Building package from source error "file is not of required architecture"

On Fri, Sep 11, 2009 at 6:32 AM, Simon Urbanek
<simon.urbanek at r-project.org> 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
<simon.urbanek at r-project.org> 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 ?

 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!

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.

BTW is the repository for the GUI public?

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.

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]