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

[Martin Maechler]

>>>>> Martin Morgan <martin.morgan at roswellpark.org>
>>>>>     on Fri, 13 May 2016 18:57:09 -0400 writes:

> 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:
> > 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?

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

> 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.
> 
> >
> > 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?
> 
> 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
> 
> >
> > Jakub
> >
> > On 13. May 2016, at 11:31, Martin Morgan
> > <martin.morgan at roswellpark.org> wrote:
> >
> >>
> >>
> >> 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? Also, should I ignore the warning
> >>> about ignoring environment value of R_HOME?
> >>
> >> 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
> >>
> >>> 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.