[R-SIG-Mac] How to get a Fortran compiler compatible to Xcode?
Marius Hofert
marius.hofert at uwaterloo.ca
Mon May 11 03:49:29 CEST 2015
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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