From radford at cs.toronto.edu  Mon Oct 18 02:39:08 2010
From: radford at cs.toronto.edu (Radford Neal)
Date: Sun, 17 Oct 2010 20:39:08 -0400
Subject: [Rd] make error for R 2.13.0 (and 2.12.0)
Message-ID: <20101018003908.GA990@cs.toronto.edu>

Regarding Tengfei Yin's post about an error trying to install
"cluster" in 2.13.0, I have gotten an error with this package when
trying to install the released version of 2.12.0.  Here is the output
on an Ubuntu Linux system:

begin installing recommended package cluster
* installing *source* package 'cluster' ...
** libs
make[3]: Entering directory `/tmp/RtmpWX7ecF/R.INSTALL2aaf76ad/cluster/src'
gcc -std=gnu99 -I/u/radford/R/R-2.12.0-rel2/include  -I/usr/local/include    -fpic  -g -O2 -c clara.c -o clara.o
g77   -fpic  -g -O2 -c daisy.f -o daisy.o
g77   -fpic  -g -O2 -c dysta.f -o dysta.o
gcc -std=gnu99 -I/u/radford/R/R-2.12.0-rel2/include  -I/usr/local/include    -fpic  -g -O2 -c fanny.c -o fanny.o
gcc -std=gnu99 -I/u/radford/R/R-2.12.0-rel2/include  -I/usr/local/include    -fpic  -g -O2 -c init.c -o init.o
g77   -fpic  -g -O2 -c meet.f -o meet.o
g77   -fpic  -g -O2 -c mona.f -o mona.o
gcc -std=gnu99 -I/u/radford/R/R-2.12.0-rel2/include  -I/usr/local/include    -fpic  -g -O2 -c pam.c -o pam.o
gcc -std=gnu99 -I/u/radford/R/R-2.12.0-rel2/include  -I/usr/local/include    -fpic  -g -O2 -c sildist.c -o sildist.o
gcc -std=gnu99 -I/u/radford/R/R-2.12.0-rel2/include  -I/usr/local/include    -fpic  -g -O2 -c spannel.c -o spannel.o
g77   -fpic  -g -O2 -c twins.f -o twins.o
gcc -std=gnu99 -shared -L/usr/local/lib -o cluster.so clara.o daisy.o dysta.o fanny.o init.o meet.o mona.o pam.o sildist.o spannel.o twins.o -L/usr/lib/gcc/i486-linux-gnu/3.4.6 -lg2c -lm
make[3]: Leaving directory `/tmp/RtmpWX7ecF/R.INSTALL2aaf76ad/cluster/src'
installing to /h/253/radford/R/R-2.12.0-rel2/library/cluster/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/h/253/radford/R/R-2.12.0-rel2/library/cluster/libs/cluster.so':
  /h/253/radford/R/R-2.12.0-rel2/library/cluster/libs/cluster.so: undefined symbol: cl_daisy_
ERROR: loading failed
* removing '/h/253/radford/R/R-2.12.0-rel2/library/cluster'
make[2]: *** [cluster.ts] Error 1
make[2]: Leaving directory `/h/253/radford/R/R-2.12.0-rel2/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory `/h/253/radford/R/R-2.12.0-rel2/src/library/Recommended'
make: *** [stamp-recommended] Error 2

Here is the output of gcc -v for this system:

Using built-in specs.
Target: i486-linux-gnu
Configured with: ../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.2 --program-suffix=-4.2 --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr --enable-targets=all --enable-checking=release --build=i486-linux-gnu --host=i486-linux-gnu --target=i486-linux-gnu
Thread model: posix
gcc version 4.2.4 (Ubuntu 4.2.4-1ubuntu4)

This R-2.12.0 installation generally works (based on testing a few
trivial things).  The same error occurs when trying to install 2.12.0
on Intel Solaris.

   Radford Neal



[Rd] make error for R 2.13.0 (and 2.12.0)
Radford Neal