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Bioconductor / GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.
http://bioconductor.github.io/GenomicDataCommons/
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GenomicDataCommons::status() error, when other connections seem fine. #66

Closed RichardJActon closed 5 years ago

RichardJActon commented 5 years ago

I installed the genomicDataCommons R package, as bellow:

source("https://bioconductor.org/biocLite.R")
biocLite("GenomicDataCommons")
library(GenomicDataCommons)

Then ran the connection check, and go this error:

GenomicDataCommons::status()

> Error in curl::curl_fetch_memory(url, handle = handle) : 
> Could not resolve host: gdc-api.nci.nih.gov

Doing: httr::GET('http://gdc-api.nci.nih.gov/status') returns an identical error, but doing the below works fine: 

httr::GET('https://api.gdc.cancer.gov/status')

> Response [https://api.gdc.cancer.gov/status]
>   Date: 2018-10-19 10:41
>   Status: 200
>   Content-Type: application/json
>   Size: 171 B
> {
>   "commit": "22932f557e607b117bb1e6af75729ac1ef7417d4",
>   "data_release": "Data Release 13.0 - September 27, 2018",
>   "status": "OK",
>   "tag": "1.15.1",
>   "version": 1

So there does not seem to be an issue with curl/httr working for other things I've tried updating and/or reinstalling all the relevant packages as suggested in https://github.com/Bioconductor/GenomicDataCommons/issues/35 and https://stackoverflow.com/questions/35055715/ssl-connect-error-in-httr-curl. my command line curl is behaving consistently with my R curl - that is to say, not working for http://gdc-api.nci.nih.gov/status

Any suggestings for resolving this?

SessionInfo:

R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.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            

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19           rstudioapi_0.8         xml2_1.2.0             knitr_1.20             XVector_0.18.0         GenomicRanges_1.30.3   BiocGenerics_0.24.0   
 [8] hms_0.4.2              zlibbioc_1.24.0        IRanges_2.12.0         R6_2.3.0               rlang_0.2.2            httr_1.3.1             GenomeInfoDb_1.14.0   
[15] tools_3.4.4            parallel_3.4.4         data.table_1.11.8      yaml_2.2.0             lazyeval_0.2.1         tibble_1.4.2           crayon_1.3.4          
[22] GenomeInfoDbData_1.0.0 readr_1.1.1            S4Vectors_0.16.0       bitops_1.0-6           curl_3.2               RCurl_1.95-4.11        compiler_3.4.4        
[29] pillar_1.3.0           stats4_3.4.4           jsonlite_1.5           pkgconfig_2.0.2
RichardJActon commented 5 years ago

Ah found the base url change in https://github.com/Bioconductor/GenomicDataCommons/blob/master/R/constants.R

installed the development version direct from github and that fixed the issue - it would be good if this change got pushed to Bioconductor soon though.