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

Tue Jul 28 21:13:08 CEST 2015

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
################################################################

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