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.
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.
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]
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*
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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