[R] Warning when running R - can't install packages either

[Martin Morgan]

On 05/12/2016 10:25 PM, Alba Pompeo wrote:
> Martin Morgan, I tried an HTTP mirror and it worked.
> What could be the problem and how to fix?

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and that you have outdated or other CA certificates problem, with some 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


> 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:
>> setInternet2() first thing after launching R might fix that.
>>
>>
>>> On May 12, 2016, at 07:45, Alba Pompeo <albapompeo at gmail.com> wrote:
>>>
>>> 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.
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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