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

Tue Jul 28 23:37:19 CEST 2015

Jose,

I suspect you're using a rather old Mac that is no longer supported by our tools.

The only other alternative I can think of is that you may have better luck trying to use the older Fortran compiler from CRAN at
https://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg

In order to avoid clashes with the newer compiler, you may need to run (on the command line) something like

sudo ln -sfn gfortran /usr/local/bin/gfortran-4.8

I'm not sure if it will work, but that's the best guess short of installing the Homebrew toolchain and re-compiling R which is a bit of an overkill.

Cheers,
Simon

> On Jul 28, 2015, at 3:13 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
> ################################################################
> 
> 	[[alternative HTML version deleted]]
> 
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