Re: [R-SIG-Mac] [Caution: Message contains Suspicious URL content] R 3.0.1 build from sources: Wrong library paths
Hi Simon,
On a related note, there has been progress on openmp in llvm/clang:
http://www.phoronix.com/scan.php?page=news_itempx=MTQ0NjQ
http://lists.cs.uiuc.edu/pipermail/llvmdev/2013-August/065169.html
http://clang-omp.github.io/
That might be an alternative route to consider if needed. Clang (I have not
openmp/clang) usually builds easily on Mac OS.
Best, Anirban
On Sep 13, 2013, at 2:16 AM, Simon Zehnder
szehn...@uni-bonn.demailto:szehn...@uni-bonn.de wrote:
Simon,
I found the fix: I needed the configure option --with-included-gettext. This is
now the whole sequence of processes I did:
1. Install XCode (newest version)
2. Install Command Line Tools (in XCode)
3. On the shell I used sudo xcodebuild -license
4. I installed MacTex and MacPorts
5. In MacPorts I installed the ports: gcc48 (GCC 4-8-1 Compiler),
valgrind-devel, gettext
6. I had to remove /usr/local/bin and /usr/local/sbin from my PATH variable, as
these folders do not exist.
7. I had to add /usr/texbin to the PATH variable for R to find the pdflatex
command.
8. Then I installed the Oracle JDK and added this to the config.site file in
the R-3.0.1 folder:
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_17.jdk/Contents/HomeJAVA_CPPFLAGS=-I/${JAVA_HOME}/include
-I/${JAVA_HOME}/include/darwin
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/jre/lib/server
JAVA_LIBS=-L/${JAVA_HOME}/jre/lib/server -ljvm
9. On the shell I used:
export LANG=en_US.UTF-8
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/lib/pkgconfig
10. In a '~/Downloads/build' folder run:
../R-3.0.1/configure --bindir=/usr/bin --sbindir=/usr/bin --with-system-zlib
--enable-memory-profiling --with-blas=-framework Accelerate --with-lapack
--x-includes=/usr/X11/include --x-libraries=/usr/X11/lib
--with-valgrind-instrumentation=2 OBJC=clang LDFLAGS=-L/opt/local/lib
CPPFLAGS=-I/opt/local/include --with-included-gettext
11. make make check sudo make install
12. I run on the shell (do not know why --bindir and --sbindir didn't make it)
sudo ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/bin/R
13. I had to add
export LANG=en_US.UTF-8 in .profile
(defaults write org.R-project.R force.LANG en_US.UTF-8 did not work, did it
several times with reopening the terminal)
I installed the packages nloptr (this still worked) and Rcpp (this worked now
as well - the ld error: library not found: lintel, has gone)
So far this works quite nice. If there are some updates on stability I let you
know.
My config.log can be seen here:
https://gist.github.com/anonymous/6541684
Thanks again for your help!
Simon
On Sep 12, 2013, at 5:16 PM, Simon Zehnder
szehn...@uni-bonn.demailto:szehn...@uni-bonn.de wrote:
Simon,
thanks for the help. This did make the work. I wonder why the --bindir and
--sbindir options during configure did not let that happen.
R runs on my system and here is what I precisely did:
1. Install XCode (newest version)
2. Install Command Line Tools (in XCode)
3. On the shell I used sudo xcodebuild -license
4. I installed MacTex and MacPorts
5. In MacPorts I installed the ports: gcc48 (GCC 4-8-1 Compiler),
valgrind-devel, gettext
6. I had to remove /usr/local/bin and /usr/local/sbin from my PATH variable, as
these folders do not exist.
7. I had to add /usr/texbin to the PATH variable for R to find the pdflatex
command.
8. Then I installed the Oracle JDK and added this to the config.site file in
the R-3.0.1 folder:
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_17.jdk/Contents/HomeJAVA_CPPFLAGS=-I/${JAVA_HOME}/include
-I/${JAVA_HOME}/include/darwin
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/jre/lib/server
JAVA_LIBS=-L/${JAVA_HOME}/jre/lib/server -ljvm
9. On the shell I used:
export LANG=en_US.UTF-8
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/lib/pkgconfig
10. In a '~/Downloads/build' folder run:
../R-3.0.1/configure --bindir=/usr/bin --sbindir=/usr/bin --with-system-zlib
--enable-memory-profiling --with-blas=-framework Accelerate --with-lapack
--x-includes=/usr/X11/include --x-libraries=/usr/X11/lib
--with-valgrind-instrumentation=2 OBJC=clang LDFLAGS=-L/opt/local/lib
CPPFLAGS=-I/opt/local/include
11. make make check sudo make install
12. I run on the shell (do not know why --bindir and --sbindir didn't make it)
sudo ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/bin/R
13. I had to add
export LANG=en_US.UTF-8 in .profile
(defaults write org.R-project.R force.LANG en_US.UTF-8 did not work, did it
several times with reopening the terminal)
All seemed to work fine. I installed the package nloptr (which did not install
in my last R app) and it did compile without a hassle (that's great!). But then
with Rcpp I got the error: ld: library not found for -lintl. I looked into the
files of the gcc48 of MacPorts under /opt/local/lib and I have three libraries
in there: libintl.8.dylib, libintl.a, libintl.la. I do not know though if this
error wrong linking via R's environment variables or I miss an export in my
.profile.
I also have now
Re: [R-SIG-Mac] R 3.0.1 build from sources: Wrong library paths
Berend,
I retried the command pdflatex without the extra export and it does not work.
Assumably, this is due to the fact, that I had /usr/local/bin and
/usr/local/sbin in my PATH variable and I used export
PATH=/usr/bin:/bin:/usr/sbin:/sbin to get it out of my PATH (inside my .profile
file).
In regard to XQuartz: True, I did and I will ad it to the sequence. Thanks for
the comment, I have fully overseen this!
Best
Simon
On Sep 13, 2013, at 10:19 AM, Berend Hasselman b...@xs4all.nl wrote:
On 12-09-2013, at 20:16, Simon Zehnder szehn...@uni-bonn.de wrote:
Simon,
I found the fix: I needed the configure option --with-included-gettext. This
is now the whole sequence of processes I did:
1. Install XCode (newest version)
2. Install Command Line Tools (in XCode)
3. On the shell I used sudo xcodebuild -license
4. I installed MacTex and MacPorts
5. In MacPorts I installed the ports: gcc48 (GCC 4-8-1 Compiler),
valgrind-devel, gettext
6. I had to remove /usr/local/bin and /usr/local/sbin from my PATH variable,
as these folders do not exist.
7. I had to add /usr/texbin to the PATH variable for R to find the pdflatex
command.
This bit I don't understand.
After installing MacTeX and either logging out and in or restarting
/usr/texbin should have been in PATH (at least that is the intention of
MacTeX).
Also I assume you have XQuartz installed. If so, that should also be
mentioned in your recipe.
Berend
8. Then I installed the Oracle JDK and added this to the config.site file in
the R-3.0.1 folder:
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_17.jdk/Contents/HomeJAVA_CPPFLAGS=-I/${JAVA_HOME}/include
-I/${JAVA_HOME}/include/darwin
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/jre/lib/server
JAVA_LIBS=-L/${JAVA_HOME}/jre/lib/server -ljvm
9. On the shell I used:
export LANG=en_US.UTF-8
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/lib/pkgconfig
10. In a '~/Downloads/build' folder run:
../R-3.0.1/configure --bindir=/usr/bin --sbindir=/usr/bin --with-system-zlib
--enable-memory-profiling --with-blas=-framework Accelerate --with-lapack
--x-includes=/usr/X11/include --x-libraries=/usr/X11/lib
--with-valgrind-instrumentation=2 OBJC=clang LDFLAGS=-L/opt/local/lib
CPPFLAGS=-I/opt/local/include --with-included-gettext
11. make make check sudo make install
12. I run on the shell (do not know why --bindir and --sbindir didn't make
it)
sudo ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/bin/R
13. I had to add
export LANG=en_US.UTF-8 in .profile
(defaults write org.R-project.R force.LANG en_US.UTF-8 did not work, did it
several times with reopening the terminal)
I installed the packages nloptr (this still worked) and Rcpp (this worked
now as well - the ld error: library not found: lintel, has gone)
So far this works quite nice. If there are some updates on stability I let
you know.
My config.log can be seen here:
https://gist.github.com/anonymous/6541684
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [Caution: Message contains Suspicious URL content] R 3.0.1 build from sources: Wrong library paths
On 13/09/2013 07:52, Anirban MUKHERJEE wrote: Hi Simon, On a related note, there has been progress on openmp in llvm/clang: http://www.phoronix.com/scan.php?page=news_itempx=MTQ0NjQ http://lists.cs.uiuc.edu/pipermail/llvmdev/2013-August/065169.html http://clang-omp.github.io/ That might be an alternative route to consider if needed. Clang (I have not openmp/clang) usually builds easily on Mac OS. We know (I believe it has been mentioned here before). But please remember that only the Apple clang is easy to use (does your self-build compile the quartz device? -- mine did not), and Apple lags a long way behind. The current Xcode version says it is '3.2svn' but lacks even 3.1 features such as AddressSanitizer. We will see what Xcode 5 brings when it is released. I don't think people appreciated Simon's comments about the stability needed. If you can check all of CRAN with no more than 10 issues with gcc 4.7 or 4.8, then let us know. That is about where we are with llvm-gcc 4.2 and clang 3.2- from Xcode 4.6.3. When I tried 4.7.x prior to R 3.0.0 I had over 50 failures (and CRAN is reqularly checked with 4.7.x on other platforms). And we are only in that good a state because a lot of (literally) thankless work has been done to get CRAN/BioC packages to compile with clang. -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R on Mac: framework or homebrew?
Prof Brian Ripley rip...@stats.ox.ac.uk writes: On 12/09/2013 17:15, MacQueen, Don wrote: I've been using R on OS X probably ever since there was an R on OS X, and like you I use it from the command line. In the early days I installed R from sources, but quite a few years ago I switched to using the framework version. I can't think of any disadvantage I've encountered. It is harder to have multiple versions of the framework in use at once. And that is an issue now the R release rate is slower: package developers probably want both the release version and a current R-devel. That is what I was thinking as well - in homebrew, I simply have to use , | brew switch R version ` to switch to another installed version. If I were to not use the framework version, I think I would prefer to install directly from sources, not use a package management system. There might be more initial work installing various prerequisites (things like tcl/tk, png, maybe readline, who knows what all) but it would probably be better in the long run. Some packages, such as a number of spatial packages, require installing other libraries such as rgdal, proj, and others. Currently, these are also available as frameworks, and installing those packages in a framework R is now well-supported. It might be considerably more difficult to install such packages in a non-framework R. I don't know how much would be involved, so I just suggest it as an aspect to consider. Almost nothing. Simon provides binaries for those at http://r.research.att.com/libs/ and if you want later ones they compile simply from the sources. in any case, whether R is a framework or not does not affect installing packages from sources, as you still need to tell the toolchain where to look for the headers and libraries. That is good to know. On my office iMac have almost all of CRAN installed (more than Simon provides as binaries) compiling from source. The exceptions are those 10 or so which are too broken to install on OS X and those depending on Qt, MySQL (I haven't bothered) or BRugs (i386 Windows/Linux only) Thanks a lot for all of your input. I will then, for the moment, stick to the framework (as it works), but keep the homebrew option in mind. Thanks, Rainer -- Rainer M. Krug email: RMKrugatgmaildotcom ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [Caution: Message contains Suspicious URL content] R 3.0.1 build from sources: Wrong library paths
Dear Brian, if it is able to test the compilation of the quartz device by calling quartz() in R - this works. Calling xcodebuild -version gives me: Xcode 4.6.3 and clang --version gives me LLVM 3.2svn indeed. My prime target was to be able to use OpenMP 3.1 which is actually only available (freely) in gcc = 4.7. Is there a possibility to install, check and reinstall all CRAN packages in R? Best Simon On Sep 13, 2013, at 10:52 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 13/09/2013 07:52, Anirban MUKHERJEE wrote: Hi Simon, On a related note, there has been progress on openmp in llvm/clang: http://www.phoronix.com/scan.php?page=news_itempx=MTQ0NjQ http://lists.cs.uiuc.edu/pipermail/llvmdev/2013-August/065169.html http://clang-omp.github.io/ That might be an alternative route to consider if needed. Clang (I have not openmp/clang) usually builds easily on Mac OS. We know (I believe it has been mentioned here before). But please remember that only the Apple clang is easy to use (does your self-build compile the quartz device? -- mine did not), and Apple lags a long way behind. The current Xcode version says it is '3.2svn' but lacks even 3.1 features such as AddressSanitizer. We will see what Xcode 5 brings when it is released. I don't think people appreciated Simon's comments about the stability needed. If you can check all of CRAN with no more than 10 issues with gcc 4.7 or 4.8, then let us know. That is about where we are with llvm-gcc 4.2 and clang 3.2- from Xcode 4.6.3. When I tried 4.7.x prior to R 3.0.0 I had over 50 failures (and CRAN is reqularly checked with 4.7.x on other platforms). And we are only in that good a state because a lot of (literally) thankless work has been done to get CRAN/BioC packages to compile with clang. -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [Caution: Message contains Suspicious URL content] R 3.0.1 build from sources: Wrong library paths
