Hi Azad,
Your first issue is something separate, probably due to clashing
compiler toolchains between compiled versions of R / packages. If you
want to dive into that further you'll need to give us some more
information about your compiler setup.
The second issue, with flowMatch, I believe this is because there is a
clash between Rcpp::function (used for modules) and clang's
std::function. You're probably running into this because you have
'using namespace std;' (which is bad practice btw -- please use
typedefs for items in std:: you need, or qualify with std::
explicitly).
You might be able to work around it by qualifying with Rcpp::function
explicitly.
Cheers,
Kevin
On Thu, May 1, 2014 at 3:55 PM, Ariful Azad <azad...@gmail.com> wrote:
> 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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> Rcpp-devel mailing list
> Rcpp-devel@lists.r-forge.r-project.org
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