[Rcpp-devel] Rcpp module errors with Rcpp binary installation

[Ariful Azad]

Dear All,

This question might be a repeat of an earlier question, but I will be
grateful if you can suggest any alternate solution to my problem.

------------
My system: Mac OS X 10.9 (Mavericks)
Rcpp Version: 0.11.1
R Version: 3.0.3
----------------

I installed Rcpp from binary using the install.package() function.
When I try to install a test package created by
Rcpp.package.skeleton('testModule', module=T)
I obtain the following error:

*** installing help indices
** building package indices
** testing if installed package can be loaded
sh: line 1:  7195 Abort trap: 6
'/Library/Frameworks/R.framework/Resources/bin/R' --no-save --slave 2>&1 <
'/var/folders/pn/d49rpkj95v5_9g5q5bsz0k400000gn/T//RtmpwW5RU4/file1bff7d88ce2'
Warning: class "C++Object" is defined (with package slot ‘Rcpp’) but no
metadata object found to revise subclass information---not exported?
Making a copy in package ‘testModule’
R(7195,0x7fff77cc8310) malloc: *** error for object 0x7fff77dd5330: pointer
being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
ERROR: loading failed


However, the error is gone when I install Rcpp from source. So far so good
for me.
However, I have distributed my package through Bioconducor.org. Bioconducor
is unable to build the package in Mac OS X 10.9 (Mavericks) (similarly
other users of my package). They report the following error :

flowMatch.cpp:74:2: error: reference to 'function' is ambiguous
        function( "computeMEC" , &computeMEC  , "Match clusters across
a pair of sample by mixed edge cover algorithm." ) ;

(the detail error can be found here

from http://www.bioconductor.org/checkResults/release/bioc-LATEST/flowMatch/morelia-buildsrc.html

)
I don't know what Rcpp version they are using. It looks like they are not
building Rcpp from source.  Is there any alternative suggestion to avoid
this situation? (It may to be possible to instruct every users of the
package to install Rcpp from source).
The error is apparently coming from function declaration inside RCPP_MODULE
function("hello" , &hello  , "documentation for hello ");
I disabled this line and the error is gone with Rcpp installed from Binary
for the package created using install.package().


Notes 1: I do not see this error with Rcpp 0.10.5 installed from source in
Mac OS X 10.9 (Mavericks)
Notes 2: I do not see this error with Rcpp 0.10.5 installed from binary in
Mac OS X Snow Leopard (10.6.8).
Notes3: Bioconductor (I don't know their Rcpp version) successfully built
my package on Linux (Ubuntu 12.04.4 LTS) / x86_64, Windows Server 2008
R2 Enterprise SP1 (64-bit) / x64
and Mac OS X Snow Leopard (10.6.8) / x86_64 .
But their system was not able to build my package on
Mac OS X Mavericks (10.9.2) / x86_64

The primary error they reported is

flowMatch.cpp:74:2: error: reference to 'function' is ambiguous
        function( "computeMEC" , &computeMEC  , "Match clusters across
a pair of sample by mixed edge cover algorithm." ) ;

If you are interested, the detail error can be found:
from http://www.bioconductor.org/checkResults/release/bioc-LATEST/flowMatch/morelia-buildsrc.html


Any suggestion to avoid this error in third party installation is much
appreciated.

Regards,

Ariful Azad
Post Doctoral Researcher
Lawrence Berkeley National Laboratory
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