Question: Error during GDCprepare
0
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:

library("TCGAbiolinks")
library("ComplexHeatmap")
library("SummarizedExperiment")

# 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")

GDCdownload(query.exp)
> 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

locale:
 [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                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=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     

Sincerely,

Mariana

 

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
0
gravatar for tiagochst
2.8 years ago by
tiagochst110
Brazil
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
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