Problems to install a package
On Jul 28, 2015, at 2:37 PM, Simon Urbanek wrote:
Jose, I suspect you're using a rather old Mac that is no longer supported by our tools.
If you can run Yosemite and install Xcode 6, are there further dependencies? https://developer.apple.com/library/prerelease/mac/releasenotes/General/rn-osx-10.11/index.html#//apple_ref/doc/uid/TP40016209 That page lists: Developer Beta System Requirements The OS X El Capitan Developer Beta supports the following Macs: ? iMac (Mid 2007 or newer) ? MacBook Air (Late 2008 or newer) ? MacBook (Late 2008 Aluminum, or Early 2009 or newer) ? Mac mini (Early 2009 or newer) ? MacBook Pro (Mid/Late 2007 or newer) ? Mac Pro (Early 2008 or newer) ? Xserve (Early 2009) This is essentially the same set of machines that can run Yosemite.
David. > > 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, Jos? Carlos Guerrero Ant?nez <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, Jos? Carlos Guerrero Ant?nez 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. Jos? Carlos Guerrero >>>>> Laboratorio de Desarrollo Sustentable y Gesti?n Ambiental del Territorio >>>>> (LDSGAT) >>>>> Instituto de Ecolog?a y Ciencias Ambientales (IECA) >>>>> Facultad de Ciencias >>>>> Universidad de la Rep?blica >>>>> 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. Jos? Carlos Guerrero >> Laboratorio de Desarrollo Sustentable y Gesti?n Ambiental del Territorio >> (LDSGAT) >> Instituto de Ecolog?a y Ciencias Ambientales (IECA) >> Facultad de Ciencias >> Universidad de la Rep?blica >> 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 David Winsemius Alameda, CA, USA