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[Rcpp-devel] Rcpp Module Errors

4 messages · Andrew Redd, Dirk Eddelbuettel, Jonas Rauch

Andrew Redd
# 
I apologize if this has been covered.  I've looked and see a couple of post
relating to this issue, but I'm not sure if it was ever solved. The example
modules appear to not work, at least for me.  On a related note I can't get
my modules to run either, but If I can figure out how to run the examples I
think I can get mine running.

R> sessionInfo()
R version 2.13.0 (2011-04-13)
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=C              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] Rcpp_0.9.4

To install the package skeleton:
$ r -lRcpp -e"Rcpp.package.skeleton(\"test\",module=T)"
Attaching package: 'utils'

The following object(s) are masked from 'package:Rcpp':

    .DollarNames, prompt

Creating directories ...
Creating DESCRIPTION ...
Creating NAMESPACE ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './test/Read-and-delete-me'.

Adding Rcpp settings
 >> added RcppModules: yada
 >> added Depends: Rcpp
 >> added LinkingTo: Rcpp
 >> added useDynLib directive to NAMESPACE
 >> added Makevars file with Rcpp settings
 >> added Makevars.win file with Rcpp settings
 >> added example header file using Rcpp classes
 >> added example src file using Rcpp classes
 >> added example R file calling the C++ example
 >> added Rd file for rcpp_hello_world
 >> copied the example module

build
$ R CMD build test
<<output omitted>>

and check with an error.
$R CMD check test_1.0.tar.gz
<<output omitted>>
* checking whether the name space can be loaded with stated dependencies ...
WARNING
Error: .onLoad failed in loadNamespace() for 'test', details:
  call: value[[3L]](cond)
  error: failed to load module yada from package test
Execution halted

<<output omitted>>

According to Dirk's June 15th post on the issue I include require("methods",
character=TRUE, quietly=TRUE) in the .onLoad function, now checks ok but
when trying things out I get a segmentation fault.
$ R -q --vanilla
R> library(test)
Loading required package: Rcpp
R> Module('yada','test')$bla()

 *** caught segfault ***
address 0x90, cause 'memory not mapped'

Traceback:
 1: .Call(symbol)
 2: Module(module, mustStart = TRUE)
 3: .getModulePointer(x)
 4: Module("yada", "test")$bla

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

So questions are:
    1) is anyone else getting this error?
    2) does anyone know how to fix it?

Thanks,
Andrew
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Dirk Eddelbuettel
#
On 21 June 2011 at 16:51, Andrew Redd wrote:
| I?apologize?if this has been covered. ?I've looked and see a couple of post
| relating to this issue, but I'm not sure if it was ever solved. The example
| modules appear to not work, at least for me. ?On a related note I can't get my
| modules to run either, but If I can figure out how to run the examples I think
| I can get mine running.
| 
| R> sessionInfo()
| R version 2.13.0 (2011-04-13)
| 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=C ? ? ? ? ? ? ?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] Rcpp_0.9.4
| 
| To install the package skeleton:
| $ r -lRcpp -e"Rcpp.package.skeleton(\"test\",module=T)"
| Attaching package: 'utils'
| 
| The following object(s) are masked from 'package:Rcpp':
| 
| ? ? .DollarNames, prompt
| 
| Creating directories ...
| Creating DESCRIPTION ...
| Creating NAMESPACE ...
| Creating Read-and-delete-me ...
| Saving functions and data ...
| Making help files ...
| Done.
| Further steps are described in './test/Read-and-delete-me'.
| 
| Adding Rcpp settings
| ?>> added RcppModules: yada
| ?>> added Depends: Rcpp
| ?>> added LinkingTo: Rcpp
| ?>> added useDynLib directive to NAMESPACE
| ?>> added Makevars file with Rcpp settings
| ?>> added Makevars.win file with Rcpp settings
| ?>> added example header file using Rcpp classes
| ?>> added example src file using Rcpp classes
| ?>> added example R file calling the C++ example
| ?>> added Rd file for rcpp_hello_world
| ?>> copied the example module?
| 
| build
| $ R CMD build test
| <<output omitted>>
| 
| and check with an error.
| $R CMD check test_1.0.tar.gz
| <<output omitted>>
| * checking whether the name space can be loaded with stated dependencies ...
| WARNING
| Error: .onLoad failed in loadNamespace() for 'test', details:
| ? call: value[[3L]](cond)
| ? error: failed to load module yada from package test
| Execution halted
| 
| <<output omitted>>
| 
| According to Dirk's June 15th post on the issue I include?require("methods",
| character=TRUE, quietly=TRUE) in the .onLoad function, now checks ok but when
| trying things out I get a segmentation fault.
| $ R -q --vanilla
| R> library(test)
| Loading required package: Rcpp
| R> Module('yada','test')$bla()
| 
| ?*** caught segfault ***
| address 0x90, cause 'memory not mapped'
| 
| Traceback:
| ?1: .Call(symbol)
| ?2: Module(module, mustStart = TRUE)
| ?3: .getModulePointer(x)
| ?4: Module("yada", "test")$bla
| 
| Possible actions:
| 1: abort (with core dump, if enabled)
| 2: normal R exit
| 3: exit R without saving workspace
| 4: exit R saving workspace
| Selection:?
| 
| So questions are:
| ? ? 1) is anyone else getting this error?
| ? ? 2) does anyone know how to fix it?

