[R-sig-Fedora] Nonexistent include directory "/usr/lib/gfortran/modules"

[Marc Schwartz]

Hi,

If you are installing to default system-wide locations, you will need to be SU/root in order to have the requisite privileges. If you try to install as a regular user, you will need to define alternative target locations for the library tree within your username tree.

As with Peter, it has been some time since I have used Fedora. Going on about 5 years at this point.

The confounding issue here may be that there are various iterations of the lme4 package in the wild and there may be some subtleties in the installation process. There is a README file here:

  http://cran.r-project.org/web/packages/lme4/README.html

It is also possible that you may need to use:

  install.packages('lme4', dependencies = TRUE)

in order to bring in various dependencies for the package during installation.

You may also be best served posting to the R-SIG-Mixed-Models list:

  https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

where the maintainers of lme4 tend to be located. Even though this appears to be a Fedora issue, it may be in reality an lme4 issue.

Regards,

Marc Schwartz


On Apr 19, 2014, at 5:48 PM, Steve Taylor <steve.taylor.nz at gmail.com> wrote:

> Thanks for your response Peter
> 
> Yes I have gfortran installed.  I also have R-devel-3.0.2-1.fc20.i686
> installed already.
> 
> It seems I can install the packages as superuser su.  However, there are
> still many fortran warnings about variables potentially being used before
> being initialised.  I'll ignore those for the moment.
> 
> cheers,
>   Steve
> 
> 
> On 20 April 2014 10:08, peter dalgaard <pdalgd at gmail.com> wrote:
> 
>> 
>> On 19 Apr 2014, at 23:33 , Steve Taylor <steve.taylor.nz at gmail.com> wrote:
>> 
>>> Hi there,
>>> 
>>> Can anyone help with this?
>>> 
>>> I tried to install.packages('lme4') and got lots of warning and error
>>> messages, starting with the one in the subject and ending with failed
>>> compilation.  The same went for the 'minqa' package which is needed by
>> lme4.
>>> 
>>> I have R version 3.0.2 running on Fedora 20.
>>> "yum update R" says that's the latest available.
>>> 
>>> Is my system missing something necessary for compilation?
>> 
>> gfortran, maybe? I'm a little out of touch with Fedora these days, but
>> there used to be a meta-package called R-devel or so, which would bring in
>> all tools needed for source compilation of R and most of the packages.
>> 
>>> 
>>> cheers,
>>>  Steve