[R] What happened to Canada?

[Marc Schwartz]

Hi Rolf,

See below.


> On Nov 2, 2015, at 5:40 PM, Rolf Turner <r.turner at auckland.ac.nz> wrote:
> 
> 
> Thanks for the reply, Marc.
> 
> On 03/11/15 12:09, Marc Schwartz wrote:
> 
> <SNIP>
> 
>> 
>> Rolf,
>> 
>> What do:
>> 
>>   getOption("CRAN")
>> 
>>   getOption("repos")
>> 
>> show?
> 
> The first shows "NULL", the second shows
> 
>> "http://cran.stat.auckland.ac.nz"
> 
>> Is there any chance that you have something set in ~/.Rprofile
>> pertaining to CRAN mirrors or are loading some packages that might conflict?
> 
> Indeed.  I have "repos" set (as seen above) in my .Rprofile.
> 
>> I would try it with a vanilla R session (e.g. 'R --vanilla').
> 
> I had already tried "R --vanilla" and got the same effect.  I.e. I got the same error from chooseCRANmirror() but nevertheless the menu appeared, just as before.
> 
> This time, at your prompting, I tried to install a package under
> "R --vanilla":
> 
>> install.packages("circular",lib="/home/rolf/Rlib")
> 
> I got the following warning message(s):
> 
>> Warning: unable to access index for repository
>> https://cran.r-project.org/src/contrib
>> Warning message:
>> package ‘circular’ is not available (for R version 3.2.2)
> 
> (That last warning is certainly not true.)
> 
> Note that this was *after* having chosen the Austria mirror from the menu presented by chooseCRANmirror().
> 
> Before running chooseCRANmirror(), getOption("repos") produced:
> 
>>    CRAN
>> "@CRAN@"
> 
> After running chooseCRANmirror(), getOption("repos") produced:
> 
>>                        CRAN
>> "https://cran.r-project.org"
> 
>> If it works then, there is something getting loaded or set at session
>> start that may be conflicting.
> 
> Well, it *doesn't* work, so setting "repos" in my .Rprofile was not the problem, or at least not the essence of the problem.
> 
> Any other ideas?  Ta.
> 
> cheers,
> 
> Rolf


Martin Morgan's reply seems like it is on point.

I would follow his logic regarding libcurl and https support, but it would be helpful to know how you installed R.

Fedora 17 has been EOL'd for >2 years, so I am guessing that you installed from source, since the EPEL and most Fedora repos would not typically support EOL'd distros due to the risk of dated dependencies and version related incompatibilities.

That might suggest that the config/compilation incantation may not have used libcurl or not a version with https support enabled.

There are references/pointers pertaining to libcurl in the Installation and Administration manual.

Regards,

Marc