[Rcpp-devel] problems while upgrading to Rcpp 0.11.2

sessionInfo()

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

| >
|