[Rcpp-devel] problems while upgrading to Rcpp 0.11.2

Kevin Ushey kevinushey at gmail.com
Wed Sep 3 21:49:00 CEST 2014 

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 <prana at 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 at 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 at 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 at max:~/git/rinside/inst/examples/standard$ ./rinside_vertica
> > | > Hello, world!
> > | > edd at 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 at 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 at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20140903/d04ebc5b/attachment-0001.html>

More information about the Rcpp-devel mailing list