[Rcpp-devel] Building a Package created with Rcpp/RcppArmadillo on the Mac

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Oct 18 20:39:20 CEST 2011


What is the output of sessionInfo()? In particular it will be helpful
to know what versions of Rcpp and RcppArmadillo you have installed on
the mac you are trying to compile on.

Also, do "simple" things work? Can you run a trivial `inline` example,
for instance?

-steve

On Tue, Oct 18, 2011 at 12:43 PM, terrance savitsky <tds151 at gmail.com> wrote:
> Dear Rcpp experts, I'm finding difficulty to build a package (created on
> Win) that uses Rcpp and RcppArmadillo on the Mac.  I've attempted the build
> on multiple machines to rule out local issues.   I find a June 27 post on
> the Rcpp list
> (http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2011-June/002548.html)
> that experiences very similar "dlopen" issues as I show below, though the
> cause is attributed to proper construction of C++ templates.  In my case, I
> do not create any templated classes; only use those in Rcpp and
> RcppArmadillo.  In this regard, please note the upstream syntax errors when
> attempting to include libRcpp.a.
> This post is a continuation of my previous, though I decided to change the
> title and re-post as I thought it would be more useful for future searches
> if composed this way.
>
>  Here are the error messages:
>
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/lib/x86_64/libRcpp.a:
> line 1: syntax error near unexpected token `newline'
>
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/lib/x86_64/libRcpp.a:
> line 1: `!<arch>'
>
> g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o
> growcurves.so DPre.o lgm.o mmC.o mmCchol.o mmCmiar.o mmCmvplusDP.o
> mmCplusDP.o mmI.o mmIgroup.o mmIgroupDP.o mmIplusDP.o mmmult.o
> -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRlapack
> -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRblas -lgfortran
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
>
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/lib/x86_64/libRcpp.a:
> line 1: syntax error near unexpected token `newline'
>
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/lib/x86_64/libRcpp.a:
> line 1: `!<arch>'
>
> installing to
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/growcurves/libs/x86_64
>
> ** R
>
> ** data
>
> ** inst
>
> ** preparing package for lazy loading
>
> ** help
>
> *** installing help indices
>
> ** building package indices ...
>
> ** testing if installed package can be loaded
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
>   unable to load shared object
> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/growcurves/libs/x86_64/growcurves.so':
>
>
> dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/growcurves/libs/x86_64/growcurves.so,
> 6): Symbol not found: __ZTIN4Rcpp12not_a_matrixE
>
>   Referenced from:
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/growcurves/libs/x86_64/growcurves.so
>
>   Expected in: flat namespace
>
>  in
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/growcurves/libs/x86_64/growcurves.so
>
> Error: loading failed
>
> Execution halted
>
> ERROR: loading failed
>
> * removing
> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/growcurves'
>
> --
> Thank you for your help and expertise, Terrance Savitsky
>
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>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact


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