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

Timothy Bates tim.bates at ed.ac.uk
Fri Jul 31 12:33:15 CEST 2015 

This happened for me too: that Intel Core 2 is just too old for the compiler.

I used it as a stimulus to buy a new laptop… As a bonus, everything is ~10x faster
Best, tim

> On 30 Jul 2015, at 8:33 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
> 
> Davor,
> 
> we're not talking about the warning - we're talking about the error (illegal instruction = too old CPU).
> 
> Cheers,
> S
> 
> 
>> On Jul 30, 2015, at 3:28 PM, Davor Cubranic <cubranic at stat.ubc.ca> wrote:
>> 
>> 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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