outdated API link - Githubissues

aninguyen commented 6 years ago

Could you check if the GenomicDataCommons package has the latest URL for the GDC API? Below are some of my outputs.

From within R:

GenomicDataCommons::status() Error in curl::curl_fetch_memory(url, handle = handle) : Could not resolve host: gdc-api.nci.nih.gov; Unknown error

From Linux command line: $ curl -v -I https://gdc-api.nci.nih.gov/status

getaddrinfo(3) failed for gdc-api.nci.nih.gov:443
Couldn't resolve host 'gdc-api.nci.nih.gov'
Closing connection 0 curl: (6) Couldn't resolve host 'gdc-api.nci.nih.gov'

$ curl -v -I https://api.gdc.cancer.gov/status
Trying 192.170.230.246...
TCP_NODELAY set
Connected to api.gdc.cancer.gov (192.170.230.246) port 443 (#0)

So the latest API URL (https://api.gdc.cancer.gov/) should be used in the R package. Thanks!

seandavi commented 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?

aninguyen commented 6 years ago

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

aninguyen commented 6 years ago

Turns out my whole Bioconductor was out of date.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!

seandavi commented 6 years ago

Glad to her it worked out for you.

ChiWPak commented 6 years ago

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?

seandavi commented 6 years ago

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.

ChiWPak commented 6 years ago

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!

Bioconductor / GenomicDataCommons

outdated API link #60