[R-SIG-Mac] Rcpp 0.8.3 on Mac OS X 10.5.8
Ken Knoblauch
ken.knoblauch at inserm.fr
Tue Jul 13 19:32:20 CEST 2010
Thanks. I don't use macports.
Ken
Quoting Conrad Stack <stack at psu.edu>:
> 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 écrit :
>>>>>
>>>>>> 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 écrit :
>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Romain Francois
>>>>> Professional R Enthusiast
>>>>> +33(0) 6 28 91 30 30
>>>>> http://romainfrancois.blog.free.fr
>>>>> |- http://bit.ly/bc8jNi : Rcpp 0.8.4
>>>>> |- http://bit.ly/dz0RlX : bibtex 0.2-1
>>>>> `- http://bit.ly/a5CK2h : Les estivales 2010
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Ken Knoblauch
>>>> Inserm U846
>>>> Stem-cell and Brain Research Institute
>>>> Department of Integrative Neurosciences
>>>> 18 avenue du Doyen Lépine
>>>> 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
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>>>
>>>
>>
>>
>> --
>> Ken Knoblauch
>> Inserm U846
>> Stem-cell and Brain Research Institute
>> Department of Integrative Neurosciences
>> 18 avenue du Doyen Lépine
>> 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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>
>
>
> --
> Conrad Stack
> -----------------------
> PSU Department of Biology
> 208 Mueller Lab
> University Park, PA 16802
> cell: 814.409.8310
> email: conrad.stack at gmail.com
>
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
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
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