [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                 ggplot2_3.1.0                
 [11] sva_3.30.1                    digest_0.6.18                
 [13] foreach_1.4.4                 htmltools_0.3.6              
 [15] magrittr_1.5                  memoise_1.1.0                
 [17] cluster_2.0.7-1               doParallel_1.0.14            
 [19] limma_3.38.3                  ComplexHeatmap_1.20.0        
 [21] Biostrings_2.50.2             readr_1.3.1                  
 [23] annotate_1.60.1               sesameData_1.0.0             
 [25] R.utils_2.8.0                 prettyunits_1.0.2            
 [27] colorspace_1.4-1              blob_1.1.1                   
 [29] rvest_0.3.2                   ggrepel_0.8.0                
 [31] xfun_0.5                      crayon_1.3.4                 
 [33] RCurl_1.95-4.12               jsonlite_1.6                 
 [35] genefilter_1.64.0             survival_2.44-1              
 [37] zoo_1.8-5                     iterators_1.0.10             
 [39] glue_1.3.1                    survminer_0.4.3              
 [41] gtable_0.3.0                  sesame_1.0.0                 
 [43] zlibbioc_1.28.0               XVector_0.22.0               
 [45] GetoptLong_0.1.7              wheatmap_0.1.0               
 [47] shape_1.4.4                   scales_1.0.0                 
 [49] DESeq_1.34.1                  DBI_1.0.0                    
 [51] edgeR_3.24.3                  ggthemes_4.1.0               
 [53] Rcpp_1.0.1                    xtable_1.8-3                 
 [55] progress_1.2.0                cmprsk_2.2-7                 
 [57] bit_1.1-14                    matlab_1.0.2                 
 [59] preprocessCore_1.44.0         km.ci_0.5-2                  
 [61] htmlwidgets_1.3               httr_1.4.0                   
 [63] RColorBrewer_1.1-2            pkgconfig_2.0.2              
 [65] XML_3.98-1.19                 R.methodsS3_1.7.1            
 [67] locfit_1.5-9.1                DNAcopy_1.56.0               
 [69] tidyselect_0.2.5              rlang_0.3.3                  
 [71] later_0.8.0                   AnnotationDbi_1.44.0         
 [73] munsell_0.5.0                 tools_3.5.2                  
 [75] downloader_0.4                generics_0.0.2               
 [77] RSQLite_2.1.1                 ExperimentHub_1.8.0          
 [79] broom_0.5.1                   stringr_1.4.0                
 [81] yaml_2.2.0                    knitr_1.22                   
 [83] bit64_0.9-7                   survMisc_0.5.5               
 [85] purrr_0.3.2                   randomForest_4.6-14          
 [87] EDASeq_2.16.3                 nlme_3.1-137                 
 [89] mime_0.6                      R.oo_1.22.0                  
 [91] xml2_1.2.0                    biomaRt_2.38.0               
 [93] compiler_3.5.2                curl_3.3                     
 [95] interactiveDisplayBase_1.20.0 tibble_2.1.1                 
 [97] geneplotter_1.60.0            stringi_1.4.3                
 [99] GenomicFeatures_1.34.7        lattice_0.20-38              
[101] Matrix_1.2-17                 KMsurv_0.1-5                 
[103] pillar_1.3.1                  BiocManager_1.30.4           
[105] GlobalOptions_0.1.0           data.table_1.12.0            
[107] bitops_1.0-6                  httpuv_1.5.0                 
[109] rtracklayer_1.42.2            R6_2.4.0                     
[111] latticeExtra_0.6-28           hwriter_1.3.2                
[113] promises_1.0.1                ShortRead_1.40.0             
[115] gridExtra_2.3                 codetools_0.2-16             
[117] assertthat_0.2.1              rjson_0.2.20                 
[119] GenomicAlignments_1.18.1      Rsamtools_1.34.1             
[121] GenomeInfoDbData_1.2.0        mgcv_1.8-28                  
[123] hms_0.4.2                     grid_3.5.2                   
[125] tidyr_0.8.3                   ggpubr_0.2                   
[127] shiny_1.2.0
TCGAbiolinks GDCprepare error • 607 views
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Entering edit mode
tiagochst ▴ 150
@tiagochst-7121
Last seen 2.2 years ago
Brazil

Hello,

This bug was solved two days ago, but I am not sure the fix is in Bioconductor yet. You update with the GitHub version with BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

Best regards, Tiago

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Entering edit mode

Thanks very much for your reply. I updated with github version and now it works.

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