Closed aninguyen closed 6 years ago
Thanks for the report. Could you update to the newest version of GenomicDataCommons? I addressed this a few months ago. If you have problems after updating, could you do me a favor and drop the output of sessionInfo()
here?
GenomicDataCommons::status() Error in curl::curl_fetch_memory(url, handle = handle) : Could not resolve host: gdc-api.nci.nih.gov; Unknown error sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.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] GenomicDataCommons_1.2.0 magrittr_1.5 BiocInstaller_1.28.0
loaded via a namespace (and not attached): [1] Rcpp_0.12.17 xml2_1.2.0 XVector_0.18.0 [4] GenomicRanges_1.30.3 BiocGenerics_0.24.0 hms_0.4.2 [7] zlibbioc_1.24.0 IRanges_2.12.0 R6_2.2.2 [10] rlang_0.2.1 httr_1.3.1 GenomeInfoDb_1.14.0 [13] tools_3.5.0 parallel_3.5.0 data.table_1.11.4 [16] lazyeval_0.2.1 tibble_1.4.2 crayon_1.3.4 [19] GenomeInfoDbData_1.0.0 readr_1.1.1 S4Vectors_0.16.0 [22] bitops_1.0-6 curl_3.2 RCurl_1.95-4.11 [25] compiler_3.5.0 pillar_1.3.0 stats4_3.5.0 [28] jsonlite_1.5 pkgconfig_2.0.1
Turns out my whole Bioconductor was out of date. Following these instructions to update all Bioconductor packages helped: https://bioconductor.org/install/#troubleshoot-biocinstaller Thanks for your help!
Glad to her it worked out for you.
I'm getting this same error
GenomicDataCommons::status()
Error in curl::curl_fetch_memory(url, handle = handle) :
Could not resolve host: gdc-api.nci.nih.gov
I can connect to correct url
httr::GET('https://api.gdc.cancer.gov/status')
Response [https://api.gdc.cancer.gov/status]
Date: 2018-09-01 13:10
Status: 200
Content-Type: application/json
Size: 168 B
{
"commit": "8acb9697bd3e944def954f8d1c0b5c22a0fbc8fa",
"data_release": "Data Release 12.0 - August 23, 2018",
"status": "OK",
"tag": "1.15.1",
"version": 1
Here's my sessionInfo()
sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
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] TCGAbiolinks_2.6.12 GenomicDataCommons_1.2.0 magrittr_1.5
loaded via a namespace (and not attached):
[1] colorspace_1.3-2 selectr_0.4-1
[3] rjson_0.2.20 hwriter_1.3.2
[5] circlize_0.4.4 XVector_0.18.0
[7] GenomicRanges_1.30.3 GlobalOptions_0.1.0
[9] ggpubr_0.1.8 matlab_1.0.2
[11] ggrepel_0.8.0 bit64_0.9-7
[13] AnnotationDbi_1.40.0 xml2_1.2.0
[15] codetools_0.2-15 splines_3.4.4
[17] R.methodsS3_1.7.1 doParallel_1.0.11
[19] DESeq_1.30.0 geneplotter_1.56.0
[21] knitr_1.20 jsonlite_1.5
[23] Rsamtools_1.30.0 km.ci_0.5-2
[25] broom_0.5.0 annotate_1.56.2
[27] cluster_2.0.7-1 R.oo_1.22.0
[29] readr_1.1.1 compiler_3.4.4
[31] httr_1.3.1 backports_1.1.2
[33] assertthat_0.2.0 Matrix_1.2-14
[35] lazyeval_0.2.1 limma_3.34.9
[37] prettyunits_1.0.2 tools_3.4.4
[39] bindrcpp_0.2.2 gtable_0.2.0
[41] glue_1.3.0 GenomeInfoDbData_1.0.0
[43] dplyr_0.7.6 ggthemes_4.0.1
[45] ShortRead_1.36.1 Rcpp_0.12.18
[47] Biobase_2.38.0 Biostrings_2.46.0
[49] nlme_3.1-137 rtracklayer_1.38.3
[51] iterators_1.0.10 stringr_1.3.1
[53] rvest_0.3.2 XML_3.98-1.16
[55] edgeR_3.20.9 zoo_1.8-3
[57] zlibbioc_1.24.0 scales_1.0.0
[59] aroma.light_3.8.0 hms_0.4.2
[61] parallel_3.4.4 SummarizedExperiment_1.8.1
[63] RColorBrewer_1.1-2 ComplexHeatmap_1.17.1
[65] curl_3.2 memoise_1.1.0
[67] gridExtra_2.3 KMsurv_0.1-5
[69] ggplot2_3.0.0 downloader_0.4
[71] biomaRt_2.34.2 latticeExtra_0.6-28
[73] stringi_1.2.4 RSQLite_2.1.1
[75] genefilter_1.60.0 S4Vectors_0.16.0
[77] foreach_1.4.4 RMySQL_0.10.15
[79] GenomicFeatures_1.30.3 BiocGenerics_0.24.0
[81] BiocParallel_1.12.0 shape_1.4.4
[83] GenomeInfoDb_1.14.0 rlang_0.2.2
[85] pkgconfig_2.0.2 matrixStats_0.54.0
[87] bitops_1.0-6 lattice_0.20-35
[89] purrr_0.2.5 bindr_0.1.1
[91] GenomicAlignments_1.14.2 cmprsk_2.2-7
[93] bit_1.1-14 tidyselect_0.2.4
[95] plyr_1.8.4 R6_2.2.2
[97] IRanges_2.12.0 DelayedArray_0.4.1
[99] DBI_1.0.0 mgcv_1.8-24
[101] pillar_1.3.0 survival_2.42-6
[103] RCurl_1.95-4.11 tibble_1.4.2
[105] EDASeq_2.12.0 crayon_1.3.4
[107] survMisc_0.5.5 GetoptLong_0.1.7
[109] progress_1.2.0 locfit_1.5-9.1
[111] grid_3.4.4 sva_3.26.0
[113] data.table_1.11.4 blob_1.1.1
[115] ConsensusClusterPlus_1.42.0 digest_0.6.16
[117] xtable_1.8-3 tidyr_0.8.1
[119] R.utils_2.7.0 stats4_3.4.4
[121] munsell_0.5.0 survminer_0.4.3
What is the latest version of GenomicDataCommons
that should work?
I tried reinstalling biocInstaller...didn't help. Any clues how I can resolve the issue?
Hi, @ChiWPak. You will need to upgrade R to the current version (3.5.x) and then reinstall Bioconductor and GenomicDataCommons. Sorry for the inconvenience.
Hi Sean: Oof - my afternoon! Thanks for the reply, I'll start the process and let you know the outcome.
EDIT: Upgrading to R 3.5.1, reinstalling Bioconductor, and getting GenomicDataCommons_1.4.1
worked for me too - thanks!
Could you check if the GenomicDataCommons package has the latest URL for the GDC API? Below are some of my outputs.
From within R:
From Linux command line: $ curl -v -I https://gdc-api.nci.nih.gov/status
Closing connection 0 curl: (6) Couldn't resolve host 'gdc-api.nci.nih.gov'
$ curl -v -I https://api.gdc.cancer.gov/status
So the latest API URL (https://api.gdc.cancer.gov/) should be used in the R package. Thanks!