Problem compiling packages

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

-- 
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

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', ? 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]]

	[[alternative HTML version deleted]]

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

-- 
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', ? 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]]

	[[alternative HTML version deleted]]

-- 
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