[R] Compilation error during package installation

From: wanding ZHOU <wz4_at_rice.edu>
Date: Thu, 26 Jun 2008 17:00:41 -0500


Hi,

I am a Newbie for R. I just installed R-base on my notebook with openSuSE 11. However, I always got compilation errors in installing add-on packages. For example, when installing "igraph" I got the following error:


gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R
-I. -g -O2 -DPACKAGE_VERSION=\"0.5\" -DINTERNAL_ARPACK
-DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c adjlist.c -o
adjlist.o
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R
-I. -g -O2 -DPACKAGE_VERSION=\"0.5\" -DINTERNAL_ARPACK
-DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c arpack.c -o arpack.o
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R
-I. -g -O2 -DPACKAGE_VERSION=\"0.5\" -DINTERNAL_ARPACK
-DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c array.c -o array.o
gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R
-I. -g -O2 -DPACKAGE_VERSION=\"0.5\" -DINTERNAL_ARPACK
-DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c atlas.c -o atlas.o
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R
-I. -g -O2 -DPACKAGE_VERSION=\"0.5\" -DINTERNAL_ARPACK
-DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c attributes.c -o
attributes.o
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R
-I. -g -O2 -DPACKAGE_VERSION=\"0.5\" -DINTERNAL_ARPACK
-DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c basic_query.c -o
basic_query.o
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R
-I. -g -O2 -DPACKAGE_VERSION=\"0.5\" -DINTERNAL_ARPACK
-DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c bfgs.c -o bfgs.o
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined
igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined
igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but
never defined
g++ -I/usr/lib/R/include -I/usr/local/include -DUSING_R -fpic -g -O2
-c bliss.cc -o bliss.o

In file included from bliss_graph.hh:27,

                 from bliss.cc:19:

bliss_kstack.hh: In constructor ‘igraph::KStack<Type>::KStack(int)’: bliss_kstack.hh:74: error: there are no arguments to ‘malloc’ that depend on a template parameter, so a declaration of ‘malloc’ must be available
bliss_kstack.hh:74: error: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated) bliss_kstack.hh: In member function ‘void igraph::KStack<Type>::init(int)’:
bliss_kstack.hh:84: error: there are no arguments to ‘malloc’ that depend on a template parameter, so a declaration of ‘malloc’ must be available
In file included from bliss_graph.hh:28,
                 from bliss.cc:19:

bliss_kqueue.hh: In member function ‘void igraph::KQueue<Type>::init(unsigned int)’: bliss_kqueue.hh:73: error: there are no arguments to ‘malloc’ that depend on a template parameter, so a declaration of ‘malloc’ must be available
make: *** [bliss.o] Error 1
chmod: cannot access `/usr/lib/R/library/igraph/libs/*': No such file or directory
ERROR: compilation failed for package 'igraph' ** Removing '/usr/lib/R/library/igraph'

The downloaded packages are in

        /tmp/RtmpU0Z5C3/downloaded_packages
Updating HTML index of packages in '.Library' Warning message:
In install.packages("igraph") :
  installation of package 'igraph' had non-zero exit status


It says "no argument to 'malloc'". Any idea on what's wrong here?

Thanks in advance.

Wanding



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