Re: [Rd] New package test results available

From: Thomas Petzoldt <>
Date: Wed, 11 Feb 2009 07:50:35 +0100

Thomas Petzoldt wrote:

> Prof Brian Ripley schrieb:

>> We've added a column at
>> of test results using the Sun Studio compiler: it is intended that
>> these will be updated weekly.
>> The Sun Studio compiler is that used on Solaris: these runs were on
>> the Linux version. All the other platforms are using gcc 4, so this
>> provides an opportunity for checking for use of gcc-specific features
>> and also standards conformance (the Sun compilers have a long-time
>> reputation for close conformance to the language standards).
>> There are known problems where packages use C++ or JNI interfaces
>> (e.g. rgdal and EBImage) as the libraries and JVM were compiled under
>> gcc's conventions (even though a Sun JVMi is used). About half the
>> packages using rJava segfault, which seems to a JNI issue.
>> Some packages use gcc-specific compiler flags:
>> LogConcDEAD Matching amap geometry memisc taskPR
>> but the vast majority of the errors reported are C++ errors. One
>> class that may not be immediately obvious is the use of C headers in
>> C++: you are supposed to write e.g.
>> #includd <cmath>
>> NOT
>> #include <math.h>
>> Symptoms of this can be seen for packages
>> BayesTree EMCC MCMCfglmm MarkedPointProcess Matching Matrix
>> RQuantlib RandomFields Rcpp SoPhy compHclust dpmix igraph minet
>> mixer modeest monomvm multic pcaPP rgenoud robfilter segclust
>> simecol subselect
> The reason can also be including <R.h> (as done in simecol) that 
> includes <math.h>
> Do I understand it correctly that this means that including <R.h> is 
> wrong in C++?
> I read "Writing R extensions" several times, but was not aware that this 
> was a mistake. If I replace <R.h> by <cmath> then it works on my 
> systems, but I want to be certain that there are no other side effects.
> Thanks in advance for clarification!
> Thomas Petzoldt

I changed it as requested, and include

#include <cmath>
#include <Rinternals.h>

... but still get the same error:

"simecol.cpp", line 224: Error: Overloading ambiguity between "floor(double)" and "std::floor(float)". 1 Error(s) detected.

What's wrong here? My code is very short and extremely simple, without any new objects (yet), but fact only "plain C with some C++" extension.

What I'm making wrong? Would it be necessary that we all have a Linux installation with Sun Studio at hand?

Thanks a lot

Thomas P.

Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie
01062 Dresden            

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