TCGAbiolinks
TCGAbiolinks copied to clipboard
BioinformaticsFMRP
GDC server down, try to use this package later
Any reason that I'm gettin this error? I followed your github installation ( in the readme) ` Error in value[3L] : GDC server down, try to use this package later
sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils
[5] datasets methods base
other attached packages: [1] TCGAbiolinks_2.6.12 apcluster_1.4.7
loaded via a namespace (and not attached):
[1] backports_1.1.5
[2] circlize_0.4.8
[3] Hmisc_4.2-0
[4] aroma.light_3.8.0
[5] plyr_1.8.4
[6] selectr_0.4-1
[7] ConsensusClusterPlus_1.42.0
[8] lazyeval_0.2.2
[9] splines_3.4.3
[10] BiocParallel_1.12.0
[11] GenomeInfoDb_1.14.0
[12] ggplot2_3.2.1
[13] sva_3.26.0
[14] digest_0.6.21
[15] foreach_1.4.7
[16] htmltools_0.3.6
[17] magrittr_1.5
[18] checkmate_1.9.4
[19] memoise_1.1.0
[20] cluster_2.1.0
[21] doParallel_1.0.15
[22] limma_3.34.9
[23] remotes_2.1.0
[24] ComplexHeatmap_1.17.1
[25] Biostrings_2.46.0
[26] readr_1.3.1
[27] annotate_1.56.2
[28] matrixStats_0.55.0
[29] R.utils_2.9.0
[30] prettyunits_1.0.2
[31] colorspace_1.4-1
[32] blob_1.2.0
[33] rvest_0.3.4
[34] ggrepel_0.8.0
[35] xfun_0.10
[36] dplyr_0.7.7
[37] crayon_1.3.4
[38] RCurl_1.95-4.12
[39] jsonlite_1.6
[40] genefilter_1.60.0
[41] bindr_0.1.1
[42] zeallot_0.1.0
[43] survival_2.44-1.1
[44] zoo_1.8-6
[45] iterators_1.0.12
[46] glue_1.3.1
[47] survminer_0.4.6
[48] gtable_0.3.0
[49] zlibbioc_1.24.0
[50] XVector_0.18.0
[51] GetoptLong_0.1.7
[52] DelayedArray_0.4.1
[53] shape_1.4.4
[54] BiocGenerics_0.24.0
[55] scales_1.0.0
[56] DESeq_1.30.0
[57] DBI_1.0.0
[58] edgeR_3.20.9
[59] ggthemes_4.2.0
[60] Rcpp_0.12.19
[61] xtable_1.8-4
[62] progress_1.2.2
[63] htmlTable_1.13.2
[64] foreign_0.8-72
[65] bit_1.1-14
[66] matlab_1.0.2
[67] km.ci_0.5-2
[68] Formula_1.2-3
[69] stats4_3.4.3
[70] htmlwidgets_1.5.1
[71] httr_1.4.1
[72] RColorBrewer_1.1-2
[73] acepack_1.4.1
[74] pkgconfig_2.0.3
[75] XML_3.98-1.16
[76] R.methodsS3_1.7.1
[77] nnet_7.3-12
[78] locfit_1.5-9.1
[79] tidyselect_0.2.5
[80] rlang_0.4.0
[81] AnnotationDbi_1.40.0
[82] munsell_0.5.0
[83] tools_3.4.3
[84] downloader_0.4
[85] generics_0.0.2
[86] RSQLite_2.1.1
[87] broom_0.5.2
[88] stringr_1.4.0
[89] knitr_1.25
[90] bit64_0.9-7
[91] survMisc_0.5.5
[92] purrr_0.3.2
[93] bindrcpp_0.2.2
[94] EDASeq_2.12.0
[95] nlme_3.1-141
[96] R.oo_1.22.0
[97] xml2_1.2.0
[98] biomaRt_2.34.2
[99] compiler_3.4.3
[100] rstudioapi_0.10
[101] curl_4.2
[102] ggsignif_0.6.0
[103] tibble_2.1.3
[104] geneplotter_1.56.0
[105] stringi_1.4.3
[106] GenomicFeatures_1.30.3
[107] lattice_0.20-38
[108] Matrix_1.2-17
[109] KMsurv_0.1-5
[110] vctrs_0.2.0
[111] pillar_1.4.2
[112] BiocManager_1.30.7
[113] GlobalOptions_0.1.1
[114] data.table_1.12.0
[115] bitops_1.0-6
[116] rtracklayer_1.38.3
[117] GenomicRanges_1.30.3
[118] R6_2.4.0
[119] latticeExtra_0.6-28
[120] hwriter_1.3.2
[121] RMySQL_0.10.17
[122] ShortRead_1.36.1
[123] gridExtra_2.3
[124] IRanges_2.12.0
[125] codetools_0.2-16
[126] assertthat_0.2.1
[127] SummarizedExperiment_1.8.1
[128] DESeq2_1.18.1
[129] rjson_0.2.20
[130] GenomicAlignments_1.14.2
[131] Rsamtools_1.30.0
[132] S4Vectors_0.16.0
[133] GenomeInfoDbData_1.0.0
[134] mgcv_1.8-24
[135] parallel_3.4.3
[136] hms_0.5.1
[137] grid_3.4.3
[138] rpart_4.1-15
[139] tidyr_0.8.1
[140] ggpubr_0.2.3
[141] Biobase_2.38.0
[142] base64enc_0.1-3 `
Hello, try to upgrade your R version and download again TCGAbiolinks, it has solved this issue for me.
