Open dBenedek opened 1 year ago
Hello,
I arm trying to use the
TCGAbiolinks:::getProjectSummary("TCGA-HNSC")
command, but I get the following message:
Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [api.gdc.cancer.gov] Resolving timed out after 10000 milliseconds
The same happens with GDCquery().
GDCquery()
I would appreciate your help!
Session info:
R Under development (unstable) (2022-02-17 r81757) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] 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] biomaRt_2.51.3 TCGAbiolinks_2.23.8 forcats_0.5.1 stringr_1.4.0 [5] dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 [9] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1 loaded via a namespace (and not attached): [1] readxl_1.3.1 backports_1.4.1 AnnotationHub_3.3.9 [4] BiocFileCache_2.3.4 systemfonts_1.0.4 plyr_1.8.6 [7] splines_4.2.0 usethis_2.1.5 GenomeInfoDb_1.31.4 [10] digest_0.6.29 htmltools_0.5.2 fansi_1.0.2 [13] magrittr_2.0.2 memoise_2.0.1 tzdb_0.2.0 [16] limma_3.51.5 remotes_2.4.2 Biostrings_2.63.1 [19] annotate_1.73.0 modelr_0.1.8 matrixStats_0.61.0 [22] R.utils_2.11.0 svglite_2.1.0 prettyunits_1.1.1 [25] colorspace_2.0-2 blob_1.2.2 rvest_1.0.2 [28] rappdirs_0.3.3 haven_2.4.3 xfun_0.29 [31] callr_3.7.0 crayon_1.5.0 RCurl_1.98-1.6 [34] jsonlite_1.7.3 genefilter_1.77.0 survival_3.2-13 [37] glue_1.6.1 kableExtra_1.3.4 gtable_0.3.0 [40] zlibbioc_1.41.0 XVector_0.35.0 webshot_0.5.3 [43] DelayedArray_0.21.2 pkgbuild_1.3.1 BiocGenerics_0.41.2 [46] scales_1.2.1 DBI_1.1.2 edgeR_3.37.0 [49] Rcpp_1.0.8 viridisLite_0.4.0 xtable_1.8-4 [52] progress_1.2.2 bit_4.0.4 stats4_4.2.0 [55] DT_0.22 htmlwidgets_1.5.4 httr_1.4.2 [58] ellipsis_0.3.2 pkgconfig_2.0.3 XML_3.99-0.8 [61] R.methodsS3_1.8.1 dbplyr_2.1.1 locfit_1.5-9.4 [64] utf8_1.2.2 tidyselect_1.1.1 rlang_1.0.5 [67] later_1.3.0 AnnotationDbi_1.57.1 munsell_0.5.0 [70] BiocVersion_3.15.0 cellranger_1.1.0 tools_4.2.0 [73] cachem_1.0.6 downloader_0.4 cli_3.3.0 [76] generics_0.1.2 RSQLite_2.2.10 ExperimentHub_2.3.5 [79] devtools_2.4.3 broom_0.7.12 evaluate_0.15 [82] fastmap_1.1.0 yaml_2.3.4 processx_3.5.2 [85] knitr_1.37 bit64_4.0.5 fs_1.5.2 [88] KEGGREST_1.35.0 mime_0.12 R.oo_1.24.0 [91] xml2_1.3.3 brio_1.1.3 compiler_4.2.0 [94] rstudioapi_0.13 filelock_1.0.2 curl_4.3.2 [97] png_0.1-7 interactiveDisplayBase_1.33.0 testthat_3.1.2 [100] reprex_2.0.1 stringi_1.7.6 ps_1.6.0 [103] TCGAbiolinksGUI.data_1.15.1 desc_1.4.0 lattice_0.20-45 [106] Matrix_1.4-0 vctrs_0.3.8 pillar_1.7.0 [109] lifecycle_1.0.1 BiocManager_1.30.16 data.table_1.14.2 [112] bitops_1.0-7 httpuv_1.6.5 GenomicRanges_1.47.6 [115] R6_2.5.1 promises_1.2.0.1 IRanges_2.29.1 [118] sessioninfo_1.2.2 assertthat_0.2.1 pkgload_1.2.4 [121] SummarizedExperiment_1.25.3 rprojroot_2.0.2 withr_2.4.3 [124] S4Vectors_0.33.10 GenomeInfoDbData_1.2.7 hms_1.1.1 [127] grid_4.2.0 rmarkdown_2.11 MatrixGenerics_1.7.0 [130] Biobase_2.55.0 shiny_1.7.1 lubridate_1.8.0
Hello,
I arm trying to use the
command, but I get the following message:
The same happens with
GDCquery().I would appreciate your help!
Session info: