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] R 3.0.1 build from sources: Wrong library paths
I did some progress on my problem: Using LDFLAGS and CPPFLAGS on the shell instead of in the config.site file changes the directories and make can find all the libraries. The next thing that came up, was the Mac-specific Cocoa issue. When I compile R sources with OBJC=gcc -arch x86_64 I get the following outputs: config.log: https://gist.github.com/anonymous/6534550 make.log: https://gist.github.com/anonymous/6534560 with errors starting in line 883 of the make.log. So it seems the gcc cannot handle the .m files properly. Then I used OBJC=clang and I get the following output: config.log: https://gist.github.com/anonymous/6534614 make.log: https://gist.github.com/anonymous/6534606 Here I get (see line 879 in the make.log) some weird warning. I know these are only warnings, they do not influence the way R works later on, but I am interested why gcc cannot handle the Cocoa files at all and clang has these warnings. Best Simon On Sep 11, 2013, at 11:08 PM, Simon Zehnder szehn...@uni-bonn.de wrote: Dear R-Users and R-Devels, I made a brand new install of Mac OS X Mountain Lion 10.8.4 on a new hard drive and want to build R from sources. As I use OpenMP 3.1 in my C++ extensions I used MacPorts to get the gcc48 compiler collection. Installation run without a hassle and I set the mp-gcc48 active. I downloaded the R-3.0.1 tar.gz and extracted it. Then I changed the config.site to the following: https://gist.github.com/anonymous/6529767 Furthermore I had to change my PATH variable in the .profile as it included /usr/local/bin:/usr/local/sbin and I have not such a folder in my /usr. Now when I run configure I get the following config.log https://gist.github.com/anonymous/6529743 with the warning: ld: warning: directory not found for option '-L/usr/local/lib' on line 217. This warning becomes an error if running the make command. I still see the C linker using -L/usr/local/lib which does not exist. I changed the LDFLAGS in the config.site to -L/opt/local/lib but Rs configure script seems to be very resistant to my new proposal. I need some help. How should I proceed? Which FLAGS can change the directory the make script searches for libraries? What configure options should be used with R-3.0.1 on OS X 10.8.4 using gcc-4.8.1? Best Simon ___ 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] R 3.0.1 build from sources: Wrong library paths
I compiled R and made a check-all without errors (only for the PDF manuals - but this is ok). Then I used sudo make install to install it to the R.framework. Now, when I want to use R on the shell no command can be found, as the installation has not installed the binaries in /usr/bin. If I try to change my PATH variable and add /Library/Frameworks/R.framework/Ressources/bin it does not change a thing, I still get the error: -bash: R: command not found. The only thing to make it work is to go into the folder /Libraries/Frameworks/R.framework/Ressources/bin/ and start it via ./R. I remember no such behaviour for prior builds of R. It seems Mac has changed something since my last compilation of R sources. Can anyone help? Best Simon On Sep 12, 2013, at 10:49 AM, Simon Zehnder szehn...@uni-bonn.de wrote: I did some progress on my problem: Using LDFLAGS and CPPFLAGS on the shell instead of in the config.site file changes the directories and make can find all the libraries. The next thing that came up, was the Mac-specific Cocoa issue. When I compile R sources with OBJC=gcc -arch x86_64 I get the following outputs: config.log: https://gist.github.com/anonymous/6534550 make.log: https://gist.github.com/anonymous/6534560 with errors starting in line 883 of the make.log. So it seems the gcc cannot handle the .m files properly. Then I used OBJC=clang and I get the following output: config.log: https://gist.github.com/anonymous/6534614 make.log: https://gist.github.com/anonymous/6534606 Here I get (see line 879 in the make.log) some weird warning. I know these are only warnings, they do not influence the way R works later on, but I am interested why gcc cannot handle the Cocoa files at all and clang has these warnings. Best Simon On Sep 11, 2013, at 11:08 PM, Simon Zehnder szehn...