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

Fri Jul 31 21:01:40 CEST 2015

Hi,

In these r-forge projects,
https://r-forge.r-project.org/R/?group_id=1853
https://r-forge.r-project.org/R/?group_id=1876
http://r-forge.r-project.org/R/?group_id=1875

All these packages run in my old Core 2 Duo machine, OS X Yosemite and R
version updated.

In the case of package RMacoqui was created and compiled first on Windows.

Best regards,

2015-07-31 15:46 GMT-03:00 peter dalgaard <pdalgd at gmail.com>:

>
> > 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
>
> _______________________________________________
> R-SIG-Mac mailing list
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>

-- 
################################################################
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
################################################################

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