On 13/09/2013 11:16, Simon Zehnder wrote: Dear Brian, if it is able to test the compilation of the quartz device by calling quartz() in R - this works. Calling xcodebuild -version gives me: Xcode 4.6.3 and clang --version gives me LLVM 3.2svn indeed. My prime target was to be able to use OpenMP 3.1 which is actually only available (freely) in gcc = 4.7. Is there a possibility to install, check and reinstall all CRAN packages in R? I was not asking about the clang in Xcode ... my point was that not all non-Apple versions of clang can compile quartz(). As for your question about CRAN package checks: CRAN does it daily so it must be possible. Best Simon On Sep 13, 2013, at 10:52 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 13/09/2013 07:52, Anirban MUKHERJEE wrote: Hi Simon, On a related note, there has been progress on openmp in llvm/clang: http://www.phoronix.com/scan.php?page=news_itempx=MTQ0NjQ http://lists.cs.uiuc.edu/pipermail/llvmdev/2013-August/065169.html http://clang-omp.github.io/ That might be an alternative route to consider if needed. Clang (I have not openmp/clang) usually builds easily on Mac OS. We know (I believe it has been mentioned here before). But please remember that only the Apple clang is easy to use (does your self-build compile the quartz device? -- mine did not), and Apple lags a long way behind. The current Xcode version says it is '3.2svn' but lacks even 3.1 features such as AddressSanitizer. We will see what Xcode 5 brings when it is released. I don't think people appreciated Simon's comments about the stability needed. If you can check all of CRAN with no more than 10 issues with gcc 4.7 or 4.8, then let us know. That is about where we are with llvm-gcc 4.2 and clang 3.2- from Xcode 4.6.3. When I tried 4.7.x prior to R 3.0.0 I had over 50 failures (and CRAN is reqularly checked with 4.7.x on other platforms). And we are only in that good a state because a lot of (literally) thankless work has been done to get CRAN/BioC packages to compile with clang. -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [Caution: Message contains Suspicious URL content] R 3.0.1 build from sources: Wrong library paths
On Sep 13, 2013, at 6:16 AM, Simon Zehnder wrote: Dear Brian, if it is able to test the compilation of the quartz device by calling quartz() in R - this works. Calling xcodebuild -version gives me: Xcode 4.6.3 and clang --version gives me LLVM 3.2svn indeed. My prime target was to be able to use OpenMP 3.1 which is actually only available (freely) in gcc = 4.7. That's not true - Intel OpenMP RTL (http://www.openmprtl.org/ ) is free (BSD license), goes even up to OpenMP 4.0 features and has much better performance. GOMP has terrible performance on OS X (one of the two reasons why we disable it in the binaries), so if you care about OMP you probably don't want to use gcc anyway (or plug out GOMP for the Intel one). Is there a possibility to install, check and reinstall all CRAN packages in R? Install is easy - you feed install.packages() with package list from available.packages() and you can even use Ncpus. Check is annoying since there is no equivalent R function (AFAIK). All of us have their own functions they use for this. But what's more complicated is that you'll need to install all dependent libraries in the system - and there are a lot of them. Cheers, Simon Best Simon On Sep 13, 2013, at 10:52 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 13/09/2013 07:52, Anirban MUKHERJEE wrote: Hi Simon, On a related note, there has been progress on openmp in llvm/clang: http://www.phoronix.com/scan.php?page=news_itempx=MTQ0NjQ http://lists.cs.uiuc.edu/pipermail/llvmdev/2013-August/065169.html http://clang-omp.github.io/ That might be an alternative route to consider if needed. Clang (I have not openmp/clang) usually builds easily on Mac OS. We know (I believe it has been mentioned here before). But please remember that only the Apple clang is easy to use (does your self-build compile the quartz device? -- mine did not), and Apple lags a long way behind. The current Xcode version says it is '3.2svn' but lacks even 3.1 features such as AddressSanitizer. We will see what Xcode 5 brings when it is released. I don't think people appreciated Simon's comments about the stability needed. If you can check all of CRAN with no more than 10 issues with gcc 4.7 or 4.8, then let us know. That is about where we are with llvm-gcc 4.2 and clang 3.2- from Xcode 4.6.3. When I tried 4.7.x prior to R 3.0.0 I had over 50 failures (and CRAN is reqularly checked with 4.7.x on other platforms). And we are only in that good a state because a lot of (literally) thankless work has been done to get CRAN/BioC packages to compile with clang. -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
