[Rd] gcc ubsan alignement test --minimal gcc version?
Dear All, I'm trying to implement the section of the manual pertaining to the gcc-ubsan test carried by CRAN on my local computer (ubuntu 14.04): http://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-UBSAN/README.txt I was wondering whether someone could tell what the minimal version of the gcc tool chain needed to run the gcc-ASAN and gcc-UBSAN alignment tests on ones local computer is. CRAN seems to use gcc 5.2.0 to do these tests, but the current version of gcc shipped with ubuntu is 4.9.2 (to be updated to 5.1.0 with the 15.10 release latter this month). I hope this is the correct list to post this. Thanks in advance, __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] gcc ubsan alignement test --minimal gcc version?
Dear Prof. Ripley, Thank you for your answer. I think I am way over my head here. (Using Doker adds a level of complexity that I'm afraid I can't manage for now so I am happy with building Rdevel and using it in to run these tests). After building Rdevel with what I think are the correct options** (just to avoid mistakes I have also fully removed R from my system just before and insured that the following packages are all updated) apt-get install bash-completion bison debhelper default-jdk g++ gcc gfortran groff-base libblas-dev libbz2-dev libcairo2-dev libcurl4-openssl-dev libjpeg-dev liblapack-dev liblzma-dev libncurses5-dev libpango1.0-dev libpcre3-dev libpng-dev libreadline-dev libtiff5-dev libx11-dev libxt-dev mpack subversion tcl8.5-dev texinfo texlive-base texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended tk8.5-dev valgrind x11proto-core-dev xauth xdg-utils xfonts-base xvfb zlib1g-dev cd /tmp svn co http://svn.r-project.org/R/trunk R-devel cd /tmp/R-devel R_PAPERSIZE=letter R_BATCHSAVE="--no-save --no-restore" PAGER=/usr/bin/pager PERL=/usr/bin/perl R_UNZIPCMD=/usr/bin/unzip R_ZIPCMD=/usr/bin/zip R_PRINTCMD=/usr/bin/lpr LIBnn=lib AWK=/usr/bin/awk CFLAGS="-pipe -std=gnu99 -Wall -pedantic -O2" CXXFLAGS="-pipe -Wall -pedantic -O2" CC="gcc -fsanitize=address,undefined" CXX="g++ -fsanitize=address,undefined" CXX1X="g++ -fsanitize=address,undefined" FC="gfortran -fsanitize=address,undefined" F77="gfortran -fsanitize=address,undefined" ./configure --enable-R-shlib --without-blas --without-lapack --with-readline --without-recommended-packages --program-suffix=dev --disable-openmp make make install make clean But I'm not sure how to proceed from there. I tried the obvious thing: Rdevel CMD build my_offending_package Rdevel CMD check --as-cran my_offending_package But I have not been able to replicate the bug I see on cran: /usr/local/gcc5/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/include/emmintrin.h:140:21: runtime error: load of misaligned address 0x6187fc84 for type 'const double', which requires 8 byte alignment 0x6187fc84: note: pointer points here 00 00 80 3f 00 00 80 3f 00 00 80 3f 00 00 80 3f 00 00 80 3f 00 00 80 3f 00 00 80 3f 00 00 80 3f **Though the original authors bear no responsibility for these scripts, I have found many of these commands on this file: https://github.com/rocker-org/r-devel-san/blob/master/Dockerfile On 2015-10-14 10:10, Prof Brian Ripley wrote: On 13/10/2015 14:46, kaveh wrote: Dear All, I'm trying to implement the section of the manual pertaining to the gcc-ubsan test carried by CRAN on my local computer (ubuntu 14.04): http://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-UBSAN/README.txt I was wondering whether someone could tell what the minimal version of the gcc tool chain needed to run the gcc-ASAN and gcc-UBSAN alignment tests on ones local computer is. CRAN seems to use gcc 5.2.0 to do these tests, but the current version of gcc shipped with ubuntu is 4.9.2 (to be updated to 5.1.0 with the 15.10 release latter this month). I hope this is the correct list to post this. The correct thing to do is to read the manual (either the R manual or your gcc manual). The R manual says 'AddressSanitizer (‘ASan’) is a tool with similar aims to the memory checker in valgrind. It is available with suitable builds of gcc 4.8.0 or clang 3.1 and later on common Linux and OS X platforms.' '‘UBSanitizer’ is a tool for C/C++ source code selected by -fsanitize=undefined in suitable builds of clang, and GCC as from 4.9.0.' Note that including these capabilities and their runtimes is optional at least for clang (until recently Apple omitted them), so you need to check your own system's documentation. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Why is my R package still compiling with the O2 flag?
