[R-SIG-Mac] Problem compiling packages

peter dalgaard pdalgd at gmail.com
Thu Nov 28 16:43:36 CET 2013 

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
>> 
>> 
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>> 
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>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> 
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> 
> _______________________________________________
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-- 
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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