[R-SIG-Mac] How to get a Fortran compiler compatible to Xcode?
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Mon May 11 04:00:37 CEST 2015
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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