When I install an R package with cpp codes such as rrcov via CRAN (under R 3.1.1, using no Makevars file and under Ubuntu 14.04 using GCC 4.8), the cpp code is compiled with the -o3 flag (in fact, looking at the Makeconf file this seem to again be the default since R 3.1.1) But when I install my own package via CRAN it is compiled with the -o2 flag. My questions are what is causing my package's cpp code to be compiled in -o2 and how to fix this? Here is the content of the src/Makeconf file of my package (it is fairly standard I believe for a package using RcppEigen): PKG_CXXFLAGS = -I../inst/include -DEIGEN_DONT_PARALLELIZE $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CXXFLAGS) CXX_STD = CXX11 and that of rrcov (which I m using for illustration's sake): PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Why is my R package still compiling with the O2 flag?
Dear Prof Ripley, Thanks for the pointer to CXX1XFLAGS: it helped me solve the problem. As usual, thanks for your prompt and helpful answer, Best regards, On 2014-09-26 11:30, Prof Brian Ripley wrote: You have not given us the 'at a minimum' information required by the posting guide, and it is -O2 etc (not O2 and not -o2). Also, cpp is the C pre-processor: if you mean C++, say so. The default compiler flags are set by whoever compiled R: it is entirely possibly they were set differently for C++98 and C++11 (which looks relevant). It seems you need to read 'R Installation and Admnistration' which has a comprehensive description of these flags. On 26/09/2014 10:00, kaveh wrote: When I install an R package with cpp codes such as rrcov via CRAN (under R 3.1.1, using no Makevars file and under Ubuntu 14.04 using GCC 4.8), the cpp code is compiled with the -o3 flag (in fact, looking at the Makeconf file this seem to again be the default since R 3.1.1) But when I install my own package via CRAN it is compiled with the -o2 flag. My questions are what is causing my package's cpp code to be compiled in -o2 and how to fix this? Here is the content of the src/Makeconf file of my package (it is fairly standard I believe for a package using RcppEigen): PKG_CXXFLAGS = -I../inst/include -DEIGEN_DONT_PARALLELIZE $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CXXFLAGS) CXX_STD = CXX11 and that of rrcov (which I m using for illustration's sake): PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] DIY Rtools?
Dear List, I'm currently working on an R package that works great when compiled with GCC 4.8 under linux but which doesn't seem to work so well when compiled by the win builder (http://win-builder.r-project.org/). After asking around a bit, the primary culprit could be the older version of GCC used in Rtools. Now, for academic purposes, I would like to have a zip version of this package (not to distribute through CRAN mind you, but to submit alongside the associated paper). My questions are as follows: -Am I correct to think that Rtool uses GCC 4.6.3? -If so, is there a way to build windows runable R package using a more recent version of GCC? Thanks in advance for sharing your views on this, Bests regards, __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] DIY Rtools?
