[R] igraph (was Compilation error during package installation)

Gabor Csardi csardi at rmki.kfki.hu
Fri Jun 27 13:11:08 CEST 2008 

Wanding, 

I'm the maintainer of igraph, but missed your previous email. 

Yes, currently the released version of igraph fails to compile 
with gcc 4.3.x. I made the required modifications to fix this, 
but these are still in the igraph development tree, as there has been
no release since that.

You can do the one of the following things:
1) You download and install 
   http://cneurocvs.rmki.kfki.hu/igraph/download/igraph_0.5.1.tar.gz
   This is an almost final 0.5.1 version, there will be some more 
   minor updates. 
2) You just wait a week for igraph 0.5.1.
3) You download our development tree and build an R package for yourself.

Probably 1) is easiest.

Best,
Gabor

Btw. there is also an igraph mailing list, see igraph.sf.net -> community ->
igraph-help

On Fri, Jun 27, 2008 at 11:49:29AM +0100, Prof Brian Ripley wrote:
> 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

> ______________________________________________
> 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.


-- 
Csardi Gabor <csardi at rmki.kfki.hu>    UNIL DGM

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