Question: Error during GDCprepare
gravatar for Mariana Boroni
2.8 years ago by
Mariana Boroni10 wrote:

Hi all, I am facing a problem with TCGAbiolinks, when I'm using the GDCprepare command: 

This is what I ma doing:


# Download the expression data
query.exp <- GDCquery(project = c("TCGA-ESCA"),
                      legacy = TRUE,
                      data.category = "Gene expression",
                      data.type = "Gene expression quantification",
                      platform = "Illumina HiSeq",
                      file.type = "results")

> ESCA.exp <- GDCprepare(query = query.exp, save = TRUE, save.filename = "ESCA_Exp.rda")
  |===============================================================================================================================| 100%Extra content at the end of the document
Error: 1: Extra content at the end of the document

Any idea what could be wrong and if there is a way to fix it? Appreciate any help or suggestions.

Here's my session info: 

> sessionInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

 [1] LC_CTYPE=pt_BR.UTF-8       LC_NUMERIC=C               LC_TIME=pt_BR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=pt_BR.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=pt_BR.UTF-8       LC_NAME=C                 

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

other attached packages:
[1] SummarizedExperiment_1.0.2 Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
[5] IRanges_2.4.8              S4Vectors_0.8.11           BiocGenerics_0.16.1        ComplexHeatmap_1.10.2     
[9] TCGAbiolinks_2.1.6        

loaded via a namespace (and not attached):
  [1] circlize_0.3.8                          aroma.light_3.0.0                       plyr_1.8.4                             
  [4] igraph_1.0.1                            lazyeval_0.2.0                          ConsensusClusterPlus_1.24.0            
  [7] splines_3.2.3                           BiocParallel_1.4.3                      ggplot2_2.1.0                          
 [10] TH.data_1.0-7                           digest_0.6.10                           foreach_1.4.3                          
 [13] BiocInstaller_1.20.3                    gdata_2.17.0                            magrittr_1.5                           
 [16] cluster_2.0.4                           doParallel_1.0.10                       limma_3.26.9                           
 [19] Biostrings_2.38.4                       readr_1.0.0                             annotate_1.48.0                        
 [22] matrixStats_0.50.2                      R.utils_2.3.0                           sandwich_2.3-4                         
 [25] colorspace_1.2-6                        rvest_0.3.2                             ggrepel_0.5                            
 [28] haven_0.2.1                             dplyr_0.5.0                             jsonlite_1.0                           
 [31] RCurl_1.95-4.8                          hexbin_1.27.1                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [34] graph_1.48.0                            genefilter_1.52.1                       lme4_1.1-12                            
 [37] supraHex_1.8.0                          survival_2.39-5                         zoo_1.7-13                             
 [40] iterators_1.0.8                         ape_3.5                                 gtable_0.2.0                           
 [43] zlibbioc_1.16.0                         XVector_0.10.0                          sjstats_0.4.0                          
 [46] GetoptLong_0.1.4                        sjmisc_1.8                              kernlab_0.9-24                         
 [49] Rgraphviz_2.14.0                        shape_1.4.2                             prabclus_2.2-6                         
 [52] DEoptimR_1.0-6                          scales_0.4.0                            DESeq_1.22.1                           
 [55] futile.options_1.0.0                    mvtnorm_1.0-5                           DBI_0.5                                
 [58] GGally_1.2.0                            edgeR_3.12.1                            ggthemes_3.2.0                         
 [61] Rcpp_0.12.6                             xtable_1.8-2                            matlab_1.0.2                           
 [64] mclust_5.2                              preprocessCore_1.32.0                   httr_1.2.1                             
 [67] gplots_3.0.1                            RColorBrewer_1.1-2                      fpc_2.1-10                             
 [70] modeltools_0.2-21                       reshape_0.8.5                           XML_3.98-1.4                           
 [73] R.methodsS3_1.7.1                       flexmix_2.3-13                          nnet_7.3-12                            
 [76] reshape2_1.4.1                          AnnotationDbi_1.32.3                    munsell_0.4.3                          
 [79] tools_3.2.3                             downloader_0.4                          RSQLite_1.0.0                          
 [82] broom_0.4.1                             stringr_1.1.0                           knitr_1.14                             
 [85] robustbase_0.92-6                       caTools_1.17.1                          dendextend_1.3.0                       
 [88] coin_1.1-2                              EDASeq_2.4.1                            nlme_3.1-128                           
 [91] whisker_0.3-2                           R.oo_1.20.0                             xml2_1.0.0                             
 [94] biomaRt_2.26.1                          curl_1.2                                affyio_1.40.0                          
 [97] tibble_1.2                              geneplotter_1.48.0                      stringi_1.1.1                          
[100] futile.logger_1.4.3                     GenomicFeatures_1.22.13                 lattice_0.20-33                        
[103] trimcluster_0.1-2                       Matrix_1.2-7                            psych_1.6.6                            
[106] nloptr_1.0.4                            effects_3.1-1                           stringdist_0.9.4.1                     
[109] GlobalOptions_0.0.10                    data.table_1.9.6                        cowplot_0.6.2                          
[112] bitops_1.0-6                            dnet_1.0.9                              rtracklayer_1.30.4                     
[115] R6_2.1.3                                latticeExtra_0.6-28                     affy_1.48.0                            
[118] hwriter_1.3.2                           ShortRead_1.28.0                        KernSmooth_2.23-15                     
[121] codetools_0.2-14                        lambda.r_1.1.9                          MASS_7.3-45                            
[124] gtools_3.5.0                            assertthat_0.1                          chron_2.3-47                           
[127] rjson_0.2.15                            mnormt_1.5-4                            GenomicAlignments_1.6.3                
[130] Rsamtools_1.22.0                        multcomp_1.4-6                          diptest_0.75-7                         
[133] sjPlot_2.0.2                            tidyr_0.6.0                             class_7.3-14                           
[136] minqa_1.2.4     




tcgabiolinks gdcprepare • 566 views
ADD COMMENTlink modified 2.8 years ago by tiagochst110 • written 2.8 years ago by Mariana Boroni10
Answer: Error during GDCprepare
gravatar for tiagochst
2.8 years ago by
tiagochst110 wrote:
This bug was in the biomart package. The server was down for maintenance. Now it is working.
ADD COMMENTlink written 2.8 years ago by tiagochst110
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 273 users visited in the last hour