[R-SIG-Mac] How to get a Fortran compiler compatible to Xcode?

Kevin Ushey kevinushey at gmail.com
Mon May 11 03:14:29 CEST 2015 

`texi2any` is packaged as part of `texinfo` (note that this is
documented throughout R-admin), and the latest version is available
for download (hosted by Simon Urbanek) at:

    http://r.research.att.com/libs/texinfo-5.2-darwin10.tar.gz

Or, if you're using homebrew, just use

    brew install texinfo

Kevin

On Sun, May 10, 2015 at 6:06 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> This is where you look for add-ons
>      http://r.research.att.com/libs
> for OS X.
>
> For texi2any I would install a new version of MacTex.
>
> Finally, see the R-admin manual.
>
> Best,
> Kasper
>
> On Sun, May 10, 2015 at 8:38 PM, Marius Hofert <marius.hofert at uwaterloo.ca>
> wrote:
>>
>> Hi Kevin,
>>
>> Thanks a lot for helping. That pushed me on the right track. I then
>> needed some more tools (Java/XQuartz) and could then install R from
>> source. Only make pdf; make info failed, saying that 'texi2any'
>> couldn't be found on the system. I couldn't find any hints online or
>> in the R administration manual on how to install/get it. I do have
>> texi2pdf, though. Do you know how to get texi2any?  (hope this is
>> still fine to be discussed in this thread, if not, I can open a new
>> one).
>>
>> Thanks & cheers,
>> Marius
>>
>>
>>
>> On Sun, May 10, 2015 at 2:45 PM, Kevin Ushey <kevinushey at gmail.com> wrote:
>> > Hi Marius,
>> >
>> > I've had success compiling (the latest versions of) R from source
>> > using Apple's command line tools (shipped with Xcode), alongside
>> > gfortran 4.8.2 installed from here (as hosted by Simon Urbanek):
>> >
>> >     http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
>> >
>> > Alternatively, (and what I tend to do by default on OS X), you can get
>> > the latest release of `gfortran` using one of the custom Apple
>> > 'package managers', e.g. with homebrew (http://brew.sh/), you can use
>> >
>> >     brew install gcc
>> >
>> > which will get you an up-to-date copy of `gcc` (not really needed
>> > since you'll have Apple clang), but also `gfortran` (which is needed
>> > as it's no longer shipped with the Apple command line tools).
>> >
>> > After this, as long as `gfortran` is on your PATH (e.g. by symlinking
>> > the binary into /usr/local/bin), you should be good to go for building
>> > R from source -- it will then be able to automatically discover where
>> > the Fortran libraries live, and so on.
>> >
>> > Kevin
>> >
>> > On Sun, May 10, 2015 at 11:00 AM, peter dalgaard <pdalgd at gmail.com>
>> > wrote:
>> >> You do need to read this:
>> >>
>> >> http://cran.r-project.org/doc/manuals/r-release/R-admin.html
>> >>
>> >> People are not inclined to write significant amounts of the same
>> >> information to the list...
>> >>
>> >> -Peter D
>> >>
>> >>
>> >>> On 10 May 2015, at 19:27 , Marius Hofert <marius.hofert at uwaterloo.ca>
>> >>> wrote:
>> >>>
>> >>> Dear Peter,
>> >>>
>> >>> Thanks for your quick help.
>> >>>
>> >>> I'm not so familiar with the technicalities (and try to learn): Where
>> >>> is the file 'config.site' located in your system? Is this supposed to
>> >>> be a file which provides settings for 'configure'?
>> >>>
>> >>> Thanks & cheers,
>> >>> Marius
>> >>>
>> >>> PS: Also thanks for the hint towards r.research... I'll look into that
>> >>> once everything else is running. I already have some things running,
>> >>> e.g., texinfo, not sure if the 'texinfo' you mentioned is a specific
>> >>> one (but I'll see then).
>> >>>
>> >>>
>> >>>
>> >>> On Sun, May 10, 2015 at 1:04 PM, peter dalgaard <pdalgd at gmail.com>
>> >>> wrote:
>> >>>>
>> >>>>> On 10 May 2015, at 17:13 , Marius Hofert
>> >>>>> <marius.hofert at uwaterloo.ca> wrote:
