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Warning when running R - can't install packages either

10 messages · Alba Pompeo, Jeff Newmiller, Tom Hopper +3 more

Alba Pompeo
# 
Hello.

I've tried to run R, but I receive many warnings and can't do simple
stuff such as installing packages.

Here's the full log when I run it.

http://pastebin.com/raw/2BkNpTte

Does anyone know what could be wrong here?

Thanks a lot.
Jeff Newmiller
# 
Looks to me like something outside of R is blocking network access by R. That could be anything from you don't have networking setup to some security policy or firewall configuration. I doubt this will be the right place to resolve those issues.
Martin Morgan
#
On 05/12/2016 07:45 AM, Alba Pompeo wrote:
do you have any success when choosing a non-https mirror, #28 in your 
screenshot?

Martin Morgan
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Tom Hopper
# 
setInternet2() first thing after launching R might fix that.
Alba Pompeo
# 
Martin Morgan, I tried an HTTP mirror and it worked.
What could be the problem and how to fix?
Also, should I ignore the warning about ignoring environment value of R_HOME?
Thanks.
On Thu, May 12, 2016 at 5:59 PM, Tom Hopper <tomhopper at gmail.com> wrote:
Martin Morgan
#
On 05/12/2016 10:25 PM, Alba Pompeo wrote:
The problem is in the warning message

1: In download.file(url, destfile = f, quiet = TRUE) :
URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'Problem 
with the SSL CA cert (path? access rights?)'

and an easier way to reproduce / troubleshoot the problem is

     download.file("https://cran.r-project.org/CRAN_mirrors.csv", 
tempfile())

The details of this process are described in ?download.file. My guess 
would be that you have 'libcurl' available

 > capabilities()["libcurl"]
libcurl
    TRUE

that it supports https (mine does, in the protocol attribute):

 > libcurlVersion()
[1] "7.35.0"
attr(,"ssl_version")
[1] "OpenSSL/1.0.1f"
attr(,"libssh_version")
[1] ""
attr(,"protocols")
  [1] "dict"   "file"   "ftp"    "ftps"   "gopher" "http"   "https" 
"imap"
  [9] "imaps"  "ldap"   "ldaps"  "pop3"   "pop3s"  "rtmp"   "rtsp" 
"smtp"
[17] "smtps"  "telnet" "tftp"

and that you have outdated or other CA certificates problem, with some 
hints for troubleshooting in the first and subsequent paragraphs of the 
'Secure URL' section.

Martin Morgan
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Martin Morgan
#
On 05/12/2016 10:25 PM, Alba Pompeo wrote:
It depends on why you set the value in your environment in the first 
place; maybe you were trying to use a particular installation of R, but 
setting R_HOME is not the way to do that (I use an alias, e.g., 
R-3.3='~/bin/R-3-3-branch/bin/R --no-save --no-restore --silent')

Martin
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Jakub Jirutka
# 
Hi,

I?m maintainer of the R package in Alpine Linux.

I read on multiple places that some packages needs R_HOME variable set to the location where is R installed, so I?ve added it to the system-wide profile. Is this correct, or a misinformation?

What system dependencies does R need to compile modules from CRAN? On Alpine the following dependencies are needed to build R: bzip2-dev curl-dev gfortran lapack-dev pcre-dev perl readline-dev xz-dev zlib-dev. Are all of these dependencies needed for compiling modules?

Jakub
On 13. May 2016, at 11:31, Martin Morgan <martin.morgan at roswellpark.org> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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Hi Jakub,

This is really a separate question. It is not really end-user related, 
and should be asked on the R-devel mailing list. Nonetheless, some 
answers below.

        
On 05/13/2016 03:55 PM, Jakub Jirutka wrote:

            

      
      
      
    

        
R_HOME is set when R starts

~$ env|grep R_HOME
~$ R --vanilla -e "Sys.getenv('R_HOME')"
 > Sys.getenv('R_HOME')
[1] "/home/mtmorgan/bin/R-3-3-branch"

and (after reading the documentation in ?R_HOME it the R help system)

~$ R RHOME
/home/mtmorgan/bin/R-3-3-branch

so there is no need to set it in a system-wide profile. It is sometimes 
referenced inside an R package source tree that uses C or other compiled 
code in a Makevars file, as described in the 'Writing R Extensions' manual

https://cran.r-project.org/doc/manuals/r-release/R-exts.html
e.g., the section on configure and cleanup

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Configure-and-cleanup

In these circumstances it has been set by the R process that is 
compiling the source code.

            

      
      
      
    

        
As you say, those look like dependencies required to build R itself.

Individual packages may have dependencies on these or other system 
libraries, but many packages do not have system dependencies. It is up 
to the package maintainer to ensure that appropriate checks are made to 
discover the system resource; there are probably dozens or even hundreds 
of system dependencies amongst all of the CRAN packages. Typically the 
task of satisfying those dependencies is left to the user (or to those 
creating distributions of R packages, e.g., 
https://cran.r-project.org/bin/linux/debian/)

Martin Morgan

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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3 days later

    

      
      

        


  

        

      Martin Maechler
    

    

      
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Short executive summary to all the nice explanations and
examples (by the other Martin M) below:

  Yes, this is misinformation.
  You should *NOT* set R_HOME in a (system wide /  user) profile.

Martin Maechler