From uwe_f_mayer at yahoo.com  Fri Aug 21 05:00:11 2009
From: uwe_f_mayer at yahoo.com (uwe_f_mayer at yahoo.com)
Date: Fri, 21 Aug 2009 05:00:11 +0200 (CEST)
Subject: [Rd] R installation problem with recommended packages (PR#13899)
Message-ID: <20090821030011.9597C282EFC0@mail.pubhealth.ku.dk>

Full_Name: Uwe F. Mayer
Version: 2.9.1
OS: SunOS myhost 5.10 Generic_120012-14 i86pc i386 i86pc Solaris
Submission from: (NULL) (216.113.168.130)


Standard configuration (that is, not specifying --without-recommended-packages)
leads to the following error:

gmake[2]: Leaving directory `/usr/local/opt/build/R-2.9.1/src/library'
gmake[1]: Leaving directory `/usr/local/opt/build/R-2.9.1/src/library'
gmake[1]: Entering directory
`/usr/local/opt/build/R-2.9.1/src/library/Recommended'
gmake[2]: Entering directory
`/usr/local/opt/build/R-2.9.1/src/library/Recommended'
begin installing recommended package VR
ERROR unable to create '/usr/local/opt/build/R-2.9.1/library/MASS'
gmake[2]: *** [VR.ts] Error 1
gmake[2]: Leaving directory
`/usr/local/opt/build/R-2.9.1/src/library/Recommended'
gmake[1]: *** [recommended-packages] Error 2
gmake[1]: Leaving directory
`/usr/local/opt/build/R-2.9.1/src/library/Recommended'
gmake: *** [stamp-recommended] Error 2

I have full write permissions to /usr/local/opt and down the tree, but I do not
have write permissions to /usr/ up the tree.

R does in fact build completely and can be installed otherwise (with some
trickery at other places), this is what it reports:

> version
               _                           
platform       x86_64-pc-solaris2.10       
arch           x86_64                      
os             solaris2.10                 
system         x86_64, solaris2.10         
status                                     
major          2                           
minor          9.1                         
year           2009                        
month          06                          
day            26                          
svn rev        48839                       
language       R                           
version.string R version 2.9.1 (2009-06-26)

A related error can be triggered from within R:

> install.packages("glmpath",
lib="/usr/local/opt/x86_64-pc-solaris2.10/R-2.9.1/lib64/R/library")
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/glmpath_0.94.tar.gz'
Content type 'application/x-gzip' length 265253 bytes (259 Kb)
opened URL
==================================================
downloaded 259 Kb

Warning in dir.create(lockdir, recursive = TRUE) :
  cannot create dir '/usr/local', reason 'Operation not applicable'
ERROR: failed to create lock directory
'/usr/local/opt/x86_64-pc-solaris2.10/R-2.9.1/lib64/R/library/00LOCK'

The downloaded packages are in
 '/tmp/RtmppArq4M/downloaded_packages'
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("glmpath", lib =
"/usr/local/opt/x86_64-pc-solaris2.10/R-2.9.1/lib64/R/library") :
  installation of package 'glmpath' had non-zero exit status

--------------------------------------------------

This is how R-2.9.1 was configured:

../../src/R-2.9.1/configure
--prefix=/usr/local/opt/x86_64-pc-solaris2.10/R-2.9.1
--exec-prefix=/usr/local/opt/x86_64-pc-solaris2.10/R-2.9.1 --disable-nls
--with-readline --with-gnu-ld CC="gcc -m64
-I/usr/local/opt/x86_64-pc-solaris2.10/include
-L/usr/local/opt/x86_64-pc-solaris2.10/lib" F77="gfortran -m64" CXX="g++ -m64"
FC="gfortran -m64" LIBnn=lib64 LD=/usr/local/opt/x86_64-pc-solaris2.10/bin/ld
SHLIB_LDFLAGS="-shared

This is what gcc -v says:

Using built-in specs.
Target: x86_64-pc-solaris2.10
Configured with: ../../src/gcc-4.4.0/configure
--prefix=/usr/local/opt/x86_64-pc-solaris2.10/gcc-4.4.0
--with-gmp=/usr/local/opt/x86_64-pc-solaris2.10
--with-mpfr=/usr/local/opt/x86_64-pc-solaris2.10 --disable-nls
--enable-languages=c,c++,fortran -with-gnu-as --without-gnu-ld
--with-ld=/usr/ccs/bin/ld --with-as=/usr/sfw/bin/gas CC='gcc -m64' CXX='g++
-m64' CFLAGS='-m64 -g -O2' CXXFLAGS='-m64 -g -O2' LDFLAGS=-m64
Thread model: posix
gcc version 4.4.0 (GCC)



[Rd] R installation problem with recommended packages (PR#13899)
uwe_f_mayer at yahoo.com