>> >>>>>
>> >>>>> Hi,
>> >>>>>
>> >>>>> I'm running Mac OS X Yosemite 10.10.3 on a MacBook Pro (Retina,
>> >>>>> 13", 2015). I would like to install R from source (various
>> >>>>> versions etc.) and thus installed Xcode (latest version:
>> >>>>> 6.3.1). How can I get a Fortran compiler which is compatible with
>> >>>>> Xcode 6.3.1?
>> >>>>>
>> >>>>> Here is what I tried:
>> >>>>> 1) I used to download and install gfortran-lion-5666-3.pkg from
>> >>>>> http://r.research.att.com/tools but I now obtain "... can't be
>> >>>>> installed on this disk. This package requires Xcode 4.1 with
>> >>>>> gcc-4.2 (build 5666.3)". It seems that my (newer) Xcode version
>> >>>>> is not recognized.
>> >>>>> 2) I then installed gfortran-4.2.3.dmg from CRAN -> Download R
>> >>>>> for (Mac) OS X -> tools. This worked fine, but then I ran into this
>> >>>>> issue:
>> >>>>> I wanted to install MPI and thus downloaded and unpacked
>> >>>>> openmpi-1.8.5.tar.gz from http://www.open-mpi.org/software/ompi/
>> >>>>> but ./configure leads to an error:
>> >>>>>
>> >>>>> ...
>> >>>>> checking if C and Fortran are link compatible... no
>> >>>>>
>> >>>>> **********************************************************************
>> >>>>> It appears that your Fortran compiler is unable to link against
>> >>>>> object files created by your C compiler.  This typically indicates
>> >>>>> one of a few possibilities:
>> >>>>>
>> >>>>> - A conflict between CFLAGS and FCFLAGS
>> >>>>> - A problem with your compiler installation(s)
>> >>>>> - Different default build options between compilers (e.g., C
>> >>>>>   building for 32 bit and Fortran building for 64 bit)
>> >>>>> - Incompatible compilers
>> >>>>>
>> >>>>> Such problems can usually be solved by picking compatible compilers
>> >>>>> and/or CFLAGS and FCFLAGS.  More information (including exactly what
>> >>>>> command was given to the compilers and what error resulted when the
>> >>>>> commands were executed) is available in the config.log file in this
>> >>>>> directory.
>> >>>>>
>> >>>>> **********************************************************************
>> >>>>> configure: error: C and Fortran compilers are not link compatible.
>> >>>>> Can not continue.
>> >>>>> sklar-2:openmpi-1.8.5 mhofert$
>> >>>>>
>> >>>>> I found this post
>> >>>>>
>> >>>>> (http://grokbase.com/t/r/r-sig-mac/14awnd0341/compiling-r-3-1-1-sources-under-os-x-yosemite)
>> >>>>> which seems to be related, but since there are no clear
>> >>>>> instructions/scripts given, I still don't have a solution.
>> >>>>>
>> >>>>> How can I get a suitable/compatible Fortran compiler?
>> >>>>>
>> >>>>
>> >>>> I think you already have one, you just need to set flags properly -
>> >>>> the typical problem is that, with default settings, you get C compiled for
>> >>>> 64 bits and Fortran for 32 bit.
>> >>>>
>> >>>> I have this:
>> >>>>
>> >>>> $ more config.site
>> >>>> r_arch=${r_arch:=x86_64}
>> >>>> CC="gcc -arch $r_arch"
>> >>>> CXX="g++ -arch $r_arch"
>> >>>> F77="gfortran -arch $r_arch"
>> >>>> FC="gfortran -arch $r_arch"
>> >>>> OBJC="gcc -arch $r_arch"
>> >>>> with_blas="-framework vecLib"
>> >>>> with_lapack=yes
>> >>>> CURL_CONFIG=/usr/bin/curl-config
>> >>>>
>> >>>> Notice also, that with the newer sources, you need to install some
>> >>>> stuff from http://r.research.att.com/libs/ : pcre, xz, texinfo, plus maybe
>> >>>> some more that I have forgotten.
>> >>>>
>> >>>>
>> >>>>
>> >>>>> Thanks & cheers,
>> >>>>> Marius
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> 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
>> >>
>> >> --
>> >> 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
>> >> 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
>
>

More information about the R-SIG-Mac mailing list