Thank you very much for all these infos! Best regards, On 2014-10-30 22:54, Duncan Murdoch wrote: On 30/10/2014, 2:45 PM, kaveh wrote: Dear List, I'm currently working on an R package that works great when compiled with GCC 4.8 under linux but which doesn't seem to work so well when compiled by the win builder (http://win-builder.r-project.org/). After asking around a bit, the primary culprit could be the older version of GCC used in Rtools. Now, for academic purposes, I would like to have a zip version of this package (not to distribute through CRAN mind you, but to submit alongside the associated paper). My questions are as follows: -Am I correct to think that Rtool uses GCC 4.6.3? Yes. -If so, is there a way to build windows runable R package using a more recent version of GCC? Yes, you need to install one (I've been told they are available from the MinGW-64 project) on your path, then just use it. If it needs different options from the ones that 4.6.3 needed, it will be slightly more work: you'll need to edit the Makefile, or Makevars, or MkRules.* files in src/gnuwin32 to put those options in place. Unlike other platforms, the Windows builds have no "configuration" step, that's all done by hand (usually by Brian Ripley, thanks!). If you change to a different compiler, you may need to change some of that. Our plans are to switch to a newer compiler before the release of R 3.2.0 in the spring, but I won't promise when new Rtools will be available. Duncan Murdoch Thanks in advance for sharing your views on this, Bests regards, __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Linking to the BH package introduces CRAN warnings
Dear all, I'm working on a project that links to the BH package (http://cran.r-project.org/web/packages/BH/index.html). My packages doesn't call entry points which might terminate R nor write to stdout/stderr instead of to the console. However, it seems some of the codes in the BH package might. At any rate, when I include some boost headers such as boost/math/distributions/ through BH, I get the following warnings when submitting to the win-builder page: Found '_ZSt4cerr', possibly from 'std::cerr' (C++) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found '_ZSt4cerr', possibly from 'std::cerr' (C++) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Furthermore, these warnings disappear when remove the boost headers and replace the call to boost functions by constants. Looking at the CRAN-check diagnostics of some other packages that link to BH, I do not see similar warnings, so I suppose it is possible to fix this issue. Looking at their source code, it is not clear to me how these authors have managed to do this, but this might be because I'm not that familiar with boost to begin with. Can someone point me to some solution to this problem? Thanks in advance, __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Linking to the BH package introduces CRAN warnings
Dear Romain, /You’re kind of out of luck. These functions are both: - used by the boost headers - forbidden by R, well at least forbidden by CRAN / // Thanks for conforming my earlier fears. Since I only use this header and would like my package to eventually be on CRAN, I was thinking of bypassing BH and just putting these headers in the /inst directory and modifying them to remove the offending calls. I was wondering what your view on this is. Or perhaps there is a simpler alternative? Thanks in advance, On 2014-11-04 21:46, Romain François wrote: >> Le 4 nov. 2014 à 15:42, Dirk Eddelbuettel a écrit : >> >> >> On 4 November 2014 at 14:37, kaveh wrote: >> | Dear all, >> | >> | I'm working on a project that links to the BH package >> | (http://cran.r-project.org/web/packages/BH/index.html). >> | >> | My packages doesn't call entry points which might terminate R nor >> | write to stdout/stderr instead of to the console. >> | >> | However, it seems some of the codes in the BH package >> | might. At any rate, when I include some boost headers such as >> | boost/math/distributions/ through BH, I get the following warnings >> | when submitting to the win-builder page: >> | >> | >> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++) >> | >> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) >> | >> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++) >> | >> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) > You’re kind of out of luck. These functions are both: > - used by the boost headers > - forbidden by R, well at least forbidden by CRAN > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Linking to the BH package introduces CRAN warnings
