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R install.packages() fails: 'Peer certificate cannot be authenticated wi


From: myglc2
Subject: R install.packages() fails: 'Peer certificate cannot be authenticated with given CA certificates'
Date: Thu, 29 Sep 2016 19:09:13 -0400
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux)

With GuixSD user config ...

(use-package-modules
 base   ; glibc-utf8-locales
 ssh    ; mosh
 admin  ; tree
 aspell ; aspell-dict-en
 mail   ; notmuch mu isync
 statistics ; r
 emacs      ; emacs-ess
 certs      ; nss-certs
 )
(packages->manifest
 (list
  mosh
  tree
  aspell-dict-en ; because emacs doesn't find system install
  notmuch mu isync ; also building from git source but this gets run-time 
dependencies
  r emacs-ess
  r-devtools r-openssl r-stringr r-xml2 r-httr 
  )
 )

... if I try to install a CRAN package like this ...

install.packages("pROC")

... it fails like this ...

Warning: unable to access index for repository 
https://rweb.crmda.ku.edu/cran/src/contrib:
  cannot download all files
Warning messages:
1: In download.file(url, destfile = f, quiet = TRUE) :
  URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'Peer 
certificate cannot be authenticated with given CA certificates'
2: package ‘pROC’ is not available (for R version 3.3.1) 

But if I "defeat" HTTPS like this ...

options(repos=
            c(
                CRAN = "http://cran.rstudio.com/";
            )
        )

... it works. I would prefer to use HTTPS, so here is the question:

How do I get R to present the CA certificates?

TIA - George

Full R session log is shown below.

***
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', 
> show.error.locations=TRUE)
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
> install.packages("pROC")
Installing package into ‘/home/g1/R/x86_64-unknown-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Warning: failed to download mirrors file (cannot download all files); using 
local file 
'/gnu/store/7543j3zkn95i7ixlc9fdq9hj0zrk5yq8-r-3.3.1/lib/R/doc/CRAN_mirrors.csv'
HTTPS CRAN mirror 

 1: 0-Cloud [https]                2: Austria [https]             
 3: Belgium (Ghent) [https]        4: Chile [https]               
 5: China (Beijing 4) [https]      6: Colombia (Cali) [https]     
 7: France (Lyon 1) [https]        8: France (Lyon 2) [https]     
 9: France (Paris 2) [https]      10: Germany (Münster) [https]   
11: Iceland [https]               12: Italy (Padua) [https]       
13: Japan (Tokyo) [https]         14: Mexico (Mexico City) [https]
15: New Zealand [https]           16: Russia (Moscow) [https]     
17: Spain (A Coruña) [https]      18: Spain (Madrid) [https]      
19: Switzerland [https]           20: UK (Bristol) [https]        
21: UK (Cambridge) [https]        22: USA (CA 1) [https]          
23: USA (KS) [https]              24: USA (MI 1) [https]          
25: USA (TN) [https]              26: USA (TX) [https]            
27: USA (WA) [https]              28: (HTTP mirrors)              


Selection: 23
Warning: unable to access index for repository 
https://rweb.crmda.ku.edu/cran/src/contrib:
  cannot download all files
Warning messages:
1: In download.file(url, destfile = f, quiet = TRUE) :
  URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'Peer 
certificate cannot be authenticated with given CA certificates'
2: package ‘pROC’ is not available (for R version 3.3.1) 
> q("no")

Process R finished at Thu Sep 29 19:07:12 2016
***



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