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 -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276
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, > > RolfMartin 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
On 03/11/15 12:52, Marc Schwartz wrote:> Hi Rolf, > > See below.<SNIP>> Martin Morgan's reply seems like it is on point.Indeed. The problem arises from a lack of "libcurl" capabilities.> 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.Yes. I installed from source.> That might suggest that the config/compilation incantation may not > have used libcurl or not a version with https support enabled.After digging around a bit in config.log I see an indication that the version of libcurl needs to be >= 7.28.0. The version that I have, which seems to be the latest that is available for my poor old Fedora 17, is 7.24.0. So therein lies the problem. (Goes away and beats the keyboard to death for an hour or two ....) I have now managed to install a recent version of libcurl --- from source; no recent version is available for Fedora 17 via yum --- and after considerable travail got R to configure and build using the new libcurl. Strangely, the configure.log for R showed no sign of problems after I installed the new libcurl, but then "make check" threw an error --- apparently R could not find the new version. The default install for libcurl put it in /usr/local/share/... and R looked in /usr/share/... There must be a way to tell R to look in /usr/local/share but I couldn't figure it out and re-installed libcurl, telling the install to use /usr as the install directory. Then I configured, made and installed R and, mirabile dictu, it is now the case that chooseCRANmirror() works as advertised without throwing any error. Supplementary question: Given that I want to be "secure" I can/should no longer use my local New Zealand mirror. Does anyone reading this know if, and if so, when the New Zealand mirror will be reconfigured to provide https rather than http protocol? Ta. cheers, Rolf P. S. You wrote:> There are references/pointers pertaining to libcurl in the > Installation and Administration manual.Yes, but these (as far as I can discern) relate only to *Windoze* which civilised people such as my very good self do not use. R. -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276