[Rcpp-devel] Rcpp Module Errors

[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
| 
| 
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