(sorry -- finger slipped and submitted early) > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit)
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RInside_0.2.11 Rcpp_0.11.2 Can you provide an example of a segfault occurring independently of RInside? Kevin On Wed, Sep 3, 2014 at 12:49 PM, Kevin Ushey <kevinus...@gmail.com> wrote: > Hi Pratibha, > > I highly doubt that the segfault is related to the optimization level. > FWIW, I still cannot replicate the segfault as you described -- Ubuntu > 14.04, gcc 4.8.2, and... > > Kevin > > > On Wed, Sep 3, 2014 at 12:34 PM, Pratibha Rana <pr...@vertica.com> wrote: > >> I think I got to the bottom of the issue. I was using the -O0 option >> instead of the -O2 option while compiling the code. Including the -O2 >> option resolved the issue. >> >> Thanks >> Pratibha >> >> On 09/02/2014 04:49 PM, Dirk Eddelbuettel wrote: >> > Hi, >> > >> > On 2 September 2014 at 20:16, Pratibha Rana wrote: >> > | Hi Dirk, >> > | >> > | Yes I work for Vertica which is apparent from my email. But I do not >> > | work on the distributedR project. I work on the vertica-R integration. >> > >> > You could tell us about that too ... >> > >> > | I acknowledge that it is a local issue because the same code works >> fine >> > | in the RInside's example directory on the same machine with the same >> > | libraries that I installed from sources. I verified the dll's being >> > | loaded in both the cases. The back trace doesn't help either. I am out >> > | of ideas as to what can be wrong. I am stumped as to why Rcpp::List >> > | works fine but Rcpp::DataFrame causes a segfault. Any suggestion on >> > | debugging the cause are greatly appreciated. >> > >> > So you may be doing something different in the build process for your >> local >> > directory. You need to work out what is different. >> > >> > Can you please post this __on the list__ for a continued thread there? >> > >> > Dirk >> > >> > | >> > | Thanks >> > | Pratibha >> > | > Dear Pratibha, >> > | > >> > | > On 2 September 2014 at 19:22, Pratibha Rana wrote: >> > | > | I have a custom application that uses Rcpp and Rinside to execute >> R code. All >> > | > >> > | > [ Random thought: I might make people a bit more sympathetic for >> your cause >> > | > and questions if you pointed out that a) you are selling a db >> solution, b) >> > | > that these days Vertica is part of HP and c) the code for the R >> integration >> > | > is apparently on GitHub: https://github.com/vertica/DistributedR >> (or at least >> > | > that is where I think it may be). Why you guys never announced >> that here >> > | > is a bit of a mystery to me. ] >> > | > >> > | > | was well until I was using R-3.0.0, Rcpp 0.10.2 and RInside >> 0.2.10 but now its >> > | > | time to upgrade to the latest version and I can't get even the >> Rinside samples >> > | > | to work in place of my application. My machine has Ubuntu14.04. >> The code >> > | > >> > | > Well, consider that >> > | > >> > | > a) I (and others) develop on Ubuntu 14.04. Things work on Ubuntu >> 14.04 >> > | > >> > | > b) CRAN tests all packages on several backends, including Ubuntu, >> Debian, >> > | > FC, OS X and Windows and would tell me (as maintainer) in no >> uncertain >> > | > terms if it didn't work. >> > | > >> > | > c) So if it fails to work for you, maybe assume a local issue >> first? >> > | > >> > | > | compiles fine but when I run it, I get a segfault during Rinside >> > | > | initialization. I tried to troubleshoot by replacing my code by >> one of the >> > | > | examples rinside_sample0. The example runs fine as is but if I >> add just a >> > | > | single line "Rcpp::DataFrame p; " it segfaults again. Here is the >> complete >> > | > | code. The same code works fine inside the Rinside examples >> directory. >> > | > | >> > | > | >> > | > | #include <RInside.h> >> > | > | >> > | > | int main(int argc, char *argv[]) >> > | > | { >> > | > | >> > | > | std::getchar(); >> > | > >> > | > That line makes little sense. I omitted it. >> > | > >> > | > | >> > | > | RInside R(argc, argv); >> > | > | >> > | > | R["txt"] = "Hello, world!