brisk022
commented
5 years ago The old api URL no longer redirects. You need to upgrade GenomicDataCommons to version 1.4 or above.
Alternatively, if you need to stay with your installed version (v1.2), you can download the source from Bioconductor, change the URL in R/constants.R (.gdc_base on the first line) from "https://gdc-api.nci.nih.gov" to "https://api.gdc.cancer.gov", and re-install from the updated source using devtools::install_local(<sourceDir>, force = T).
seandavi
Hi,
I have a problem to use the query.met<-GDCquery(project="TCGA-LAML",legacy=TRUE,data.category="DNA methylation",platform="Illumina Human Methylation 450") Error in value[3L] : GDC server down, try to use this package later In addition, there is an error about GenomicDataCommons::status() Error in curl::curl_fetch_memory(url, handle = handle) : Could not resolve host: gdc-api.nci.nih.gov
sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0 LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0 locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 [6] LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicDataCommons_1.2.0 TCGAbiolinks_2.9.5 DESeq2_1.18.1 [4] EnsDb.Hsapiens.v86_2.99.0 BiocInstaller_1.28.0 EnsDb.Mmusculus.v79_2.99.0 [7] ensembldb_2.2.2 AnnotationFilter_1.2.0 SummarizedExperiment_1.8.1 [10] DelayedArray_0.4.1 matrixStats_0.54.0 VennDiagram_1.6.20 [13] futile.logger_1.4.3 tximport_1.6.0 TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 [16] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0 Biobase_2.38.0 [19] gridExtra_2.3 gtable_0.2.0 bindrcpp_0.2.2 [22] forcats_0.3.0 stringr_1.3.1 purrr_0.2.5 [25] readr_1.1.1 tibble_1.4.2 tidyverse_1.2.1 [28] tidyr_0.8.1 ggpubr_0.1.8 magrittr_1.5 [31] dplyr_0.7.6 reshape_0.8.7 ggplot2_3.0.0 [34] rtracklayer_1.38.3 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 [37] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 [40] limma_3.34.9 loaded via a namespace (and not attached): [1] utf8_1.1.4 R.utils_2.7.0 tidyselect_0.2.4 htmlwidgets_1.2 RSQLite_2.1.1 [6] BiocParallel_1.12.0 devtools_1.13.6 DESeq_1.30.0 munsell_0.5.0 codetools_0.2-15 [11] withr_2.1.2 colorspace_1.3-2 knitr_1.20 rstudioapi_0.7 labeling_0.3 [16] git2r_0.23.0 GenomeInfoDbData_1.0.0 hwriter_1.3.2 KMsurv_0.1-5 bit64_0.9-7 [21] rhdf5_2.22.0 downloader_0.4 lambda.r_1.2.3 ggthemes_4.0.1 EDASeq_2.12.0 [26] R6_2.2.2 doParallel_1.0.11 locfit_1.5-9.1 bitops_1.0-6 assertthat_0.2.0 [31] promises_1.0.1 scales_0.5.0.9000 nnet_7.3-12 sva_3.26.0 rlang_0.2.1 [36] genefilter_1.60.0 cmprsk_2.2-7 GlobalOptions_0.1.0 splines_3.4.4 lazyeval_0.2.1 [41] acepack_1.4.1 selectr_0.4-1 checkmate_1.8.5 broom_0.5.0 yaml_2.2.0 [46] modelr_0.1.2 backports_1.1.2 httpuv_1.4.4.1 Hmisc_4.1-1 RMySQL_0.10.15 [51] tools_3.4.4 RColorBrewer_1.1-2 Rcpp_0.12.18 plyr_1.8.4 base64enc_0.1-3 [56] progress_1.2.0 zlibbioc_1.24.0 RCurl_1.95-4.11 prettyunits_1.0.2 rpart_4.1-13 [61] GetoptLong_0.1.7 cowplot_0.9.3 zoo_1.8-3 haven_1.1.2 ggrepel_0.8.0 [66] cluster_2.0.7-1 data.table_1.11.4 futile.options_1.0.1 circlize_0.4.4 survminer_0.4.3 [71] ProtGenerics_1.10.0 aroma.light_3.8.0 hms_0.4.2 mime_0.5 xtable_1.8-3 [76] XML_3.98-1.16 readxl_1.1.0 shape_1.4.4 compiler_3.4.4 biomaRt_2.34.2 [81] crayon_1.3.4 R.oo_1.22.0 htmltools_0.3.6 mgcv_1.8-24 later_0.7.4 [86] Formula_1.2-3 geneplotter_1.56.0 lubridate_1.7.4 DBI_1.0.0 formatR_1.5 [91] matlab_1.0.2 ComplexHeatmap_1.17.1 ShortRead_1.36.1 Matrix_1.2-14 cli_1.0.0 [96] R.methodsS3_1.7.1 bindr_0.1.1 pkgconfig_2.0.2 km.ci_0.5-2 GenomicAlignments_1.14.2 [101] foreign_0.8-71 xml2_1.2.0 foreach_1.4.4 annotate_1.56.2 XVector_0.18.0 [106] rvest_0.3.2 digest_0.6.17 ConsensusClusterPlus_1.42.0 Biostrings_2.46.0 cellranger_1.1.0 [111] htmlTable_1.12 survMisc_0.5.5 edgeR_3.20.9 curl_3.2 shiny_1.1.0 [116] Rsamtools_1.30.0 rjson_0.2.20 nlme_3.1-137 jsonlite_1.5 fansi_0.3.0 [121] pillar_1.3.0 lattice_0.20-35 httr_1.3.1 survival_2.42-3 interactiveDisplayBase_1.16.0 [126] glue_1.3.0 iterators_1.0.10 bit_1.1-14 stringi_1.2.3 blob_1.1.1 [131] AnnotationHub_2.10.1 latticeExtra_0.6-28 memoise_1.1.0
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How can I solve the problem? Thanks a lot.