[R-SIG-Mac] Problem compiling packages
Guillaume Blanchet
gblanchet.list at gmail.com
Fri Nov 29 07:52:05 CET 2013
Hi Peter and Robert !
Thank you very much for the help !
Problem solved !!
Have a good day !
Guillaume
Le 2013-11-28 à 17:43, peter dalgaard <pdalgd at gmail.com> a écrit :
> Or, as I suggested a while back:
>
> TAR=/usr/bin/tar R CMD etc.
>
> The offender is
>
> /Library/Frameworks/R.framework/Resources/etc/Renviron:TAR=${TAR-'/usr/bin/gnutar'}
>
> which you could beat into submission in the obvious way, and which perhaps "we" (i.e., not me...) could fixup on Mavericks installs.
>
> -pd
>
>
>>> Do we have any authoritative advice as to what should go into config.site? Mine seems to work unchanged, but I'm not sure I have a clue about what they are doing anymore.
>>
>> I have
>>
>> % cat config.site
>> CC="clang -mtune=native"
>> OBJC=$CC
>> F77="gfortran-4.2 -arch x86_64 -mtune=native"
>> FC=$F77
>> CXX="clang++ -mtune=native"
>> CFLAGS="-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion"
>>
>> Those are rather picky C flags, of course: intended to pick up issues with long vectors.
>>
>> gcc/g++ are not the same as clang/clang++, although the only differences I have detected are what they report themselves as. As I don't know if there are any material differences I chose to use clang explicitly. Similarly calling gfortran-4.2 explicitly to avoid any other versions (and I would even consider using /usr/local/bin/gfortran-4.2).
>>
>>> -pd
>>>
>>> On 30 Oct 2013, at 15:38 , Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
>>>
>>>> This is an attempt to collect together various pieces of advice.
>>>>
>>>> If you update to Mavericks and want to compile packages (or run some) with the CRAN binary R, you will need to
>>>>
>>>> - Update R to 3.0.2 or later if you use R.app.
>>>>
>>>> - Re-install XQuartz. The Mavericks update re-populates /usr/X11 with links which tell you to install XQuartz (even if it is currently installed).
>>>>
>>>> - Re-install the Apple Java 6 runtime if you use rJava. Try any of the rJava examples and you will be prompted for an install.
>>>>
>>>> - Install Xcode 5.0.1 if you had not previously done so.
>>>>
>>>> - Re-install the Xcode command-line tools. Xcode for Mavericks has moved most things inside Xcode (specifically under /Applications/Xcode.app/Contents/Developer) and the command-line tools previously installed seemed almost to work, but not entirely.
>>>>
>>>> xcode-select --install
>>>>
>>>> seems to be the recommended way to do so under Mavericks.
>>>>
>>>>
>>>> If you previously had them installed, the Xcode 4.6.3 compilers (such as llvm-g++-4.2) should still work. Otherwise you could select clang as your compiler: see http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages . There are also compilers called 'gcc' and 'g++' in Xcode 5.0.1: these are clang-based but are not quite the same as clang/clang++. Although g++ reports
>>>>
>>>> % g++ --version
>>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
>>>>
>>>> it looks at the libcxx headers at
>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/ . And the packages which do not compile under clang++ do not compile under g++ .
>>>>
>>>> Packages using a C++ interface may need re-compiling if you use clang++ (or g++) as your C++ compiler. The external software at http://r.research.att.com/libs/ which I know does is gdal and zeromq. It would be prudent to compile Rcpp with the same compiler as a Rcpp-using package, although not always necessary.
>>>>
>>>>
>>>> --
>>>> Brian D. Ripley, ripley at stats.ox.ac.uk
>>>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
>>>> University of Oxford, Tel: +44 1865 272861 (self)
>>>> 1 South Parks Road, +44 1865 272866 (PA)
>>>> Oxford OX1 3TG, UK Fax: +44 1865 272595
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>
>>
>> --
>> Brian D. Ripley, ripley at stats.ox.ac.uk
>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford, Tel: +44 1865 272861 (self)
>> 1 South Parks Road, +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK Fax: +44 1865 272595
>
>
>
> On 28 Nov 2013, at 16:17 , Robert J Goedman <goedman at icloud.com> wrote:
>
>> Guillaume,
>>
>> The problem is that R can't find /usr/bin/gnutar. One way of fixing this is to install gnutar or to create a symbolic link to tar, which is available on Mavericks.
>>
>> Rob J. Goedman
>> goedman at icloud.com
>>
>>
>>
>>
>> On Nov 28, 2013, at 7:11 AM, Guillaume Blanchet <gblanchet.list at gmail.com> wrote:
>>
>>> Hi !
>>>
>>> I have recently updated my OS to Maverick and from this moment, I have been unable to compile any packages (with or without C code in them). However, I can install source package on my machine without any problem. In other words, the command line
>>>
>>> R CMD INSTALL pkg
>>>
>>> works perfectly fine, where as the command line
>>>
>>> R CMD INSTALL --build pkg
>>>
>>> sends me the following insults after trying to compile any package (here for the package spacemakeR):
>>>
>>> * installing to library ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library’
>>> * installing *source* package ‘spacemakeR’ ...
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** installing vignettes
>>> ‘tutorial.Rnw’ using ‘UTF-8’
>>> ** testing if installed package can be loaded
>>> sh: /usr/bin/gnutar: No such file or directory
>>> gzip: can't stat: /Users/guslevesque/Documents/Recherche/Subversion/sedar/pkg/spacemakeR_0.0-5_R_x86_64-apple-darwin10.8.0.tar (/Users/guslevesque/Documents/Recherche/Subversion/sedar/pkg/spacemakeR_0.0-5_R_x86_64-apple-darwin10.8.0.tar): No such file or directory
>>> Avis dans file.rename(file.path(startdir, filename), file.path(startdir, :
>>> impossible de renommer le fichier '/Users/guslevesque/Documents/Recherche/Subversion/sedar/pkg/spacemakeR_0.0-5_R_x86_64-apple-darwin10.8.0.tar.gz' en '/Users/guslevesque/Documents/Recherche/Subversion/sedar/pkg/spacemakeR_0.0-5.tgz', à cause de 'No such file or directory'
>>> packaged installation of ‘spacemakeR’ as ‘spacemakeR_0.0-5.tgz’
>>> * DONE (spacemakeR)
>>>
>>>
>>> Note that I have carefully followed advices posted on this list and I have install XQuartz, XCode 5.0.2 and XCode command line tools and made following modifications to the ~/.R/Makevars file:
>>>
>>> CC=clang
>>> CXX=clang++
>>> CFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
>>> CXXFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
>>>
>>> Any ideas what is causing this problem ?
>>>
>>> Thanks in advance for all the help !
>>>
>>> Guillaume Blanchet
>>>
>>> P.S.: I almost forgot, I am working with R 3.0.2
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> --
> Peter Dalgaard, Professor
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
>
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