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guidance on solving SSL error? #35
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Does this work for you, Vince?
Output should look something like:
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Hi, @vjcitn. This looks like a problem with ssl verification. After starting R and loading httr, can you do this and then install the package in the same R session? httr::set_config(httr::config(ssl_verifypeer=0L)) This has been seen elsewhere including swirldev/swirl#475. I think the ultimate fix is to update the SSL package for your system. What OS are you on? |
And another reference with suggestions for linux. http://stackoverflow.com/questions/35055715/ssl-connect-error-in-httr-curl |
Thanks for looking into this. I am on Mac OSX 10.11.6 .
Enter a frame number, or 0 to exit 1: httr::GET("https://gdc-api.nci.nih.gov/status") Selection: 0
Matrix products: default locale: attached base packages: other attached packages: loaded via a namespace (and not attached): |
Thanks, @vjcitn. If you do this before the httr::GET, do you still get the error? httr::set_config(httr::config(ssl_verifypeer=0L)) |
indeed the error occurs after set_config
httr::set_config(httr::config(ssl_verifypeer=0L))
httr::GET('https://gdc-api.nci.nih.gov/status')
*Error in curl::curl_fetch_memory(url, handle = handle) : *
* SSL connect error*
Enter a frame number, or 0 to exit
1: httr::GET("https://gdc-api.nci.nih.gov/status")
2: request_perform(req, hu$handle$handle)
3: request_fetch(req$output, req$url, handle)
4: request_fetch.write_memory(req$output, req$url, handle)
5: curl::curl_fetch_memory(url, handle = handle)
…On Fri, Mar 3, 2017 at 4:30 PM, Sean Davis ***@***.***> wrote:
Thanks, @vjcitn <https://github.com/vjcitn>. If you do this before the
httr::GET, do you still get the error?
httr::set_config(httr::config(ssl_verifypeer=0L))
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Sorry for the runaround. I have not been able to reproduce this locally, but two of you are seeing the same issue, so I know we need to track it down. And how about: httr::set_config(httr::config(ssl_verifypeer=0L, ssl_verifyhost=0L)) If that doesn't do the trick, how about: httr::set_config(httr::config(ssl_verifypeer=0L, ssl_verifyhost=0L, sslversion=3)) Thanks for the help and patience. |
So, it looks like an update to Let me know how it goes. |
I hate to drag this out so long. I upgraded openssl and attempted to
inform the package build environment about where to
look for the current openssl
%vjcair> openssl version -a
OpenSSL 1.0.2k 26 Jan 2017
built on: reproducible build, date unspecified
platform: darwin64-x86_64-cc
options: bn(64,64) rc4(ptr,int) des(idx,cisc,16,int) idea(int)
blowfish(idx)
compiler: clang -I. -I.. -I../include -fPIC -fno-common -DOPENSSL_PIC
-DZLIB_SHARED -DZLIB -DOPENSSL_THREADS -D_REENTRANT -DDSO_DLFCN
-DHAVE_DLFCN_H -arch x86_64 -O3 -DL_ENDIAN -Wall -DOPENSSL_IA32_SSE2
-DOPENSSL_BN_ASM_MONT -DOPENSSL_BN_ASM_MONT5 -DOPENSSL_BN_ASM_GF2m
-DSHA1_ASM -DSHA256_ASM -DSHA512_ASM -DMD5_ASM -DAES_ASM -DVPAES_ASM
-DBSAES_ASM -DWHIRLPOOL_ASM -DGHASH_ASM -DECP_NISTZ256_ASM
OPENSSLDIR: "/usr/local/etc/openssl"
%vjcair>
%vjcair> pwd
/Users/stvjc
%vjcair> vi SSLSTUFF
%vjcair> export LDFLAGS=-L/usr/local/opt/openssl/lib:$LDFLAGS
%vjcair> export CPPFLAGS=-I/usr/local/opt/openssl/include:$CPPFLAGS
%vjcair> export
PKG_CONFIG_PATH=/usr/local/opt/openssl/lib/pkgconfig:$PKG_CONFIG_PATH
then using R CMD INSTALL --clean --preclean for current downloads of curl
and httr packages, we still have
httr::set_config(httr::config(ssl_verifypeer=0L, ssl_verifyhost=0L,
sslversion=3))
httr::GET('https://gdc-api.nci.nih.gov/status')
*Error in curl::curl_fetch_memory(url, handle = handle) : *
* SSL connect error*
Enter a frame number, or 0 to exit
1: httr::GET("https://gdc-api.nci.nih.gov/status")
2: request_perform(req, hu$handle$handle)
3: request_fetch(req$output, req$url, handle)
4: request_fetch.write_memory(req$output, req$url, handle)
5: curl::curl_fetch_memory(url, handle = handle)
Does R itself need to be rebuilt with the newer openSSL?
…On Sat, Mar 4, 2017 at 4:51 PM, Sean Davis ***@***.***> wrote:
So, it looks like an update to openssl is necessary. See 34b95b0
<34b95b0>
for details; a vignette section has attempted to outline the problem and
the potential solutions. On mac os, it appears that using brew to install
openssl, link it, and then reinstall curl and httr should do the trick.
Let me know how it goes.
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Thanks, @vjcitn. I really appreciate your patience in working through this. @hadley, @jeroenooms, or @kbroman, any thoughts on this issue? Any insight would be greatly appreciated. |
Here is a solution. It is likely a good idea to verify that command-line curl gets a good response
the response is relatively long but begins with `%vjcair> curl -v -I https://gdc-api.nci.nih.gov/status
If that is not working it does not seem that the R interface will work either. In order to get to this point, I needed to get a relatively current instance of openssl and
At this point I can install the R package for curl, but, in my case, not without putting
as a component of LDFLAGS in $HOME/.R/Makevars Once curl package is installed with a suitable openssl and libcurl, we can do
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Is this resolved? I have not been able to reproduce this error on MacOS 10.12 or MacOS 10.9 using any version of |
I consider it resolved. |
At a very high level, upgrade of openssl, upgrade/reinstallation of libcurl, and then re-installation in R of httr and curl seems to have been the fix. |
I don't think that was the problem. Note that OSX native It could very well have been a temporary server misconfiguration. |
Thanks, @jeroenooms. In any case, it appears that Vince and Martin were able to come to a solution for Vince. |
source 0.99.7
%vjcair> R CMD build GenomicDataCommons
Quitting from lines 91-98 (api.Rmd)
Error: processing vignette 'api.Rmd' failed with diagnostics:
SSL connect error
Execution halted
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