[R-SIG-Mac] .... Matrix broken on Mac...

Prof Brian Ripley ripley at stats.ox.ac.uk
Wed Dec 3 11:26:34 CET 2008 

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 <datkins at fuller.edu>
>>>>>>     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
>    >> <datkins at fuller.edu> 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
>    >>> datkins at u.washington.edu
>    >>>
>    >>>
>    >>>> 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
>    >>>
>    >>> _______________________________________________
>    >>> R-sig-mixed-models at r-project.org mailing list
>    >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>    >>>
>    >>
>
> _______________________________________________
>    DA> R-sig-mixed-models at r-project.org mailing list
>    DA> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

-- 
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

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