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 <[email protected]> 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 <[email protected]> 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, [email protected] >>>> 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 >>>> [email protected] >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> >> >> -- >> Brian D. Ripley, [email protected] >> 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 <[email protected]> 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 >> [email protected] >> >> >> >> >> On Nov 28, 2013, at 7:11 AM, Guillaume Blanchet <[email protected]> >> 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 >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> 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: [email protected] Priv: [email protected] > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
