From elff at sowi.uni-mannheim.de  Tue Feb 10 10:49:46 2009
From: elff at sowi.uni-mannheim.de (Martin Elff)
Date: Tue, 10 Feb 2009 10:49:46 +0100
Subject: [Rd] New package test results available
In-Reply-To: <alpine.LFD.2.00.0902070651160.18308@gannet.stats.ox.ac.uk>
References: <alpine.LFD.2.00.0902070651160.18308@gannet.stats.ox.ac.uk>
Message-ID: <200902101049.46516.elff@sowi.uni-mannheim.de>

Dear Professor Ripley,

as you pointed out, package 'memisc' caused a compilation error with
the Sun Studio compiler because of gcc-specific compilation flags. The obvious 
reason was that the 'src' directory had a 'Makevars' file 
containing "PKGC_FLAGS="-Wall -pedantic". 

In the new revision of my package uploaded this weekend, the Makevars
file is removed, but nevertheless according to the protocol of the
automatic package checking with Sun Studio (of 2009-02-10 05:53:33), a 
compilation error occurs because of the gcc-specific compilation 
options "-Wall -pedantic". I checked the CRAN-version of the package for any 
instances of Makefiles or Makevar files, but none is present. Also I grepped 
my sources for any instance of "-Wall", with negative results. So I wonder 
what I should do to avoid Sun Studio errors caused by these options.

Any hint is appreciated.
Thanks, 

Martin Elff


On Saturday 07 February 2009 (08:22:49), Prof Brian Ripley wrote:
> We've added a column at
>
> http://cran.r-project.org/web/checks/check_summary.html
>
> 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 subselec

-------------------------------------------------
Dr. Martin Elff
Lecturer
LSPWIVS (Prof. van Deth)
Department of Social Sciences
University of Mannheim
A5, 6, A 328
68131 Mannheim
Germany

Phone: +49-621-181-2093
Fax: +49-621-181-2099
E-Mail: elff at sowi.uni-mannheim.de
Web: http://webrum.uni-mannheim.de/sowi/elff/
     http://www.sowi.uni-mannheim.de/lspwivs/



[Rd] New package test results available
Martin Elff