Warning when running R - can't install packages either

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?

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.