[R] igraph (was Compilation error during package installation)
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Jun 27 12:49:29 CEST 2008
Please discuss this with the package maintainer (see the posting guide).
He will need lots of details you have omitted, including the precise OS
and the C++ compiler used.
BTW, this illustrates a common problem with packages using C++, which
people often test only under one compiler, and until recently (4.3.x) g++
has been notoriously lax in reporting non-conformance to ISO C++. There
are about 30 CRAN packages that fail to install under the Sun C++
compiler, but igraph did at one point recently (there is now a problem
with the use of C headers in C++ code).
On Thu, 26 Jun 2008, wanding ZHOU wrote:
> 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:
> ___________________________________________________________________
> * Installing *source* package 'igraph' ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking for fmemopen... yes
> checking for open_memstream... yes
> checking for rintf... yes
> checking for finite... yes
> checking how to run the C preprocessor... gcc -E
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking sys/times.h usability... yes
> checking sys/times.h presence... yes
> checking for sys/times.h... yes
> checking for xml2-config... none
> checking for __gmpz_add in -lgmp... no
> configure: creating ./config.status
> config.status: creating src/config.h
> config.status: creating R/config.R
> config.status: creating src/Makevars
> ** libs
>
> 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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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