[R-SIG-Mac] Problems to install a package
peter dalgaard
pdalgd at gmail.com
Fri Jul 31 20:46:34 CEST 2015
> On 31 Jul 2015, at 12:33 , Timothy Bates <tim.bates at ed.ac.uk> wrote:
>
> 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
Hum, well, I wasn't actually planning to switch out my MB Air just now.
I'm actually baffled that I haven't bumped into this before. Both my laptop and my office desktop are Core 2 Duo machines (and the latter is the one that builds the R source releases!).
Anyone have some harder info on this? Is it the case that gfortran-4.8 cannot compile code for the C2D architecture, or is it just that the compiler binaries on Simon's site were built for later architectures and are not backwards compatible. The latter could be fixed by rebuilding the compiler.
-pd
>
>> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
More information about the R-SIG-Mac
mailing list