If it helps at all I had the exact same error installing Rcpp v0.8.1 (the
package from CRAN). My setup: gcc 4.3 (g++-mp-4.3 macports version), os
10.5.8, using R 2.11 (macports version). The solution was to reinstall
macports, use v0.8.3 and everything worked fine.
On Tue, Jul 13, 2010 at 12:04 PM, Ken Knoblauch
<ken.knoblauch at inserm.fr>wrote:
Hi Simon,
The information wasn't in the mail that he forwarded but
I had communicated it in a previous mail. Sorry.
[Macintosh-83:~] knoblauch% gcc --version
i686-apple-darwin9-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5577)
[Macintosh-83:~] knoblauch% uname -r
9.8.0
I'm currently working with Mac OS X 10.5.8 and have Xcode 3.1.4.
Also,
Macintosh-83:~] knoblauch% gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.
if that is of use.
I'll give reinstalling Xcode a try. I hadn't thought of
that. Thanks.
Ken
Quoting Simon Urbanek <simon.urbanek at r-project.org>:
On Jul 13, 2010, at 8:13 AM, Ken Knoblauch wrote:
Thanks. I'm in mode d'attente...
I did not see the exact OS version mentioned anywhere but as Romain
pointed out it's working just fine on OS X 10.5.8 with gcc 5577:
hagal:~$ gcc --version
i686-apple-darwin9-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5577)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
hagal:~$ uname -r
9.8.0
[...]
* installing *source* package 'Rcpp' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c Date.cpp -o
Date.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c
DateVector.cpp
-o DateVector.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c Datetime.cpp
-o Datetime.o
[...]
So my only advice really is to re-install Xcode...
Cheers,
Simon
Quoting Romain Francois <romain.francois at dbmail.com>:
Le 13/07/10 13:59, Ken Knoblauch a ?crit :
Salut Romain,
Thanks for your rapid response. Toujours pas de chance.
Just for verification, my gcc
[Macintosh-83:~] knoblauch% gcc --version
i686-apple-darwin9-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5577)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is
NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
IIRC, this is the version (both OS and compiler version) that is used
on CRAN so there is nothing fundamentally wrong about these.
I'm cc'ing the r-sig-mac mailing list where people might have more
clues, as I am afraid I'm short :-(
Romain
[Macintosh-83:~] knoblauch% svn checkout
svn://svn.r-forge.r-project.org/svnroot/rcpp/pkg
A pkg/RcppExamples
...
[Macintosh-83:~] knoblauch% cd pkg
[Macintosh-83:~/pkg] knoblauch% R CMD INSTALL -l
~/Library/R/2.11/library/ Rcpp
* installing *source* package ?Rcpp? ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c Date.cpp -o
Date.o
../inst/include/Rcpp/internal/export.h: In function 'void
Rcpp::internal::export_range__dispatch(SEXPREC*, InputIterator,
Rcpp::traits::r_type_primitive_tag)':
../inst/include/Rcpp/internal/export.h:56: internal compiler error: Bus
error
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://developer.apple.com/bugreporter> for instructions.
make: *** [Date.o] Error 1
ERROR: compilation failed for package ?Rcpp?
* removing ?/Users/knoblauch/Library/R/2.11/library/Rcpp?
* restoring previous ?/Users/knoblauch/Library/R/2.11/library/Rcpp?
So, still the same problem. Could this be a Leopard vs Snow Leopard
problem?
Thanks.
best,
Ken
PS, I'll subscribe shortly, but went ahead and tried your
suggestion first.
Quoting Romain Francois <romain at r-enthusiasts.com>:
Bonjour Ken,
We usually encourage people to use the mailing list (cc'ed) rather
than
the maintainer address (you would need to subsribe first)
http://lists.r-forge.r-project.org/mailman/listinfo/rcpp-devel
I think this was fixed and the version 0.8.4 is on CRAN incoming.
Could you try the svn version and let us know if it compiles fine, it
certainly does for me on Snow Leopard.
$ svn checkout svn://svn.r-forge.r-project.org/svnroot/rcpp/pkg
$ R CMD INSTALL Rcpp
Thanks for your interest in Rcpp.
FWIW, my version of gcc (on snow leopard) is:
$ gcc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is
NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
... time passes ...
Now this does sound familiar and I think we have seen some similar
errors when Rcpp was inadvertently built with gcc 4.0 on CRAN
Romain
Le 13/07/10 13:38, Ken Knoblauch a ?crit :
Hi,
I'm wondering if you can provide any suggestions for installing
Rcpp on Mac or whether I should await the appearance of a binary?
This is the error message that I get:
R CMD INSTALL --no-multiarch -l ~/Library/R/2.11/library/
Rcpp_0.8.3.tar.gz
* installing *source* package ?Rcpp? ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I../inst/include/ -I/usr/local/include -fPIC -g -O2 -c Date.cpp -o
Date.o
../inst/include/Rcpp/internal/export.h: In function 'void
Rcpp::internal::export_range__dispatch(SEXPREC*, InputIterator,
Rcpp::traits::r_type_primitive_tag)':
../inst/include/Rcpp/internal/export.h:56: internal compiler error:
Bus
error
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://developer.apple.com/bugreporter> for instructions.
make: *** [Date.o] Error 1
ERROR: compilation failed for package ?Rcpp?
* removing ?/Users/knoblauch/Library/R/2.11/library/Rcpp?
* restoring previous ?/Users/knoblauch/Library/R/2.11/library/Rcpp?
Is this a question of having the right compiler or ???
I did this from the command line but my sessionInfo is:
R version 2.11.1 Patched (2010-07-09 r52501)
i386-apple-darwin9.8.0
locale:
[1] 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
[7] base
I don't have problems compiling any other packages from source except
lme4a, so I would be greatful for any guidance.
Thanks.
Best,
Ken
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen L?pine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html