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

[Davor Cubranic]

It’s not just old Macs: I see the same warning on a late-2013 MacBook Pro (so the second-latest generation):

$ gfortran --version
gfortran: warning: couldn’t understand kern.osversion ‘14.4.0
GNU Fortran (GCC) 4.8.2
Copyright (C) 2013 Free Software Foundation, Inc.

Davor

> On Jul 28, 2015, at 2:37 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
> 
> 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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> 
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