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 -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org _______________________________________________ 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
