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fang291831388
•
0
@fang291831388-11375
Last seen 8.3 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
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?