(PR#14226) -- Re: libgfortran misplaced in Mac OS X R install

Another possibility is to link statically to libgfortran. ?That has pros and
cons, but for libgfortran not many cons apart from space for multiple copies
in sundry packages (and is what is done on Windows, BTW).

There are several ways to arrange that. ?As far as I recall I temporarily
removed /usr/local/lib/libgfortran*.dylib: another way is to edit FLIBS in
Makeconf (but then you do need to know which copies of that file you need to
edit).

As far as I know we don't document in the standard manuals how to build
distributable binary Mac packages, and perhaps we should do so in due course
(or at least point at where the information can be found).

On Thu, 4 Mar 2010, Simon Urbanek wrote:

Hi Michael,

On Mar 3, 2010, at 12:01 , Michael Spiegel wrote:

I am the guy who compiles the OpenMx binaries. ?We would be delighted to
place our package on CRAN, once the project is stable enough so that we are
comfortable releasing it to the larger public. ?Let's try to track down
where I made a mistake. ?Our Makevars.in file contains the line:

PKG_LIBS=$(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS)

In addition, on the build machine I noticed that a copy of
libgfortran.2.dylib exists at /usr/local/lib. ?I believe the Xcode install
placed a copy of it there.

No, it is part of the GNU Fortran installation. Anything you compile with
a Fortran requires that you have that Fortran installed at run time, because
Fortran uses its own run-time libraries (if the Fortran you compiled with
used dynamic libraries). This implies that if you distribute your package
you have to tell users to install the same Fortran you used to compile it.

However, unlike other unices Mac users don't necessarily have development
tools installed, so on CRAN we make an effort to modify the binaries such
that they work even without the tools they have been compiled with. There
are several possible approaches, but since R itself already uses the same
Fortran, we ship a copy of the Fortran libraries inside R and modify
packages such that they use it instead of the one from dev tools (see below
for details).

To create the binary release, I run ?R CMD INSTALL --build.

That is not sufficient to create a binary of your package, because it
contains a configure script (this is unrelated to the above - see R-admin
2.6). What you want to use is something like this (assuming R 2.10.1 Leopard
build and Fortran from CRAN):

R --arch=i386 CMD INSTALL OpenMx_0.2.9-1147.tar.gz
R --arch=x86_64 CMD INSTALL --libs-only OpenMx_0.2.9-1147.tar.gz
R --arch=ppc CMD INSTALL --libs-only OpenMx_0.2.9-1147.tar.gz
cd /Library/Frameworks/R.framework/Versions/2.10/Resources/library

# fix the Fortran paths to point to R 2.10 instead
for lib in `ls OpenMx/libs/*/*.so`; do
install_name_tool -change /usr/local/lib/libgfortran.2.dylib \

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libgfortran.2.dylib
\
?$lib
done

# change permissions for distribution
sudo chown -Rh root:admin OpenMx
sudo chmod -R g+w OpenMx

# pack it up
tar fvcz ~/OpenMx_0.2.9-1147.tgz OpenMx


You can check that you have the correct paths using otool -L:

ginaz:library$ otool -L OpenMx/libs/*/*.so
OpenMx/libs/i386/OpenMx.so:
? ? ? ?OpenMx.so (compatibility version 0.0.0, current version 0.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libgfortran.2.dylib
(compatibility version 3.0.0, current version 3.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libRblas.dylib
(compatibility version 0.0.0, current version 0.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libRlapack.dylib
(compatibility version 2.10.0, current version 2.10.1)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libR.dylib
(compatibility version 2.10.0, current version 2.10.1)

?/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
(compatibility version 150.0.0, current version 476.19.0)
? ? ? ?/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)
? ? ? ?/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 111.1.4)
? ? ? ?/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
(compatibility version 1.0.0, current version 242.0.0)
OpenMx/libs/ppc/OpenMx.so:
? ? ? ?OpenMx.so (compatibility version 0.0.0, current version 0.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libgfortran.2.dylib
(compatibility version 3.0.0, current version 3.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libRblas.dylib
(compatibility version 0.0.0, current version 0.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libRlapack.dylib
(compatibility version 2.10.0, current version 2.10.1)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libR.dylib
(compatibility version 2.10.0, current version 2.10.1)

