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

Peter Dalgaard pdalgd at gmail.com
Mon Oct 18 09:03:58 CEST 2010

On 10/18/2010 02:39 AM, Radford Neal wrote:
> 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:

Hmm, g77 along with a recent gcc? It is usually gfortran on current
linux systems. It's strange that it got past the configure step though.
What did the configure output look like? A look at "nm cluster.so" could
also be informative.


> 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
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Peter Dalgaard
Center for Statistics, Copenhagen Business School
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

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