Dear Romain, Thanks for all these info, I will ponder this versus using some of the alternatives in the R sources Best regards, On 2014-11-04 22:01, Romain François wrote: > >> Le 4 nov. 2014 à 21:52, kaveh > <mailto:vakili.kaveh.em...@gmail.com>> a écrit : >> >> >> Dear Romain, >> >> >> >> /You’re kind of out of luck. These functions are both: >> - used by the boost headers >> - forbidden by R, well at least forbidden by CRAN >> / >> >> // >> >> Thanks for conforming my earlier fears. Since I only use >> this header and would like my package to eventually be >> on CRAN, I was thinking of bypassing BH and just putting >> these headers in the /inst directory and modifying them >> to remove the offending calls. I was wondering what your >> view on this is. Or perhaps there is a simpler alternative? >> >> Thanks in advance, > > If you go through the hoops of modifying these headers to fulfill R’s > requirements, I’m sure it would be of interest to others if you > contribute these back to BH. > > The danger obviously is that this gets out of sync with boost, which > would create work for merging your changes to new boost files from the > future. > > Some parts of boost (e.g. uBlas) have macros to control whether or not > std::cerr is used at all. > https://github.com/eddelbuettel/bh/blob/cb1427c27dc068c8328fd1d2f4b1b8a8da1957c2/inst/include/boost/numeric/ublas/exception.hpp#L215 > > But I don’t think this is of any relevance to the files you want to use. > > Romain > >> On 2014-11-04 21:46, Romain François wrote: >>>> Le 4 nov. 2014 à 15:42, Dirk Eddelbuettel a écrit : >>>> >>>> >>>> On 4 November 2014 at 14:37, kaveh wrote: >>>> | Dear all, >>>> | >>>> | I'm working on a project that links to the BH package >>>> | (http://cran.r-project.org/web/packages/BH/index.html). >>>> | >>>> | My packages doesn't call entry points which might terminate R nor >>>> | write to stdout/stderr instead of to the console. >>>> | >>>> | However, it seems some of the codes in the BH package >>>> | might. At any rate, when I include some boost headers such as >>>> | boost/math/distributions/ through BH, I get the following warnings >>>> | when submitting to the win-builder page: >>>> | >>>> | >>>> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++) >>>> | >>>> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) >>>> | >>>> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++) >>>> | >>>> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) >>> You’re kind of out of luck. These functions are both: >>> - used by the boost headers >>> - forbidden by R, well at least forbidden by CRAN >>> >> > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Linking to the BH package introduces CRAN warnings
Dear Hadley, Thank you for this information, maybe the CRAN gods will look favourably on this case too, Best regards, On 2014-11-04 23:32, Hadley Wickham wrote: | However, it seems some of the codes in the BH package | might. At any rate, when I include some boost headers such as | boost/math/distributions/ through BH, I get the following warnings | when submitting to the win-builder page: | | |Found '_ZSt4cerr', possibly from 'std::cerr' (C++) | |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) | |Found '_ZSt4cerr', possibly from 'std::cerr' (C++) | |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) You’re kind of out of luck. These functions are both: - used by the boost headers - forbidden by R, well at least forbidden by CRAN Mybe - I had this note in RSQLite, and CRAN seemed ok with my explanation: * checking compiled code ... NOTE File ‘/Users/hadley/Documents/databases/RSQLite.Rcheck/RSQLite/libs/RSQLite.so’: Found ‘___stderrp’, possibly from ‘stderr’ (C) Object: ‘sqlite-all.o’ This is in C code from the embedded SQLite database. Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Linking to the BH package introduces CRAN warnings
Sire, The header that is included is boost/math/distributions/ If I remove it and replace the calls to its members by plain constants, the warning disappear (I just tried this again on http://win-builder.r-project.org/). This leads me to the suspicion that the header is causing the error message. I will post a simpler source code, tomorrow on this list. Best regards, On 2014-11-04 23:52, Dirk Eddelbuettel wrote: Gentlemen, On 4 November 2014 at 23:36, kaveh wrote: | Dear Hadley, | | Thank you for this information, maybe the CRAN gods | will look favourably on this case too, You seemed to have missed a point my earlier email tried to stress: Inclusion of BH does not lead to the warning. All this depends on WHICH headers are included, and the OP will need to sort this out by modifying his code. Dirk | Best regards, | | On 2014-11-04 23:32, Hadley Wickham wrote: | >>> | However, it seems some of the codes in the BH package | >>> | might. At