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List:       r-sig-mac
Subject:    Re: [R-SIG-Mac] R 3.0.1 build from sources: Wrong library paths
From:       Simon Zehnder <szehnder () uni-bonn ! de>
Date:       2013-09-13 8:29:34
Message-ID: DE3B0A38-02A1-4687-83A5-FF1B71DA2B49 () uni-bonn ! de
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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 <bhh@xs4all.nl> wrote:

> 
> On 12-09-2013, at 20:16, Simon Zehnder <szehnder@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 
> > 
> 

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