On Sep 11, 2009, at 15:41 , Peter Cowan wrote:
On Fri, Sep 11, 2009 at 6:32 AM, Simon Urbanek
<[email protected]> wrote:
Peter,
On Sep 11, 2009, at 2:05 AM, Peter Cowan wrote:
Bouncing to the list after failing to reply-all
On Thu, Sep 10, 2009 at 5:25 PM, Simon Urbanek
<[email protected]> wrote:
Peter,
you have probably compiled ncl in 64-bit (default on SL) but
you're using
32-bit R, so it won't work. Either use 64-bit R or compile ncl for
32-bit.
I suspected something obvious of the like. Unfortunately, I've
not been
able to get 64 bit R working for me. When I try the following for
the CRAN
version:
Birch$ R --arch x86_64
/usr/bin/R: line 207:
/Library/Frameworks/R.framework/Resources/etc/x86_64/ldpaths: No
such
file or directory
Yes, CRAN R is 32-bit only.
Yes, this makes sense, but I was a bit confused by this comment on
r.research.att.com
"Leopard builds, 64-bit binaries and packages are becoming available
from CRAN as of R 2.8.0."
Does that mean r.research.att.com ?
No, the package binaries are available directly from CRAN:
http://cran.r-project.org/bin/macosx/leopard/contrib/
I don't find a link on CRAN.
So I got the 2.9.2 patched version distributed as a tar.gz from
<http://r.research.att.com/> (thanks for providing this Simon!),
but that
doesn't work with the 64bit GUI build on the same site (it won't
even
launch, because it need 2.10.0).
Oh, true, the 2.9 GUI is simply not there. I'll have to look to see
what
went wrong.
Thanks!
Hm.. the builds are in fact there on the build machine, but are
missing from the website index ... some more digging needed ...
Please use the direct link in the meantime:
http://r.research.att.com/R-GUI-5473-2.9-leopard-Leopard64.dmg
So I installed the 32/64 Universal 2.9.0,
[BTW: you can simply overwrite the installation with the 2.9.2
patched
binary to upgrade it - the only part you really needed from the
universal
package was the GUI]
Okay, I was concerned there might be a version mismatch between 2.9.2
and the 2.9.0 gui so I didn't do that.
Patch-level releases of R are [supposed to be] binary-compatible, so
it should be safe.
BTW is the repository for the GUI public?
Yes, see FAQ:
2.4 How to build and install the R.app
The sources for the R.app GUI are currently not included in the global
R source distribution. They are available in the form of a Xcode
project on the R for Mac OS X CRAN pages (released versions) as well
as the SVN repository. In order to check out the latest development
version, use
svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI
I see the .tar on CRAN.
but now building any package gives errors [1] perhaps because SL
doesn't
install ppc64 libraries?
Yes, unfortunately. The hot fix is
rm -rf /Library/Frameworks/R.framework/Resources/bin/exec/ppc*
Brilliant! This works perfectly. Thank you for not only contributing
software but patiently helping me understand it.
Sure, you're welcome.
Cheers,
Simon
I the same (or similar warning) using the R-devel nightly.
I apologize if this to is obvious. When I install xcode, do I
need to
install the tools for prior OSs to get ppc compilers?
The compilers are there all right, it's the libraries that are
missing. They
are now only part of the 10.5 SDK in Xcode which is not used by R.
Cheers,
Simon
[1]
======
(WARNING: partial output only, ask package author to use Rprintf
instead!)
newick.c: In function ‘readNewickString’:
newick.c:233: warning: format not a string literal and no format
arguments
ld: warning: in /usr/lib/dylib1.10.5.o, missing required
architecture
ppc64 in file
ld: warning: in /usr/lib/libSystemStubs.a, missing required
architecture ppc64 in file
ld: warning: in
/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation,
missing required architecture ppc64 in file
ld: warning: in /usr/lib/libSystem.dylib, missing required
architecture ppc64 in file
ld: in /usr/lib/libSystem.B.dylib, missing required architecture
ppc64 in
file
collect2: ld returned 1 exit status
make: *** [ape.so] Error 1
ERROR: compilation failed for package ‘ape’
* Removing
‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/ape’
* Restoring previous
‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/ape’
========
Cheers,
Simon
On Sep 10, 2009, at 7:58 PM, Peter Cowan wrote:
I'm running 10.6 from clean install, with the supplied Xcode,
and R
2.9.2. I am unable to build a package (specifically the phylobase
package [1]) which built fine under 10.5.8. Even more
confusingly it
seems to build fine for others using 10.6. The end of the
install
log (appended below) contains the these potentially informative
errors:
ld: warning: in ncl/ncl/.libs/libncl.a, file is not of required
architecture
ld: warning: duplicate dylib /usr/local/lib/libgcc_s.1.dylib
The latter error I get with any source package, but doesn't seem
to
prevent them from being installed.
The package also makes use of the Rcpp interface to use an
included
library (NCL). It is this included library that seems to not
build
correctly, which could very well be related to the old version of
Rcpp, or the makefiles responsible for building it.
I've tried all manner of tweaking, upgrading, and list
searching, but
the (probably obvious) solution still eludes me. Any pointers
in the
right direction are greatly appreciated.
Peter
[1] https://r-forge.r-project.org/projects/phylobase/
=========================
sessionInfo()
R version 2.9.2 (2009-08-24)
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
=========================
birch$ which gfortran
/usr/local/bin/gfortran
birch$ gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by
law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named
COPYING
============================
[original error snipped]
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