[R-SIG-Mac] Problems to install a package

[Kevin Ushey]

It looks like 'gfortran' was successfully unpacked (since R is
locating it), but I guess it's 'too old' and doesn't work on Yosemite.
The error printed is basically 'gfortran' saying, "I don't understand
the kernel associated with this operating system", likely because it's
too new -- and I guess that's causing the compiler errors.

You'll have to obtain a more up-to-date version of 'gfortran' -- I
would recommend following the earlier instructions posted in this
thread. (I promise that homebrew is relatively painless to install and
use, although there is a bit more setup required that I alluded to in
my earlier post)

As a parting note, after installing 'gfortran', the easiest way to
make R 'aware' of the new compiler is to create a file at the location
`~/.R/Makevars`. Roughly speaking, this file can be used to set what
compilers and compiler flags are used when compiling code from R. Note
that you'll have to create it if it doesn't exist. Within that file,
you should be able to use something like:

    FF=gfortran
    FLIBS=`gfortran -print-search-dirs | grep ^libraries: | sed
's|libraries: =||' | sed 's|:| -L|g' | sed 's|^|-L|'`

Of course, another alternative is to contact the authors of RMacoqui
and ask them to make a binary version of the package available to you,
so you don't need to mess with compilers...

Good luck,
Kevin

On Tue, Jul 28, 2015 at 12:13 PM, José Carlos Guerrero Antúnez
<jcgantunez at gmail.com> wrote:
> Hi,
>
> First, thank you for your answers, and I have to admit that don't prepare to
> do a bit more work, because I'm a user that I have no programming skills,
> and therefore, I depend on people like you, to use these programs.
>
> According to the easier instruction, and I downloaded
> gfortran-4.8.2-darwin13.tar.bz2
>
> You'll want to unpack it in the root folder at `/` (or move it there after
> unpacking); the directory structure is such that the necessary
> pieces are dumped into `/usr/local/` and R will by default be able to
> discover everything needed.
>
> It will not let me move the item "usr" to the root folder "/"
>
> Now I have this error message,
>
>> install.packages("~/Desktop/RMacoqui_1.0.tar.gz", repos = NULL, type =
>> "source",
>> lib="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
> * installing *source* package ‘RMacoqui’ ...
> ** libs
> gfortran-4.8   -fPIC  -g -O2  -c RMacoqui.f -o RMacoqui.o
> gfortran-4.8: warning: couldn’t understand kern.osversion ‘14.4.0
> f951: internal compiler error: Illegal instruction: 4
>
> f951: internal compiler error: Abort trap: 6
> gfortran-4.8: internal compiler error: Abort trap: 6 (program f951)
> make: *** [RMacoqui.o] Abort trap: 6
> ERROR: compilation failed for package ‘RMacoqui’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RMacoqui’
> Warning in install.packages :
>   installation of package ‘/Users/joseca_IMac/Desktop/RMacoqui_1.0.tar.gz’
> had non-zero exit status
>
> Many thanks again,
>
>
> Best regards,
>
>
>
>
> 2015-07-27 23:49 GMT-03:00 Kevin Ushey <kevinushey at gmail.com>:
>>
>> There error here is, as it says:
>>
>> > make: gfortran-4.8: No such file or directory
>>
>> In other words, `make` is attempting to call `gfortran-4.8` to compile
>> FORTRAN code in your package, but is unable to find it -- likely
>> because it's not installed.
>>
>> Since 'gfortran' is no longer distributed as part of Apple's command
>> line tools, you'll need to install it from another source -- Simon
>> Urbanek hosts a version of 'gfortran' at http://r.research.att.com/
>> (more specifically, in the `libs` directory at
>> http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2).
>> You'll want to unpack it in the root folder at `/` (or move it there
>> after unpacking); the directory structure is such that the necessary
>> pieces are dumped into `/usr/local/` and R will by default be able to
