Why the package readr can't be find?
0
0
Entering edit mode
@fang291831388-11375
Last seen 5.4 years ago

When I try to run the example of TCGAbiolinks, i get this error message:

     library("TCGAbiolinks", lib.loc="~/R/x86_64-pc-linux-gnu-library/3.3")
     query <- GDCquery(project = "TARGET-AML",
                       data.category = "Transcriptome Profiling",
                       data.type = "Gene Expression Quantification", 
                       workflow.type = "HTSeq - Counts")
Error in date_names_lang(date_names) :
  cannot open file '~/R/x86_64-pc-linux-gnu-library/3.3/readr/R/sysdata.rdb': No such file or directory

But i am sure this package is in that position.  I also try to reinstall this package, but it doesn't work. Really need help. Thank you.

Here is my sessioninfo:

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             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_2.0.6

loaded via a namespace (and not attached):
  [1] circlize_0.3.8                          aroma.light_3.2.0                       plyr_1.8.4                             
  [4] igraph_1.0.1                            lazyeval_0.2.0                          ConsensusClusterPlus_1.36.0            
  [7] splines_3.3.1                           BiocParallel_1.6.6                      GenomeInfoDb_1.8.3                     
 [10] ggplot2_2.1.0                           TH.data_1.0-7                           digest_0.6.10                          
 [13] foreach_1.4.3                           BiocInstaller_1.22.3                    gdata_2.17.0                           
 [16] magrittr_1.5                            cluster_2.0.4                           doParallel_1.0.10                      
 [19] limma_3.28.20                           ComplexHeatmap_1.10.2                   Biostrings_2.40.2                      
 [22] readr_1.0.0                             annotate_1.50.0                         matrixStats_0.50.2                     
 [25] R.utils_2.3.0                           sandwich_2.3-4                          colorspace_1.2-6                       
 [28] rvest_0.3.2                             ggrepel_0.5                             haven_0.2.1                            
 [31] dplyr_0.5.0                             RCurl_1.95-4.8                          jsonlite_1.0                           
 [34] hexbin_1.27.1                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 graph_1.50.0                           
 [37] genefilter_1.54.2                       lme4_1.1-12                             supraHex_1.10.0                        
 [40] survival_2.39-5                         zoo_1.7-13                              iterators_1.0.8                        
 [43] ape_3.5                                 gtable_0.2.0                            zlibbioc_1.18.0                        
 [46] XVector_0.12.1                          sjstats_0.4.0                           GetoptLong_0.1.4                       
 [49] sjmisc_1.8                              kernlab_0.9-24                          Rgraphviz_2.16.0                       
 [52] shape_1.4.2                             prabclus_2.2-6                          BiocGenerics_0.18.0                    
 [55] DEoptimR_1.0-6                          scales_0.4.0                            DESeq_1.24.0                           
 [58] mvtnorm_1.0-5                           DBI_0.5                                 GGally_1.2.0                           
 [61] edgeR_3.14.0                            ggthemes_3.2.0                          Rcpp_0.12.6                            
 [64] xtable_1.8-2                            matlab_1.0.2                            mclust_5.2                             
 [67] preprocessCore_1.34.0                   stats4_3.3.1                            httr_1.2.1                             
 [70] gplots_3.0.1                            RColorBrewer_1.1-2                      fpc_2.1-10                             
 [73] modeltools_0.2-21                       reshape_0.8.5                           XML_3.98-1.4                           
 [76] R.methodsS3_1.7.1                       flexmix_2.3-13                          nnet_7.3-12                            
 [79] reshape2_1.4.1                          AnnotationDbi_1.34.4                    munsell_0.4.3                          
 [82] tools_3.3.1                             downloader_0.4                          RSQLite_1.0.0                          
 [85] broom_0.4.1                             stringr_1.1.0                           knitr_1.14                             
 [88] robustbase_0.92-6                       caTools_1.17.1                          dendextend_1.3.0                       
 [91] coin_1.1-2                              EDASeq_2.6.2                            nlme_3.1-128                           
 [94] whisker_0.3-2                           R.oo_1.20.0                             xml2_1.0.0                             
 [97] biomaRt_2.28.0                          curl_1.2                                affyio_1.42.0                          
[100] tibble_1.2                              geneplotter_1.50.0                      stringi_1.1.1                          
[103] GenomicFeatures_1.24.5                  lattice_0.20-33                         trimcluster_0.1-2                      
[106] Matrix_1.2-7                            psych_1.6.6                             nloptr_1.0.4                           
[109] effects_3.1-1                           stringdist_0.9.4.1                      GlobalOptions_0.0.10                   
[112] data.table_1.9.6                        cowplot_0.6.2                           bitops_1.0-6                           
[115] dnet_1.0.9                              rtracklayer_1.32.2                      GenomicRanges_1.24.2                   
[118] R6_2.1.3                                latticeExtra_0.6-28                     affy_1.50.0                            
[121] hwriter_1.3.2                           ShortRead_1.30.0                        KernSmooth_2.23-15                     
[124] IRanges_2.6.1                           codetools_0.2-14                        MASS_7.3-45                            
[127] gtools_3.5.0                            assertthat_0.1                          chron_2.3-47                           
[130] SummarizedExperiment_1.2.3              rjson_0.2.15                            mnormt_1.5-4                           
[133] GenomicAlignments_1.8.4                 Rsamtools_1.24.0                        multcomp_1.4-6                         
[136] S4Vectors_0.10.3                        diptest_0.75-7                          parallel_3.3.1                         
[139] sjPlot_2.0.2                            grid_3.3.1                              tidyr_0.6.0                            
[142] class_7.3-14                            minqa_1.2.4                             Biobase_2.32.0      
software error tcgabiolinks readr • 1.2k views
ADD COMMENT
0
Entering edit mode

Just to be clear, `ls ~/R/x86_64-pc-linux-gnu-library/3.3/readr/R/sysdata.rdb` shows the file exists in that location? What are the file permissions?

ADD REPLY

Login before adding your answer.

Traffic: 391 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6