I got the same error from devtools::install_github('BioinformaticsFMRP/TCGAbiolinks'):
> library("TCGAbiolinks")
> query <- GDCquery(project = "TARGET-OS",
+ data.category = "Transcriptome Profiling",
+ data.type = "Gene Expression Quantification",
+ workflow.type = "HTSeq - Counts")
Error in value[[3L]](cond) :
GDC server down, try to use this package later
> sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.5 (Santiago)
Matrix products: default
BLAS: /data/SoftWare/R/R-4.0.1/lib64/R/lib/libRblas.so
LAPACK: /data/SoftWare/R/R-4.0.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.3.0 usethis_1.6.1 TCGAbiolinks_2.17.1
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.1.7
[3] aroma.light_3.18.0 BiocFileCache_1.12.0
[5] plyr_1.8.6 selectr_0.4-2
[7] splines_4.0.1 BiocParallel_1.22.0
[9] GenomeInfoDb_1.24.0 ggplot2_3.3.1
[11] sva_3.36.0 digest_0.6.25
[13] foreach_1.5.0 fansi_0.4.1
[15] magrittr_1.5 memoise_1.1.0
[17] doParallel_1.0.15 remotes_2.1.1
[19] openxlsx_4.1.5 limma_3.44.1
[21] Biostrings_2.56.0 readr_1.3.1
[23] annotate_1.66.0 matrixStats_0.56.0
[25] R.utils_2.9.2 askpass_1.1
[27] prettyunits_1.1.1 jpeg_0.1-8.1
[29] colorspace_1.4-1 blob_1.2.1
[31] rvest_0.3.5 rappdirs_0.3.1
[33] ggrepel_0.8.2 haven_2.3.1
[35] xfun_0.14 dplyr_1.0.0
[37] callr_3.4.3 tcltk_4.0.1
[39] crayon_1.3.4 RCurl_1.98-1.2
[41] jsonlite_1.6.1 genefilter_1.70.0
[43] zoo_1.8-8 survival_3.1-12
[45] iterators_1.0.12 glue_1.4.1
[47] survminer_0.4.7 gtable_0.3.0
[49] zlibbioc_1.34.0 XVector_0.28.0
[51] DelayedArray_0.14.0 pkgbuild_1.0.8
[53] car_3.0-8 BiocGenerics_0.34.0
[55] abind_1.4-5 scales_1.1.1
[57] DESeq_1.39.0 DBI_1.1.0
[59] edgeR_3.30.3 rstatix_0.5.0
[61] ggthemes_4.2.0 Rcpp_1.0.4.6
[63] xtable_1.8-4 progress_1.2.2
[65] foreign_0.8-80 bit_1.1-15.2
[67] km.ci_0.5-2 stats4_4.0.1
[69] httr_1.4.1 RColorBrewer_1.1-2
[71] ellipsis_0.3.1 pkgconfig_2.0.3
[73] XML_3.99-0.3 R.methodsS3_1.8.0
[75] dbplyr_1.4.4 locfit_1.5-9.4
[77] tidyselect_1.1.0 rlang_0.4.6
[79] AnnotationDbi_1.50.0 munsell_0.5.0
[81] cellranger_1.1.0 tools_4.0.1
[83] cli_2.0.2 downloader_0.4
[85] generics_0.0.2 RSQLite_2.2.0
[87] broom_0.5.6 stringr_1.4.0
[89] processx_3.4.2 fs_1.4.1
[91] knitr_1.28 bit64_0.9-7
[93] zip_2.0.4 survMisc_0.5.5
[95] purrr_0.3.4 EDASeq_2.22.0
[97] nlme_3.1-148 R.oo_1.23.0
[99] postlogic_0.1.0.1 xml2_1.3.2
[101] biomaRt_2.44.0 compiler_4.0.1
[103] curl_4.3 png_0.1-7
[105] parsetools_0.1.3 testthat_2.3.2
[107] ggsignif_0.6.0 tibble_3.0.1
[109] geneplotter_1.66.0 stringi_1.4.6
[111] ps_1.3.3 desc_1.2.0
[113] GenomicFeatures_1.40.0 forcats_0.5.0
[115] lattice_0.20-41 Matrix_1.2-18
[117] KMsurv_0.1-5 vctrs_0.3.1
[119] purrrogress_0.1.1 pillar_1.4.4
[121] lifecycle_0.2.0 BiocManager_1.30.10
[123] data.table_1.12.8 bitops_1.0-6
[125] rtracklayer_1.48.0 GenomicRanges_1.40.0
[127] R6_2.4.1 latticeExtra_0.6-29
[129] hwriter_1.3.2 ShortRead_1.46.0
[131] gridExtra_2.3 rio_0.5.16
[133] IRanges_2.22.2 pkgcond_0.1.0
[135] sessioninfo_1.1.1 codetools_0.2-16
[137] pkgload_1.1.0 assertthat_0.2.1
[139] SummarizedExperiment_1.18.1 rprojroot_1.3-2
[141] openssl_1.4.1 withr_2.2.0
[143] GenomicAlignments_1.24.0 Rsamtools_2.4.0
[145] S4Vectors_0.26.1 GenomeInfoDbData_1.2.3
[147] mgcv_1.8-31 parallel_4.0.1
[149] hms_0.5.3 testextra_0.1.0.1
[151] grid_4.0.1 tidyr_1.1.0
[153] carData_3.0-4 ggpubr_0.3.0
[155] Biobase_2.48.0
>
