[R-SIG-Mac] How to get a Fortran compiler compatible to Xcode?
Marius Hofert
marius.hofert at uwaterloo.ca
Mon May 11 05:39:18 CEST 2015
On Sun, May 10, 2015 at 11:08 PM, Kevin Ushey <kevinushey at gmail.com> wrote:
> Marius,
>
> Best guess -- you probably need to call 'configure' again.
... you have excellent guesses... it worked! Thanks a lot.
Cheers,
Marius
>
> 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
>>> >>
>>> >>
>>
>>
>
More information about the R-SIG-Mac
mailing list