Error message: SSL certificate expired

[thatslifescience]

When trying to conduct searches using the rbhl package, I'm getting the following error message:
Error in curl::curl_fetch_memory(x$url$url, handle = x$url$handle) :
SSL certificate problem: certificate has expired

I've set my API key in .Renviron. This error message came up after using bhl_namesearch(). Is this a problem on my end? Thanks!

Session Info

─ Session info ────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.0 (2020-04-24)
 os       macOS Mojave 10.14.6        
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/New_York            
 date     2020-06-02                  

─ Packages ────────────────────────────────────────────────────────────────────────
 package     * version date       lib source        
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.0)
 backports     1.1.6   2020-04-05 [1] CRAN (R 4.0.0)
 callr         3.4.3   2020-03-28 [1] CRAN (R 4.0.0)
 cli           2.0.2   2020-02-28 [1] CRAN (R 4.0.0)
 colorspace    1.4-1   2019-03-18 [1] CRAN (R 4.0.0)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.0)
 crul          0.9.0   2019-11-06 [1] CRAN (R 4.0.0)
 curl        * 4.3     2019-12-02 [1] CRAN (R 4.0.0)
 desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.0)
 devtools      2.3.0   2020-04-10 [1] CRAN (R 4.0.0)
 digest        0.6.25  2020-02-23 [1] CRAN (R 4.0.0)
 dplyr         0.8.5   2020-03-07 [1] CRAN (R 4.0.0)
 ellipsis      0.3.0   2019-09-20 [1] CRAN (R 4.0.0)
 fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.0)
 fs            1.4.1   2020-04-04 [1] CRAN (R 4.0.0)
 ggplot2       3.3.0   2020-03-05 [1] CRAN (R 4.0.0)
 glue          1.4.1   2020-05-13 [1] CRAN (R 4.0.0)
 gtable        0.3.0   2019-03-25 [1] CRAN (R 4.0.0)
 httpcode      0.3.0   2020-04-10 [1] CRAN (R 4.0.0)
 jsonlite      1.6.1   2020-02-02 [1] CRAN (R 4.0.0)
 lattice       0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
 lifecycle     0.2.0   2020-03-06 [1] CRAN (R 4.0.0)
 magrittr      1.5     2014-11-22 [1] CRAN (R 4.0.0)
 Matrix        1.2-18  2019-11-27 [1] CRAN (R 4.0.0)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.0)
 munsell       0.5.0   2018-06-12 [1] CRAN (R 4.0.0)
 pillar        1.4.4   2020-05-05 [1] CRAN (R 4.0.0)
 pkgbuild      1.0.8   2020-05-07 [1] CRAN (R 4.0.0)
 pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.0.0)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 4.0.0)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.0)
 processx      3.4.2   2020-02-09 [1] CRAN (R 4.0.0)
 ps            1.3.3   2020-05-08 [1] CRAN (R 4.0.0)
 purrr         0.3.4   2020-04-17 [1] CRAN (R 4.0.0)
 R6            2.4.1   2019-11-12 [1] CRAN (R 4.0.0)
 rbhl        * 0.9.0   2020-01-29 [1] CRAN (R 4.0.0)
 Rcpp          1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
 remotes       2.1.1   2020-02-15 [1] CRAN (R 4.0.0)
 rlang         0.4.6   2020-05-02 [1] CRAN (R 4.0.0)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 4.0.0)
 rstudioapi    0.11    2020-02-07 [1] CRAN (R 4.0.0)
 scales        1.1.1   2020-05-11 [1] CRAN (R 4.0.0)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.0)
 testthat      2.3.2   2020-03-02 [1] CRAN (R 4.0.0)
 tibble        3.0.1   2020-04-20 [1] CRAN (R 4.0.0)
 tidyselect    1.1.0   2020-05-11 [1] CRAN (R 4.0.0)
 triebeard     0.3.0   2016-08-04 [1] CRAN (R 4.0.0)
 urltools      1.7.3   2019-04-14 [1] CRAN (R 4.0.0)
 usethis       1.6.1   2020-04-29 [1] CRAN (R 4.0.0)
 vctrs         0.3.0   2020-05-11 [1] CRAN (R 4.0.0)
 withr         2.2.0   2020-04-20 [1] CRAN (R 4.0.0)
 xml2          1.3.2   2020-04-23 [1] CRAN (R 4.0.0)

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

[sckott]

Thanks @thatslifescience I've just noticed this yesterday. I've reached out to BHL

[jeroen]

This is a global problem with many servers right now due to a major CA root cert being expired that turned out to be still used on many servers.