any rate, when I include some boost headers such as | >>> | boost/math/distributions/ through BH, I get the following warnings | >>> | when submitting to the win-builder page: | >>> | | >>> | | >>> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++) | >>> | | >>> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) | >>> | | >>> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++) | >>> | | >>> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) | >> You’re kind of out of luck. These functions are both: | >> - used by the boost headers | >> - forbidden by R, well at least forbidden by CRAN | > Mybe - I had this note in RSQLite, and CRAN seemed ok with my explanation: | > | > * checking compiled code ... NOTE | >File ‘/Users/hadley/Documents/databases/RSQLite.Rcheck/RSQLite/libs/RSQLite.so’: | > Found ‘___stderrp’, possibly from ‘stderr’ (C) | >Object: ‘sqlite-all.o’ | > | >This is in C code from the embedded SQLite database. | > | > | > Hadley | > | __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Linking to the BH package introduces CRAN warnings
Dear all,
the simple code in below, when send to the
win-builder returns the following (and no other)
warning:
* checking compiled code ... WARNING
File 'quicky/libs/i386/quicky.dll':
Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
Object: 'quicky.o'
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Object: 'quicky.o'
File 'quicky/libs/x64/quicky.dll':
Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
Object: 'quicky.o'
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Object: 'quicky.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the C RNG.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
Here is the source:
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
using namespace std;
using namespace Eigen;
using Eigen::MatrixXd;
using Eigen::VectorXd;
using Eigen::VectorXi;
using Eigen::RowVectorXd;
using boost::math::chi_squared;
using boost::math::quantile;
using boost::math::complement;
using boost::math::normal_distribution;
using namespace boost::math::policies;
typedef policy<
promote_double
> my_policy_norm;
typedef policy<
promote_double
> my_policy_chi2;
typedef boost::math::normal_distribution my_norm;
typedef boost::math::chi_squared_distribution
my_chi2;
VectorXd GetQs(const VectorXd& x){
const int n=x.size();
double mytol=1e-8;
double the_max=x.maxCoeff();
double the_min=x.minCoeff();
double the_rag=(the_max-the_min);
if(the_ragfor(int i=0;iy(i)=sqrt(quantile(complement(my_chi2(1.0),x(i;
return(y);
}
extern "C"{
void quicky(int* rn,double* xi,double* yi){
const int n=*rn;
VectorXd x=Map(xi,n);
Map(yi,n)=GetQs(x);
}
}
So I guess, I should fill a bug report with the
BH maintainer?
Best regards,
On 2014-11-04 23:52, Dirk Eddelbuettel wrote:
Gentlemen,
On 4 November 2014 at 23:36, kaveh wrote:
| Dear Hadley,
|
| Thank you for this information, maybe the CRAN gods
| will look favourably on this case too,
You seemed to have missed a point my earlier email tried to stress: Inclusion
of BH does not lead to the warning.
All this depends on WHICH headers are included, and the OP will need to sort
this out by modifying his code.
Dirk
| Best regards,
|
| On 2014-11-04 23:32, Hadley Wickham wrote:
| >>> | However, it seems some of the codes in the BH package
| >>> | might. At any rate, when I include some boost headers such as
| >>> | boost/math/distributions/ through BH, I get the following warnings
| >>> | when submitting to the win-builder page:
| >>> |
| >>> |
| >>> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
| >>> |
| >>> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| >>> |
| >>> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
| >>> |
| >>> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| >> You’re kind of out of luck. These functions are both:
| >> - used by the boost headers
| >> - forbidden by R, well at least forbidden by CRAN
| > Mybe - I had this note in RSQLite, and CRAN seemed ok with my
explanation:
| >
| > * checking compiled code ... NOTE
| >File
‘/Users/hadley/Documents/databases/RSQLite.Rcheck/RSQLite/libs/RSQLite.so’:
| > Found ‘___stderrp’, possibly from ‘stderr’ (C)
| >Object: ‘sqlite-all.o’
| >
| >This is in C code from the embedded SQLite database.
| >
| >
| > Hadley
| >
|
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Linking to the BH package introduces CRAN warnings
Dear,
I was expecting this reaction.
Please do not get caught up in the details of the examples,
which I have tried to make as simple as possible for your
benefit.
The main point is that if you remove the lines associated
with
boost/math/distributions/
the warning disappears as well. Ergo,
boost/math/distributions/
is causing the warnings.
