How to get a Fortran compiler compatible to Xcode?

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

--
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