Problem connecting to gdc

[sowmyaiyer]

Successful installation done with biocLite('Bioconductor/GenomicDataCommons').

> files() Error in curl::curl_fetch_memory(url, handle = handle) : SSL connect error > httr::GET('https://gdc-api.nci.nih.gov/status') Error in curl::curl_fetch_memory(url, handle = handle) : SSL connect error > httr::GET('http://gdc-api.nci.nih.gov/status') Error in curl::curl_fetch_memory(url, handle = handle) : SSL connect error `> sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

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] ggplot2_2.2.1 GenomicDataCommons_0.99.8 magrittr_1.5
[4] dplyr_0.5.0 BiocInstaller_1.20.3

loaded via a namespace (and not attached): [1] Rcpp_0.12.9 git2r_0.14.0 plyr_1.8.4 R.methodsS3_1.7.1 R.utils_2.4.0
[6] tools_3.2.3 digest_0.6.12 jsonlite_1.3 memoise_1.0.0 tibble_1.2
[11] gtable_0.2.0 R.cache_0.12.0 shiny_1.0.0 DBI_0.5-1 curl_2.3
[16] R.rsp_0.30.0 withr_1.0.1 httr_1.2.1 knitr_1.14 xml2_1.1.1
[21] devtools_1.12.0 grid_3.2.3 data.table_1.10.4 R6_2.2.0 readr_1.0.0
[26] scales_0.4.1 htmltools_0.3.5 assertthat_0.1 mime_0.5 colorspace_1.2-7 [31] xtable_1.8-2 httpuv_1.3.3 labeling_0.3 miniUI_0.1.1 lazyeval_0.2.0
[36] munsell_0.4.3 R.oo_1.20.0 `

[seandavi]

Does the proposal here help?

[sowmyaiyer]

No it did not. Still the same error httr::GET('https://gdc-api.nci.nih.gov/status') Error in curl::curl_fetch_memory(url, handle = handle) : SSL connect error

I tried httr::set_config(httr::config(ssl_verifypeer=0L, ssl_verifyhost=0L, sslversion=3)) and httr::set_config(httr::config(ssl_verifypeer=0L, ssl_verifyhost=0L))

[sowmyaiyer]

Also, it seems to work from R command line but not from Rstudio This is from the R command line

sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

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

loaded via a namespace (and not attached): [1] httr_1.2.1 R6_2.2.0 curl_2.3

[seandavi]

Good news and bad. I just committed 34b95b09b. The good news is that the problem can be addressed by upgrading openssl on the system. The the new section in the vignette. The bad news is that this will require some work on the server, it seems, and is not "fixable" by R code. I have tried to point to at least one site with some hints, but this stuff is sometimes a bit tricky.

This should also cover the issues that @vjcitn is seeing in issue #35.

Let me know how it goes.

[seandavi]

It appears that libcurl and libcurl-devel would need an update as well, to take advantage of the new openssl. I'm not sure about the correct linux foo for making that happen on CentOS6, but this does seem to be the path forward.

[sowmyaiyer]

Thank you for looking into it. Is ftp an option instead of http?

[seandavi]

Unfortunately, no. This whole system on the server is built around a RESTful interface. That is only available using http(s) technologies. How are you doing with getting this working for yourself?

[sowmyaiyer]

I haven't approached the system admins yet. But I am confused about why it would work on the R command line if it were an OS-level issue?