>> discover everything needed.
>>
>> Alternatively (if you're prepared to do a bit more work), you can use
>> the OS X package manager homebrew to install 'gcc' and hence
>> 'gfortran'. Install homebrew following the instructions here:
>>
>>     http://brew.sh/
>>
>> and then, from the command line, call
>>
>>     brew install gcc
>>
>> This will install an up-to-date version of both 'gcc' and 'gfortran'.
>> Since it won't be installed into a directory that's 'visible' to R by
>> default, you'll need to tell R how to find it -- you can check the
>> StackOverflow questions + responses here for ideas on how to
>> accomplish that.
>>
>>
>> http://stackoverflow.com/questions/29992066/rcpp-warning-directory-not-found-for-option-l-usr-local-cellar-gfortran-4-8
>>
>> http://stackoverflow.com/questions/19920281/rcpparmadillo-compile-errors-on-os-x-mavericks/19920761#19920761
>>
>> As an aside -- I am not sure why make is attempting to call
>> `gfortran-4.8` rather than `gfortran`. You might have to check
>> `~/.R/Makevars` or other package configuration variables. (Do you
>> _really_ need to be compiling with `gfortran-4.8` specifically?)
>>
>> Hope this helps,
>> Kevin
>>
>>
>> On Mon, Jul 27, 2015 at 7:19 PM, David Winsemius <dwinsemius at comcast.net>
>> wrote:
>> >
>> > On Jul 27, 2015, at 6:49 PM, José Carlos Guerrero Antúnez wrote:
>> >
>> >> Hi,
>> >>
>> >> I have this problem when I try to install a package, I'm working with
>> >> OSX
>> >> Yosemite 10.10.4.
>> >>
>> >> Best regards,
>> >>
>> >>> install.packages("~/Downloads/RMacoqui_1.0.tar.gz", repos = NULL, type
>> >>> =
>> >> "source",
>> >> lib="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
>> >> * installing *source* package ‘RMacoqui’ ...
>> >> ** libs
>> >> gfortran-4.8   -fPIC  -g -O2  -c RMacoqui.f -o RMacoqui.o
>> >> make: gfortran-4.8: No such file or directory
>> >
>> > I suspect that you have not obtained Xcode and installed Command line
>> > tools and perhaps not installed XQuartz (although that is not the cause of
>> > any error that I see here.)
>> >
>> > Apple has pretty much always made XCode available for free. You need to
>> > register with Apple as a developer and then get the XCode version that is
>> > mated to your version of OSX.
>> >
>> >
>> >
>> > --
>> > David
>> >
>> >> make: *** [RMacoqui.o] Error 1
>> >> ERROR: compilation failed for package ‘RMacoqui’
>> >> * removing
>> >>
>> >> ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RMacoqui’
>> >> Warning in install.packages :
>> >>  installation of package ‘/Users/joseca/Downloads/RMacoqui_1.0.tar.gz’
>> >> had
>> >> non-zero exit status
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> ################################################################
>> >> Dr. José Carlos Guerrero
>> >> Laboratorio de Desarrollo Sustentable y Gestión Ambiental del
>> >> Territorio
>> >> (LDSGAT)
>> >> Instituto de Ecología y Ciencias Ambientales (IECA)
>> >> Facultad de Ciencias
>> >> Universidad de la República
>> >> Montevideo-URUGUAY
>> >> ################################################################
>> >>
>> >>       [[alternative HTML version deleted]]
>> >>
>> >> _______________________________________________
>> >> R-SIG-Mac mailing list
>> >> R-SIG-Mac at r-project.org
>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >
>> > David Winsemius
>> > Alameda, CA, USA
>> >
>> > _______________________________________________
>> > R-SIG-Mac mailing list
>> > R-SIG-Mac at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
>
>
> --
> ################################################################
> Dr. José Carlos Guerrero
> Laboratorio de Desarrollo Sustentable y Gestión Ambiental del Territorio
> (LDSGAT)
> Instituto de Ecología y Ciencias Ambientales (IECA)
> Facultad de Ciencias
> Universidad de la República
> Montevideo-URUGUAY
> ################################################################