R devel - Mar 2010 - (PR#14226) -- Re: libgfortran misplaced in Mac OS X R install (PR#14226)

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

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.
>>>
>>>
>>
>>
>
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>
>