On Mar 4, 2010, at 14:44 , Prof Brian Ripley wrote:
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).
The Xcode add-on compilers from R.research.att.com use static
libgfortran by default, so if you didn't install any other Fortran,
that will be the default.
However, there are issues when linking multiple modules that also link
libgfortran statically - dylibs are not allowed to contain multiple
common symbols on OS X (with flat namespaces) which is the case if you
get static libgfortran from two sources independently. The most
prominent example is libRlapack linked into a package that also uses
Fortran (that's why CRAN Rlapack does not use static libgfortran).
There are ways around, but it all makes the already complex issue even
more complex ;).
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).
Yes, I agree. There are bits and pieces in the R for Mac FAQ, but it
may be worth putting what I wrote below into the FAQ.
Thanks,
Simon
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 <tbr...@virginia.edu>
wrote:
From: Simon Urbanek <simon.urba...@r-project.org>
Date: March 3, 2010 8:32:52 AM MST
To: tbr...@virginia.edu
Cc: r-de...@stat.math.ethz.ch, r-b...@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 , tbr...@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.
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--
Brian D. Ripley, rip...@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
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