[R-SIG-Mac] Building package from source error "file is not of required architecture"

[Peter Cowan]

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

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).

So I installed the 32/64 Universal 2.9.0, but now building any package
gives errors [1] perhaps because SL doesn't install ppc64 libraries?
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?

[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]