@uni-bonn.de wrote: Dear R-Users and R-Devels, I made a brand new install of Mac OS X Mountain Lion 10.8.4 on a new hard drive and want to build R from sources. As I use OpenMP 3.1 in my C++ extensions I used MacPorts to get the gcc48 compiler collection. Installation run without a hassle and I set the mp-gcc48 active. I downloaded the R-3.0.1 tar.gz and extracted it. Then I changed the config.site to the following: https://gist.github.com/anonymous/6529767 Furthermore I had to change my PATH variable in the .profile as it included /usr/local/bin:/usr/local/sbin and I have not such a folder in my /usr. Now when I run configure I get the following config.log https://gist.github.com/anonymous/6529743 with the warning: ld: warning: directory not found for option '-L/usr/local/lib' on line 217. This warning becomes an error if running the make command. I still see the C linker using -L/usr/local/lib which does not exist. I changed the LDFLAGS in the config.site to -L/opt/local/lib but Rs configure script seems to be very resistant to my new proposal. I need some help. How should I proceed? Which FLAGS can change the directory the make script searches for libraries? What configure options should be used with R-3.0.1 on OS X 10.8.4 using gcc-4.8.1? Best Simon ___ 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
Re: [R-SIG-Mac] R 3.0.1 build from sources: Wrong library paths
On Sep 12, 2013, at 5:50 AM, Simon Zehnder wrote: I compiled R and made a check-all without errors (only for the PDF manuals - but this is ok). Then I used sudo make install to install it to the R.framework. Now, when I want to use R on the shell no command can be found, as the installation has not installed the binaries in /usr/bin. If I try to change my PATH variable and add /Library/Frameworks/R.framework/Ressources/bin it does not change a thing, I still get the error: -bash: R: command not found. The only thing to make it work is to go into the folder /Libraries/Frameworks/R.framework/Ressources/bin/ and start it via ./R. What the CRAN installer does is essentially sudo ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/bin/R Obviously, changing the PATH works as well - make sure you check the value of PATH in the session you're running (bash uses a cached lookup, but recent versions should have no trouble re-trying after PATH changes) -- assuming running /Libraries/Frameworks/R.framework/Ressources/bin/R works. If it doesn't then maybe check the version symlinks. Re you earlier post - FSF builds of gcc don't support ObjC with Apple runtime, so you have to use Apple's clang (as you did). In my tests few months ago gcc 4.7/4.8 was too unreliable - it was miscompiling R so things were breaking randomly at run-time. If your build seems reliable, please share with use the exact version and settings. Thanks, Simon I remember no such behaviour for prior builds of R. It seems Mac has changed something since my last compilation of R sources. Can anyone help? Best Simon On Sep 12, 2013, at 10:49 AM, Simon Zehnder szehn...@uni-bonn.de wrote: I did some progress on my problem: Using LDFLAGS and CPPFLAGS on the shell instead of in the config.site file changes the directories and make can find all the libraries. The next thing that came up, was the Mac-specific Cocoa issue. When I compile R sources with OBJC=gcc -arch x86_64 I get the following outputs: config.log: https://gist.github.com/anonymous/6534550 make.log: https://gist.github.com/anonymous/6534560 with errors starting in line 883 of the make.log. So it seems the gcc cannot handle the .m files properly. Then I used OBJC=clang and I get the following output: config.log: https://gist.github.com/anonymous/6534614 make.log: https://gist.github.com/anonymous/6534606 Here I get (see line 879 in the make.log) some weird warning. I know these are only warnings, they do not influence the way R works later on, but I am interested why gcc cannot handle the Cocoa files at all and clang has these warnings. Best Simon On Sep 11, 2013, at 11:08 PM, Simon Zehnder szehn...