See details e.g. here https://calnetweb.berkeley.edu/calnet-technologists/incommon-sectigo-certificate-service/addtrust-external-root-expiration-may-2020

or here: https://support.sectigo.com/articles/Knowledge/Sectigo-AddTrust-External-CA-Root-Expiring-May-30-2020

Recent browsers and TLS libraries already have a workaround for this problem, so they are not affected, but some older versions are. As a workaround until the server has updated their certs, you can build the R curl package from source against libcurl from homebrew:

brew install curl
export PKG_CONFIG_PATH="/usr/local/opt/curl/lib/pkgconfig"
R

And then in R:

install.packages("curl", type = "source")

And then it should work.

[sckott]

worked for me, @thatslifescience let us know if the solution above works

[thatslifescience]

It's still not working, but it could be that I'm not following the code correctly in my Mac terminal. I successfully downloaded homebrew, installed curl through brew, and ran the command line for the PKG_CONFIG_PATH. When opening R in terminal, I get the following error message:

install.packages("curl", type = "source")
--- Please select a CRAN mirror for use in this session ---
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object r'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libfontconfig.1.dylib
Referenced from: /usr/local/lib/libtk8.6.dylib
Reason: Incompatible library version: libtk8.6.dylib requires version 11.0.0 or later, but libfontconfig.1.dylib provides version 10.0.0.

I've tried installing the package in RStudio after running the command lines in terminal, still doesn't work. I also tried directly in R console and I get a new error message:

install.packages("curl", type="source")
--- Please select a CRAN mirror for use in this session --- # I select the closest USA
Warning: unable to access index for repository https://cran.case.edu/src/contrib:
cannot open URL 'https://cran.case.edu/src/contrib/PACKAGES'
Warning message:
package ‘curl’ is not available (for R version 4.0.0).

Is there a way to download the package using homebrew in RStudio?

[jeroen]

@thatslifescience are you using the official R from cran ? Also make sure you install xquartz as described on that page.

[thatslifescience]

Whoops, I was using terminal. I downloaded xquartz and I'm using official R from CRAN. In xquartz I followed jeroen's steps, but when I try to install curl I'm now getting this message:

Warning: unable to access index for repository https://cran.case.edu/src/contrib:
  cannot open URL 'https://cran.case.edu/src/contrib/PACKAGES'
Warning message:
package 'curl' is not available (for R version 4.0.0) 

I then tried the code below, which worked, but I'm assuming this did the opposite of building the package locally (and it the bhl search still didn't work):
install.packages("curl", type = "source", repos = "http://cran.rstudio.com/")

Just to be clear, once the package is installed, I'm doing the following to check if it worked:

library(curl)
library(rbhl)
Sys.setenv(BHL_KEY = "my_key")
bhl_authorsearch(name='dimmock')

[sckott]

@thatslifescience still having the problem?

[Lithobius]

This is a global problem with many servers right now due to a major CA root cert being expired that turned out to be still used on many servers.

See details e.g. here https://calnetweb.berkeley.edu/calnet-technologists/incommon-sectigo-certificate-service/addtrust-external-root-expiration-may-2020

or here: https://support.sectigo.com/articles/Knowledge/Sectigo-AddTrust-External-CA-Root-Expiring-May-30-2020

Recent browsers and TLS libraries already have a workaround for this problem, so they are not affected, but some older versions are. As a workaround until the server has updated their certs, you can build the R curl package from source against libcurl from homebrew:

brew install curl
export PKG_CONFIG_PATH="/usr/local/opt/curl/lib/pkgconfig"
R

And then in R:

install.packages("curl", type = "source")

And then it should work.

I have used this solution four times now, several months apart, on three different computers running different OSX versions and it works every time.

I just want to say thanks for posting it!!!