[R-SIG-Mac] make install fails

Kasper Daniel Hansen khansen at stat.berkeley.edu
Tue Dec 1 23:25:01 CET 2009


I think I found the culprit.  I installed the devpack before I compiled R, and looking at the contents of the tarball it does install things in /Library/Frameworks/R.framework/Resources.  That must have created the hard link.

Kasper

On Dec 1, 2009, at 5:22 PM, Kasper Daniel Hansen wrote:

> Thanks. rm -Rf /Library/Frameworks/R.framework did the trick, so it was obviously an error on my end.
> 
> My system is/was clean insofar as all I have done regarding R is use ./configure, make, make install on a freshly formatted harddrive.  One possible explanation for this could be a C-c during make install or a make install without sudo.  Granted, I do not see why either of these possibilities would create a non symlink.  This is based on a review of my bash history, which - unfortunately in this case - removes duplicate entries, so it is hard to see exactly what I did in what order.
> 
> Anyway, it is probably pointless to speculate about the cause.
> 
> Kasper
> 
> On Dec 1, 2009, at 4:49 PM, Simon Urbanek wrote:
> 
>> I see - you have a rogue directory
>> /Library/Frameworks/R.framework/Resources
>> in all normal installations that is a symlink but apparently you may have used hard copy or something such that it's not a symlink.
>> If you remove that all should be well. What you have there is definitely not a clean system ;). I have put a guard about such strange framework setup in the R-devel, just in case.
>> Cheers,
>> Simon
>> 
>> 
>> 
>> On Dec 1, 2009, at 12:13 , Kasper Daniel Hansen wrote:
>> 
>>> 
>>> On Dec 1, 2009, at 11:29 AM, Simon Urbanek wrote:
>>> 
>>>> ls -l /Library/Frameworks/R.framework
>>>> ls -l /Library/Frameworks/R.framework/Versions
>>>> ls -l /Library/Frameworks/R.framework/Versions/2.11
>>>> ls -l /Library/Frameworks/R.framework/Versions/2.11/Resources
>>> 
>>> 
>>> This is my current state, after a failed sudo make install on R-2.10 and R-devel
>>> 
>>> grue-1:~/> ls -l /Library/Frameworks/R.framework
>>> total 32
>>> lrwxr-xr-x  1 root  admin    24B Dec  1 09:41 Headers -> Versions/Current/Headers
>>> lrwxr-xr-x  1 root  admin    30B Dec  1 09:41 Libraries -> Versions/Current/Resources/lib
>>> lrwxr-xr-x  1 root  admin    31B Dec  1 09:41 PrivateHeaders -> Versions/Current/PrivateHeaders
>>> lrwxr-xr-x  1 root  admin    18B Dec  1 09:41 R -> Versions/Current/R
>>> drwxrwxr-x  4 root  admin   136B Dec  1 09:41 Resources
>>> drwxr-xr-x  5 root  admin   170B Dec  1 09:41 Versions
>>> grue-1:~/> ls -l /Library/Frameworks/R.framework/Versions
>>> total 8
>>> drwxr-xr-x  6 root  admin   204B Nov 30 19:09 2.10
>>> drwxr-xr-x  6 root  admin   204B Dec  1 09:41 2.11
>>> lrwxr-xr-x  1 root  admin     4B Dec  1 09:41 Current -> 2.11
>>> grue-1:~/> ls -l /Library/Frameworks/R.framework/Versions/2.11
>>> total 16
>>> lrwxr-xr-x   1 root  admin    17B Dec  1 09:41 Headers -> Resources/include
>>> drwxr-xr-x   2 root  admin    68B Dec  1 09:27 PrivateHeaders
>>> lrwxr-xr-x   1 root  admin    24B Dec  1 09:41 R -> Resources/lib/libR.dylib
>>> drwxr-xr-x  16 root  admin   544B Dec  1 09:41 Resources
>>> grue-1:~/> ls -l /Library/Frameworks/R.framework/Versions/2.11/Resources
>>> total 928
>>> -rw-r--r--   1 root  admin    18K Dec  1 09:41 COPYING
>>> -rw-r--r--   1 root  admin   408K Dec  1 09:41 NEWS
>>> -rwxr-xr-x   1 root  admin   8.1K Dec  1 09:41 R
>>> -rwxr-xr-x   1 root  admin    14K Dec  1 09:41 Rscript
>>> -rw-r--r--   1 root  admin    46B Dec  1 09:41 SVN-REVISION
>>> drwxr-xr-x  28 root  admin   952B Dec  1 09:41 bin
>>> drwxr-xr-x  15 root  admin   510B Dec  1 09:41 doc
>>> drwxr-xr-x   4 root  admin   136B Dec  1 09:41 etc
>>> drwxr-xr-x  10 root  admin   340B Dec  1 09:41 include
>>> drwxr-xr-x   3 root  admin   102B Dec  1 09:26 lib
>>> drwxr-xr-x  30 root  admin   1.0K Dec  1 09:27 library
>>> drwxr-xr-x   4 root  admin   136B Dec  1 09:41 man1
>>> drwxr-xr-x   3 root  admin   102B Dec  1 09:26 modules
>>> drwxr-xr-x  11 root  admin   374B Dec  1 09:27 share
>>> grue-1:~/>
>>> 
>>> Just for reference, my full build script is
>>> #!/bin/bash
>>> R_VERSION=devel
>>> SRCDIR=R-${R_VERSION}-src
>>> BUILDDIR=R-${R_VERSION}-build
>>> 
>>> if [ ! -d ${SRCDIR} ]; then
>>> svn co https://svn.r-project.org/R/trunk ${SRCDIR}
>>> fi
>>> cd ${SRCDIR}
>>> svn up || exit 1
>>> tools/rsync-recommended || exit 1
>>> tools/link-recommended || exit 1
>>> cd ..
>>> rm -rf ${BUILDDIR}
>>> mkdir ${BUILDDIR}
>>> cd ${BUILDDIR}
>>> LANG=C
>>> export LANG
>>> ../${SRCDIR}/configure SHELL='/bin/bash' \
>>> r_arch=x86_64 \
>>> CC="/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99" \
>>> CFLAGS="-g -O2 -std=gnu99 -march=nocona" \
>>> CXX="/usr/bin/g++-4.2 -arch x86_64" \
>>> CXXFLAGS="-g -O2 -march=nocona" \
>>> OBJC="/usr/bin/gcc-4.2 -arch x86_64" \
>>> F77="/usr/bin/gfortran-4.2 -arch x86_64" \
>>> FFLAGS="-g -O2 -march=nocona" \
>>> FC="/usr/bin/gfortran-4.2 -arch x86_64" \
>>> FCFLAGS="-g -O2 -march=nocona" \
>>> --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib \
>>> --with-system-zlib \
>>> --with-blas='-framework vecLib' --with-lapack
>>> 
>>> 
>>> 
>>> 
>> 
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