\n"; >> > | > | Rcpp::DataFrame pf; <-------- Runs fine if I comment >> out this line. >> > | > | R.parseEvalQ("cat(txt)"); >> > | > | >> > | > | exit(0); >> > | > | } >> > | > >> > | > Works fine here: >> > | > >> > | > edd@max:~/git/rinside/inst/examples/standard$ cat >> rinside_vertica.cpp >> > | > >> > | > #include <RInside.h> >> > | > >> > | > int main(int argc, char *argv[]) >> > | > { >> > | > >> > | > RInside R(argc, argv); >> > | > >> > | > R["txt"] = "Hello, world!\n"; >> > | > Rcpp::DataFrame pf; // <-------- Runs fine if I >> comment out this line. >> > | > R.parseEvalQ("cat(txt)"); >> > | > >> > | > exit(0); >> > | > } >> > | > edd@max:~/git/rinside/inst/examples/standard$ make rinside_vertica >> > | > ccache g++-4.8 -I/usr/share/R/include >> -I/usr/local/lib/R/site-library/Rcpp/include >> -I/usr/local/lib/R/site-library/RInside/include -g -O2 -fstack-protector >> --param=ssp-buffer-size=4 -Wformat -Werror=format-security >> -D_FORTIFY_SOURCE=2 -g -O3 -Wall -pipe -Wno-unused -pedantic -Wall >> rinside_vertica.cpp -Wl,--export-dynamic -fopenmp -L/usr/lib/R/lib -lR >> -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -lblas -llapack >> -L/usr/local/lib/R/site-library/RInside/lib -lRInside >> -Wl,-rpath,/usr/local/lib/R/site-library/RInside/lib -o rinside_vertica >> > | > edd@max:~/git/rinside/inst/examples/standard$ ./rinside_vertica >> > | > Hello, world! >> > | > edd@max:~/git/rinside/inst/examples/standard$ >> > | > >> > | > >> > | > I maybe running github versions of Rcpp and/or RInside, but the >> only thing >> > | > that may matter is that you probably should >> > | > >> > | > a) install Rcpp from source >> > | > b) install RInside from source >> > | > >> > | > and then build these examples. >> > | > >> > | > A reproducible issue may help. This was not reproducible. Or >> rather, this >> > | > may not even have been a bug. >> > | > >> > | > Regards, Dirk >> > | > >> > | > >> > | > | Here is the backtrace of the segfault >> > | > | >> > | > | >> > | > | Program received signal SIGSEGV, Segmentation fault. >> > | > | 0x00007ffff7597767 in reset_current_error() () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | (gdb) bt -10 >> > | > | #261636 0x00007ffff7597769 in reset_current_error() () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261637 0x00007ffff7597769 in reset_current_error() () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261638 0x00007ffff7597769 in reset_current_error() () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261639 0x00007ffff7597769 in reset_current_error() () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261640 0x00007ffff7598530 in Rcpp::Rcpp_eval(SEXPREC*, SEXPREC*) >> () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261641 0x00007ffff7599542 in >> Rcpp::Language_Impl<Rcpp::PreserveStorage>::eval() const () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261642 0x00007ffff75969c7 in RInside::autoloads() () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261643 0x00007ffff7595fd3 in RInside::initialize(int, char >> const* const*, bool, bool, bool) () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261644 0x00007ffff7595a4a in RInside::RInside(int, char const* >> const*, bool, bool, bool) () from >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | #261645 0x000000000040361e in main (argc=1, argv=0x7fffffffdc88) >> at rinside_sample0.cpp:14 >> > | > | (gdb) >> > | > | >> > | > | >> > | > | >> > | > | >> > | > | I also looked at the libraries that were being loaded at runtime >> and they are >> > | > | exactly the same for both the rinside examples and my app. Pasted >> below for >> > | > | completeness. I am out ofdebugging tricks to get this to work. >> Any ideas as to >> > | > | what's wrong. what am I missing? >> > | > | >> > | > | >> > | > | >> prana:trunk/third-party/install/lib/R/library/RInside/examples/standard $ >> cat /proc/21915/maps | awk '{print $6}' | grep '\.so' | sort | uniq >> > | > | /home/prana/trunk/third-party/install/lib/R/lib/libRblas.so >> > | > | /home/prana/trunk/third-party/install/lib/R/lib/libRlapack.so >> > | > | /home/prana/trunk/third-party/install/lib/R/lib/libR.