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

Kevin Ushey kevinushey at gmail.com
Mon May 11 05:08:55 CEST 2015


Marius,

Best guess -- you probably need to call 'configure' again.

Kevin
On May 10, 2015 19:00, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
wrote:

> yeah, I forgot.
>
> Do what Kevin says, grab the texinfo from the r.research.att.com/libs
> website.  Basically this is the first place to look.
>
> Kasper
>
> On Sun, May 10, 2015 at 9:49 PM, Marius Hofert <marius.hofert at uwaterloo.ca
> > wrote:
>
>> Hi,
>>
>> Thanks again, Kevin.
>>
>> @Kasper: I had a new version (as of today) of MacTeX installed and
>> texinfo came with it. I had texi2dvi, texi2pdf... but not texi2any,
>> that's why I thought it's something 'special' and couldn't find it
>> anywhere else.
>>
>> @Kevin: I tried homebrew, but it seemed to fail, saying that it won't
>> link/install as texinfo is already installed (via MacTeX) :-(.
>> Interestingly, /usr/local/Cellar/texinfo existed afterwards and it
>> contained ./5.2/bin/texi2any. I then simply linked from /usr/local/bin
>> to that file, but still obtained (also after a reboot + as su):
>>
>> sklar-2:R-3.2.0_build mhofert$ make info
>> ERROR: 'texi2any' v5.1 or later needed but missing on your system.
>> make[2]: *** [R-FAQ.info] Error 1
>> make[1]: *** [info] Error 2
>> make: [info] Error 2 (ignored)
>> sklar-2:R-3.2.0_build mhofert$ texi2any --version
>> texi2any (GNU texinfo) 5.2
>>
>> Copyright (C) 2013 Free Software Foundation, Inc.
>> License GPLv3+: GNU GPL version 3 or later <
>> http://gnu.org/licenses/gpl.html>
>> This is free software: you are free to change and redistribute it.
>> There is NO WARRANTY, to the extent permitted by law.
>>
>> Any ideas?
>>
>> Cheers,
>> Marius
>>
>>
>> On Sun, May 10, 2015 at 9:14 PM, Kevin Ushey <kevinushey at gmail.com>
>> wrote:
>> > `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
>> >>
>> >>
>>
>
>

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