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 subselect -- 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
Hi, I am the maintainer for the Rigroup package. Based on the e-mail below, I found and fixed a warning (spurious right brace) in the manual for my package under the new parser. It has been a number of years since I last revised the package and I am not sure where and how to upload it. I looked on the "developer" page but did not see anything that said where to upload revised packages. Sorry for the inconvenience but could someone please direct me to where I find the instructions for uploading revised packages. Thank you. Kevin On 7-Feb-09, at 2:22 AM, 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 subselect > > > -- > 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-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
Prof Brian Ripley schrieb:> 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 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 -- Thomas Petzoldt Technische Universitaet Dresden Institut fuer Hydrobiologie thomas.petzoldt at tu-dresden.de 01062 Dresden http://tu-dresden.de/hydrobiologie/ GERMANY
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/