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/graphics/libs/graphics.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/grDevices/libs/grDevices.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/methods/libs/methods.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/Rcpp/libs/Rcpp.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/stats/libs/stats.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/utils/libs/utils.so >> > | > | /lib/x86_64-linux-gnu/ld-2.19.so >> > | > | /lib/x86_64-linux-gnu/libc-2.19.so >> > | > | /lib/x86_64-linux-gnu/libdl-2.19.so >> > | > | /lib/x86_64-linux-gnu/libgcc_s.so.1 >> > | > | /lib/x86_64-linux-gnu/libm-2.19.so >> > | > | /lib/x86_64-linux-gnu/libnsl-2.19.so >> > | > | /lib/x86_64-linux-gnu/libnss_compat-2.19.so >> > | > | /lib/x86_64-linux-gnu/libnss_files-2.19.so >> > | > | /lib/x86_64-linux-gnu/libnss_nis-2.19.so >> > | > | /lib/x86_64-linux-gnu/libpthread-2.19.so >> > | > | /lib/x86_64-linux-gnu/librt-2.19.so >> > | > | /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 >> > | > | /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >> > | > | /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 >> > | > | /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 >> > | > | >> > | > | >> > | > | prana:trunk/myapp $ cat /proc/21730/maps | awk '{print $6}' | >> grep '\.so' | sort | uniq >> > | > | /home/prana/trunk/third-party/install/lib/R/lib/libRblas.so >> > | > | /home/prana/trunk/third-party/install/lib/R/lib/libRlapack.so >> > | > | /home/prana/trunk/third-party/install/lib/R/lib/libR.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/graphics/libs/graphics.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/grDevices/libs/grDevices.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/methods/libs/methods.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/Rcpp/libs/Rcpp.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/RInside/lib/libRInside.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/stats/libs/stats.so >> > | > | >> /home/prana/trunk/third-party/install/lib/R/library/utils/libs/utils.so >> > | > | /lib/x86_64-linux-gnu/ld-2.19.so >> > | > | /lib/x86_64-linux-gnu/libc-2.19.so >> > | > | /lib/x86_64-linux-gnu/libdl-2.19.so >> > | > | /lib/x86_64-linux-gnu/libgcc_s.so.1 >> > | > | /lib/x86_64-linux-gnu/libm-2.19.so >> > | > | /lib/x86_64-linux-gnu/libnsl-2.19.so >> > | > | /lib/x86_64-linux-gnu/libnss_compat-2.19.so >> > | > | /lib/x86_64-linux-gnu/libnss_files-2.19.so >> > | > | /lib/x86_64-linux-gnu/libnss_nis-2.19.so >> > | > | /lib/x86_64-linux-gnu/libpthread-2.19.so >> > | > | /lib/x86_64-linux-gnu/librt-2.19.so >> > | > | /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0 >> > | > | /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >> > | > | /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 >> > | > | /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 >> > | > | >> > | > | >> > | > | >> > | > | >> > | > | Thanks >> > | > | Pratibha >> > | > | _______________________________________________ >> > | > | Rcpp-devel mailing list >> > | > | Rcpp-devel@lists.r-forge.r-project.org >> > | > | >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >> > | > >> > | >> > >> >> _______________________________________________ >> Rcpp-devel mailing list >> Rcpp-devel@lists.r-forge.r-project.org >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >> > >
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