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

Simon Urbanek simon.urbanek at r-project.org
Thu Jul 30 21:33:45 CEST 2015 

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]]
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
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