Best regards,
On 2014-11-05 13:43, Dirk Eddelbuettel wrote:
On 5 November 2014 at 00:55, kaveh wrote:
| Dear all,
|
|
| the simple code in below, when send to the
| win-builder returns the following (and no other)
| warning:
|
|
| * checking compiled code ... WARNING
| File 'quicky/libs/i386/quicky.dll':
|Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
| Object: 'quicky.o'
|Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| Object: 'quicky.o'
| File 'quicky/libs/x64/quicky.dll':
|Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
| Object: 'quicky.o'
|Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| Object: 'quicky.o'
|
| Compiled code should not call entry points which might terminate R nor
| write to stdout/stderr instead of to the console, nor the C RNG.
|
| See 'Writing portable packages' in the 'Writing R Extensions' manual.
|
|
| Here is the source:
|
| #include
| #include
| #include
| #include
| #include
| #include
| #include
| #include
| #include
| #include
| #include
| #include
| #include
|
| #include
| #include
|
| #include
|
| using namespace std;
| using namespace Eigen;
| using Eigen::MatrixXd;
| using Eigen::VectorXd;
| using Eigen::VectorXi;
| using Eigen::RowVectorXd;
|
|
| using boost::math::chi_squared;
| using boost::math::quantile;
| using boost::math::complement;
| using boost::math::normal_distribution;
| using namespace boost::math::policies;
|
| typedef policy<
|promote_double
|> my_policy_norm;
| typedef policy<
|promote_double
|> my_policy_chi2;
|
| typedef boost::math::normal_distribution my_norm;
| typedef boost::math::chi_squared_distribution
| my_chi2;
|
|
| VectorXd GetQs(const VectorXd& x){
| const int n=x.size();
| double mytol=1e-8;
| double the_max=x.maxCoeff();
| double the_min=x.minCoeff();
| double the_rag=(the_max-the_min);
| if(the_rag(xi,n);
| Map(yi,n)=GetQs(x);
| }
| }
|
|
| So I guess, I should fill a bug report with the
| BH maintainer?
Err, why? BH does nothing wrong.
You are NOT forced or required to use the Boost distributions header __as R
comes with the equivalent functionality__ via the Rmath.h header file from R.
Which has functionality that Rcpp provides to you in scalar and vector form.
And there are probably several dozen examples of using the R distribution
functions from Rcpp.
So this is _precisely_ what I suggested several mails ago: do your homework,
identify which header is causing it. And the obvious next step is then to
not use the header.
Dirk
| Best regards,
|
|
| On 2014-11-04 23:52, Dirk Eddelbuettel wrote:
| > Gentlemen,
| >
| > On 4 November 2014 at 23:36, kaveh wrote:
| > | Dear Hadley,
| > |
| > | Thank you for this information, maybe the CRAN gods
| > | will look favourably on this case too,
| >
| > You seemed to have missed a point my earlier email tried to stress:
Inclusion
| > of BH does not lead to the warning.
| >
| > All this depends on WHICH headers are included, and the OP will need to sort
| > this out by modifying his code.
| >
| > Dirk
| >
| > | Best regards,
| > |
| > | On 2014-11-04 23:32, Hadley Wickham wrote:
| > | >>> | However, it seems some of the codes in the BH package
| > | >>> | might. At any rate, when I include some boost headers such as
| > | >>> | boost/math/distributions/ through BH, I get the following warnings
| > | >>> | when submitting to the win-builder page:
| > | >>> |
| > | >>> |
| > | >>> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
| > | >>> |
| > | >>> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| > | >>> |
| > | >>> |Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
| > | >>> |
| > | >>> |Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
| > | >> You’re kind of out of luck. These functions are both:
| > | >> - used by the boost headers
| > | >> - forbidden by R, well at least forbidden by CRAN
| > | > Mybe - I had this note in RSQLite, and CRAN seemed ok with my
explanation:
| > | >
| > | > * checking compiled code ... NOTE
| > | >File
‘/Users/hadley/Documents/databases/RSQLite.Rcheck/RSQLite/libs/RSQLite.so’:
| > | > Found ‘___stderrp’, possibly from ‘stderr’ (C)
| > | >Object: ‘sqlite-all.o’
| > | >
| > | >This is in C code from the embedded SQLite database.
| > | >
| > | >
| > | > Hadley
| > | >
| > |
| >
|
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
