On Wed, 3 Dec 2008, Martin Maechler wrote:
This was on the wrong mailing list (R-SIG-mixed-models),
but I strongly believe belongs here.
As one of the two maintainers of Matrix,
I'm very interested to here if really there are still/again
problems with the *R-forge* (or CRAN) version of Matrix on the Mac.
We need to be careful here about what R version (source vs binary, CRAN
build vs others, which sub-architectures?).
That Simon is building R-devel means that the CRAN version of Matrix works
on the CRAN build of R with all the sub-architectures.
We have made several efforts, partially prompted and aided by
Simon Urbanek, to get the issues (mostly related to building a
"fat binary", IIRC) resolved.
Dave, did you install the R-forge version
with
install.packages("Matrix",repos="http://R-Forge.R-project.org";)
{as it is recommended}?
which with a CRAN build gets a binary. That binary works for me (Leopard
i386, 10.5.5), but it only has i386 and ppc binaries. So I think you
should be recommending type="source" to Mac users (or at least warn 64-bit
Mac users about this).
Now the i386 Matrix.so is linked against gfortran:
tystie% otool -L Matrix.so
Matrix.so:
Matrix.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/libRlapack.dylib
(compatibility version 2.8.0, current version 2.8.0)
/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/libRblas.dylib
(compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libgfortran.2.dylib (compatibility version 3.0.0,
current version 3.0.0)
...
and the error message is about not finding libgfortran. That suggests a
problem with the R installation in question, since AFAIK this is normally
installed with R. If /usr/local/lib/libgfortran.2.dylib really is
missing, it can be installed from the tools subdirectory on CRAN (or you
could try re-installing R).
The CRAN build of Matrix is not linked against libgfortran. I suspect
that reflects a difference in how the BLAS has been set up on R-forge and
on Simon's build machine. Fortran is needed for the standard R BLAS but
not for the 'vecLib' BLAS that comes with the OS.
So I think the problem is with one user's R installation, but this was
triggered by a difference in how the CRAN and R-forge builds of R 2.8.0
were configured.
Best regards,
Martin
"DA" == Dave Atkins <[EMAIL PROTECTED]>
on Mon, 01 Dec 2008 11:39:18 -0800 writes:
DA> Douglas Bates wrote:
>> Does
>>
>> library(Matrix)
>>
>> without any reference to lme4 work for you?
DA> No, if I start a fresh R session and call Matrix on its
DA> own, I get:
>> library(Matrix)
DA> Loading required package: lattice Error in
DA> dyn.load(file, DLLpath = DLLpath, ...) : unable to load
DA> shared library
DA>
'/Library/Frameworks/R.framework/Resources/library/Matrix/libs/i386/Matrix.so':
DA>
dlopen(/Library/Frameworks/R.framework/Resources/library/Matrix/libs/i386/Matrix.so,
DA> 6): Library not loaded:
DA> /usr/local/lib/libgfortran.2.dylib Referenced from:
DA>
/Library/Frameworks/R.framework/Resources/library/Matrix/libs/i386/Matrix.so
DA> Reason: image not found Error: package/namespace load
DA> failed for 'Matrix'
>> sessionInfo()
DA> R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1
DA> locale:
DA> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
DA> attached base packages: [1] stats graphics grDevices
DA> utils datasets methods base
DA> other attached packages: [1] lattice_0.17-17
DA> loaded via a namespace (and not attached): [1]
DA> grid_2.8.0
>>
Any ideas? Anything else I can pass along?
DA> thanks, Dave
>>
>> The other person who was having difficulty loading the
>> Matrix package on a Mac was able to resolve the problem
>> although I forget the details of how it was resolved.
>>
>> The messages indicate that the problem is more with
>> Matrix than with lme4.
>>
>> On Mon, Dec 1, 2008 at 12:26 PM, Dave Atkins
>> <[EMAIL PROTECTED]> wrote:
>>> [whoops, first sent this from my current email, which
>>> the listserv didn't recognize. apologies if this comes
>>> through twice.]
>>
>> And it did come through twice. I read the messages in
>> the wrong order and authorized the posting from the other
>> address before reading this message. Sorry for the extra
>> noise.
>>
>>> Doug--
>>>
>>> You had inquired whether anyone else was having problems
>>> with Matrix on a Mac... yep. I am. You'll see below
>>> that I removed both lme4 and Matrix, re-install from
>>> r-forge, but get an error msg. sessionInfo() at bottom.
>>>
>>> Could someone point me to an earlier version of Matrix?
>>> I don't believe I had this problem prior to the most
>>> recent update.
>>>
>>> cheers, Dave
>>>
>>> Dave Atkins, PhD Research Associate Professor Center for
>>> the Study of Health and Risk Behaviors Department of
>>> Psychiatry and Behavioral Science 1100 NE 45th Street,
>>> Suite 300 Seattle, WA 98105 206-616-3879
>>> [EMAIL PROTECTED]
>>>
>>>
>>>> remove.packages("Matrix")
>>> Warning in remove.packages("Matrix") : argument 'lib' is
>>> missing: using
>>> /Library/Frameworks/R.framework/Resources/library
>>>> remove.packages("lme4")
>>> Warning in remove.packages("lme4") : argument 'lib' is
>>> missing: using
>>> /Library/Frameworks/R.framework/Resources/library
>>>> install.packages("Matrix", repos =
>>>> "http://r-forge.r-project.org";)
>>> trying URL
>>>
'http://r-forge.r-project.org/bin/macosx/universal/contrib/2.8/Matrix_0.999375-17.tgz'
>>> Content type 'application/x-gzip' length 2740286 bytes
>>> (2.6 Mb) opened URL
>>> ==================================================
>>> downloaded 2.6 Mb
>>>
>>>
>>> The downloaded packages are in
>>>
>>>
/var/folders/eF/eFm91WFiEm8IX1HSzMCn4E+++TI/-Tmp-//RtmpVgGfBC/downloaded_packages
>>>> install.packages("lme4", repos =
>>>> "http://r-forge.r-project.org";)
>>> trying URL
>>>
'http://r-forge.r-project.org/bin/macosx/universal/contrib/2.8/lme4_0.999375-27.tgz'
>>> Content type 'application/x-gzip' length 913761 bytes
>>> (892 Kb) opened URL
>>> ==================================================
>>> downloaded 892 Kb
>>>
>>>
>>> The downloaded packages are in
>>>
>>>
/var/folders/eF/eFm91WFiEm8IX1HSzMCn4E+++TI/-Tmp-//RtmpVgGfBC/downloaded_packages
>>>> library(lme4)
>>> Loading required package: Matrix Error in dyn.load(file,
>>> DLLpath = DLLpath, ...) : unable to load shared library
>>>
'/Library/Frameworks/R.framework/Resources/library/Matrix/libs/i386/Matrix.so':
>>>
>>>
dlopen(/Library/Frameworks/R.framework/Resources/library/Matrix/libs/i386/Matrix.so,
>>> 6): Library not loaded:
>>> /usr/local/lib/libgfortran.2.dylib Referenced from:
>>>
/Library/Frameworks/R.framework/Resources/library/Matrix/libs/i386/Matrix.so
>>> Reason: image not found Error: package 'Matrix' could
>>> not be loaded
>>>> sessionInfo()
>>> R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1
>>>
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages: [1] stats graphics grDevices
>>> utils datasets methods base
>>>
>>> other attached packages: [1] lattice_0.17-17
>>>
>>> loaded via a namespace (and not attached): [1]
>>> grid_2.8.0 tools_2.8.0
>>>
>>> _______________________________________________
>>> [EMAIL PROTECTED] mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>>
>>
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Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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