@uni-bonn.de wrote: Dear R-Users and R-Devels, I made a brand new install of Mac OS X Mountain Lion 10.8.4 on a new hard drive and want to build R from sources. As I use OpenMP 3.1 in my C++ extensions I used MacPorts to get the gcc48 compiler collection. Installation run without a hassle and I set the mp-gcc48 active. I downloaded the R-3.0.1 tar.gz and extracted it. Then I changed the config.site to the following: https://gist.github.com/anonymous/6529767 Furthermore I had to change my PATH variable in the .profile as it included /usr/local/bin:/usr/local/sbin and I have not such a folder in my /usr. Now when I run configure I get the following config.log https://gist.github.com/anonymous/6529743 with the warning: ld: warning: directory not found for option '-L/usr/local/lib' on line 217. This warning becomes an error if running the make command. I still see the C linker using -L/usr/local/lib which does not exist. I changed the LDFLAGS in the config.site to -L/opt/local/lib but Rs configure script seems to be very resistant to my new proposal. I need some help. How should I proceed? Which FLAGS can change the directory the make script searches for libraries? What configure options should be used with R-3.0.1 on OS X 10.8.4 using gcc-4.8.1? Best Simon ___ 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 ___ 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 3.0.1 build from sources: Wrong library paths
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 a warning when using MacPorts, which is already reported:
http://openradar.appspot.com/11894054
Here is my config.log
https://gist.github.com/anonymous/6539093
and here the output from Sys.getenv():
https://gist.github.com/anonymous/6539133
So, I cannot tell, if this should be considered a stable build on the Mac. But
maybe everything can be solved quite easily.
Best
Simon
On Sep 12, 2013, at 2:54 PM, Simon Urbanek simon.urba...@r-project.org wrote:
On Sep 12, 2013, at 5:50 AM, Simon Zehnder wrote:
I compiled R and made a check-all without errors (only for the PDF manuals -
but this is ok). Then I used
sudo make install
to install it to the R.framework. Now, when I want to use R on the shell no
command can be found, as the installation has not installed the binaries in
/usr/bin. If I try to change my PATH variable and add
/Library/Frameworks/R.framework/Ressources/bin it does not change a thing, I
still get the error: -bash: R: command not found. The only thing to make it
work is to go into the folder
/Libraries/Frameworks/R.framework/Ressources/bin/ and start it via ./R.
What the CRAN installer does is essentially
sudo ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/bin/R
Obviously, changing the PATH works as well - make sure you check the value
of PATH in the session you're running (bash uses a cached lookup, but recent
versions should have no trouble re-trying after PATH changes) -- assuming
running
/Libraries/Frameworks/R.framework/Ressources/bin/R
works. If it doesn't then maybe check the version symlinks.
Re you earlier post - FSF builds of gcc don't support ObjC with Apple
runtime, so you have to use Apple's clang (as you did). In my tests few
months ago gcc 4.7/4.8 was too unreliable - it was miscompiling R so things
were breaking randomly at run-time. If your build seems reliable, please
share with use the exact version and settings.
Thanks,
Simon
I remember no such behaviour for prior builds of R. It seems Mac has changed
something since my last compilation of R sources.
Can anyone help?
Best
Simon
On Sep 12, 2013, at 10:49 AM, Simon Zehnder szehn...@uni-bonn.de wrote:
I did some progress on my problem:
Using LDFLAGS and CPPFLAGS on the shell instead of in the config.site file
changes the directories and make can find all the libraries.
The next thing that came up, was the Mac-specific Cocoa issue. When I
compile R sources with OBJC=gcc -arch x86_64 I get the following outputs:
config.log: https://gist.github.com/anonymous/6534550
make.log: https://gist.github.com/anonymous/6534560
with
Re: [R-SIG-Mac] R 3.0.1 build from sources: Wrong library paths
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.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 a warning when using MacPorts, which is already reported:
http://openradar.appspot.com/11894054
Here is my config.log
https://gist.github.com/anonymous/6539093
and here the output from Sys.getenv():
https://gist.github.com/anonymous/6539133
So, I cannot tell, if this should be considered a stable build on the Mac.
But maybe everything can be solved quite easily.
Best
Simon
On Sep 12, 2013, at 2:54