?/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
(compatibility version 150.0.0, current version 476.19.0)
? ? ? ?/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)
? ? ? ?/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 111.1.4)
? ? ? ?/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
(compatibility version 1.0.0, current version 242.0.0)
OpenMx/libs/x86_64/OpenMx.so:
? ? ? ?OpenMx.so (compatibility version 0.0.0, current version 0.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libgfortran.2.dylib
(compatibility version 3.0.0, current version 3.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libRblas.dylib
(compatibility version 0.0.0, current version 0.0.0)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libRlapack.dylib
(compatibility version 2.10.0, current version 2.10.1)

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libR.dylib
(compatibility version 2.10.0, current version 2.10.1)

?/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
(compatibility version 150.0.0, current version 476.19.0)
? ? ? ?/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)
? ? ? ?/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 111.1.4)
? ? ? ?/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
(compatibility version 1.0.0, current version 242.0.0)


If you are dealing with only one R version, you can change the ID of your
Fortran library instead of touching the package files:

install_name_tool -id \

?/Library/Frameworks/R.framework/Versions/2.10/Resources/lib/libgfortran.2.dylib
/usr/local/lib/libgfortran.2.0.0.dylib

Note, however, that this will lead to (possibly silent) errors if you
forget to change it when switching to another R version, so I prefer to fix
the package instead.

Cheers,
Simon

The beta test users install the package using the following script:
http://openmx.psyc.virginia.edu/getOpenMx.R.

On Wed, Mar 3, 2010 at 9:48 AM, Tim Brick <tbrick at virginia.edu> wrote:

From: Simon Urbanek <simon.urbanek at r-project.org>
Date: March 3, 2010 8:32:52 AM MST
To: tbrick at virginia.edu
Cc: r-devel at stat.math.ethz.ch, R-bugs at r-project.org
Subject: Re: [Rd] libgfortran misplaced in Mac OS X R install
(PR#14226)

This is not an R bug so please don't abuse R-bugs. It is likely a bug
in the way OpenMx binaries are distributed by someone (you didn't even say
where you got them from) - OpenMx is not even on CRAN so take that to
whoever gave you the binaries. On CRAN we use the correct paths.

Cheers,
Simon


On Mar 2, 2010, at 11:45 , tbrick at virginia.edu wrote:

Full_Name: Timothy Brick
Version: 2.10
OS: Mac OS X (seen on both 10.6 and 10.5)
Submission from: (NULL) (63.255.24.5)


When using install.packages in R on Mac OS X, packages that require
gfortran
throws an error (Example below from installation of OpenMx package):

Loading required package: OpenMx
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library

'/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so':

dlopen(/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so,
6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from:
/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so
Reason: image not found

libgfortran.2.dylib does exist, but in

/Library/Frameworks/R.framework/Versions/2.10/Resouces/lib/libgfortran.2.dylib
(or /2.9/, depending on version installed).

A workaround at present involves creating a symbolic link from the
above file to
/usr/local/lib/libgfortran.2.dylib, however this requires sudo access
and is
confusing for novice users.

There is more discussion of this bug as it relates to OpenMx at:
http://openmx.psyc.virginia.edu/thread/316

Posts on other forums indicate a similar issue with other packages
including
vegan and lme4:

http://r-forge.r-project.org/forum/forum.php?thread_id=728&forum_id=194
https://stat.ethz.ch/pipermail/r-sig-mac/2009-May/006210.html

Those are very old posts and those were temporary issues in the CRAN
build system that have been promptly resolved.

--
Brian D. Ripley, ? ? ? ? ? ? ? ? ?ripley at stats.ox.ac.uk
Professor of Applied Statistics, ?http://www.stats.ox.ac.uk/~ripley/
University of Oxford, ? ? ? ? ? ? Tel: ?+44 1865 272861 (self)
1 South Parks Road, ? ? ? ? ? ? ? ? ? ? +44 1865 272866 (PA)
Oxford OX1 3TG, UK ? ? ? ? ? ? ? ?Fax: ?+44 1865 272595