I just checked my very own (and small) RcppBDT which uses Rcpp modules; it
still builds. As do the regression tests.

If your code fails, you may need to compare against the docs in the
Rcpp-modules vignette, its code and the Rcpp modules unittest:

The unit test still works here ( and ~/bin/runit.sh is a trivial shell and
littler script wrapper included below ):

edd at max:~/svn/rcpp/pkg/Rcpp/inst/unitTests$ ~/bin/runit.sh -p RUnit,Rcpp runit.Module.client.package.R 


Executing test function test.Module.package  ... * checking for file ?testRcppModule/DESCRIPTION? ... OK
* preparing ?testRcppModule?:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ?testRcppModule_0.1.tar.gz?

* installing *source* package ?testRcppModule? ...
** libs
ccache g++-4.5 -I/usr/share/R/include   -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O3 -Wall -pipe -pedantic -Wno-variadic-macros  -c Num.cpp -o Num.o
ccache g++-4.5 -I/usr/share/R/include   -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O3 -Wall -pipe -pedantic -Wno-variadic-macros  -c rcpp_hello_world.cpp -o rcpp_hello_world.o
ccache g++-4.5 -I/usr/share/R/include   -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O3 -Wall -pipe -pedantic -Wno-variadic-macros  -c rcpp_module.cpp -o rcpp_module.o
ccache g++-4.5 -I/usr/share/R/include   -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O3 -Wall -pipe -pedantic -Wno-variadic-macros  -c stdVector.cpp -o stdVector.o
g++ -shared -o testRcppModule.so Num.o rcpp_hello_world.o rcpp_module.o stdVector.o -L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/lib64/R/lib -lR
installing to /tmp/RtmpGXLL47/file53c4b34a/templib/testRcppModule/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (testRcppModule)
Loading required package: testRcppModule
 done successfully.

edd at max:~/svn/rcpp/pkg/Rcpp/inst/unitTests$ 

That is with a recent SVN version, but it should be the same for Rcpp 0.9.4
as released.

(For argument's sake here is ~/bin/runit.sh:

edd at max:~/svn/rcpp/pkg/Rcpp/inst/unitTests$ cat ~/bin/runit.sh 
#!/bin/sh

set -u 
set -e

progname=`basename $0`
options='p:h?'
 
usage_and_exit()
{
    echo "Usage: $progname [-p package[,package2,..]] [-?|-h]"
    echo "  Run unit test script for R package"
    echo "Options:"
    echo "  -p package[,package2,..]]  load additional package(s)"
    echo "  -h                         show this help"
    exit 0
}

while getopts "$options" i 
do 
    case "$i" in
        p)
            pkg=",$OPTARG"
            shift 
            shift
            ;;
        h|?)
            usage_and_exit
            ;;
    esac
done

if [ ! -f $1 ]; then
    echo "Error: No file '$1' found"
    exit 1
fi

file=`pwd`/$1

r -i -t -lRUnit${pkg} -e"cppfunction <- function(...) cxxfunction(..., plugin=\"Rcpp\"); runTestFile(\"$file\")"
edd at max:~/svn/rcpp/pkg/Rcpp/inst/unitTests$ 

Hth, Dirk

| 
| Thanks,
| Andrew
| 
| 
| ----------------------------------------------------------------------
| _______________________________________________
| 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
Jonas Rauch
# 
I had the same problem before I realized that when a Module is loaded as
part of a package (instead of manually loading the shared lib) you don't
need the whole
just try
The exposed classes and functions are automatically made available in the
namespace of the package
Loading required package: Rcpp
test::bar               test::bla2              test::rcpp_hello_world
test::bla               test::foo               test::World
test::bla1              test::hello

Regards,
Jonas
On Wed, Jun 22, 2011 at 12:51 AM, Andrew Redd <amredd at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        
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      Andrew Redd
    

    

      
      #
    

  


  

      
Jonas,
Thank you.  This exactly solved the problem.  I'm not sure if this
`Module('yada','test')$bla()` causing a segmentation fault or not is a bug
or user error.  I'll leave that for Dirk and Romain to figure out.  For now
I'll chalk it up to a user error.  Thanks for figuring this out.

-Andrew

        
On Tue, Jun 21, 2011 at 10:37 PM, Jonas Rauch <jonas.rauch at googlemail.com>wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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