[Rcpp-devel] r-forge error: undefined symbol: zgetri_

[baptiste auguie]

Indeed, I had forgotten to rerun roxygen before my last commit, sorry.
It should be OK now.

I've also put the source tarball from R CMD BUILD here,

http://dl.dropbox.com/u/352834/cda_1.0.tar.gz

Best regards,

baptiste

On 20 August 2010 08:42, Romain Francois <romain at r-enthusiasts.com> wrote:
> Le 20/08/10 07:36, baptiste auguie a écrit :
>>
>> Hi,
>>
>> My Makevars contains the following line,
>>
>> ## Use the R_HOME indirection to support installations of multiple R
>> version
>> PKG_LIBS = $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" )
>> $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
>
> That looks ok.
>
> I can't R CMD INSTALL your package now because of something else. Some
> collate issue of the R files, is this a roxygen issue by any chance ?
>
> But the compile step -- apart from some minor problems I'm sure you'll fix
> -- seem fine :
>
> $ R CMD INSTALL cda
> * installing to library ‘/Library/Frameworks/R.framework/Resources/library’
> * installing *source* package ‘cda’ ...
> ** libs
> *** arch - i386
> g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386
> -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -I"/Library/Frameworks/R.framework/Resources/library/RcppArmadillo/include"
>   -fPIC  -g -O3 -Wall -pipe -c cda.cpp -o cda.o
> cda.cpp: In function ‘int progress_bar(double, double)’:
> cda.cpp:36: warning: no return statement in function returning non-void
> cda.cpp: In function ‘Rcpp::List linearExtinction(const arma::mat&, const
> arma::cx_mat&, double)’:
> cda.cpp:285: warning: unused variable ‘pi’
> cda.cpp: In function ‘int progress_bar(double, double)’:
> cda.cpp:36: warning: control reaches end of non-void function
> g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o
> cda.so cda.o
> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/lib/i386/libRcpp.a
> -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack
> -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -lgfortran
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installation dans
> /Library/Frameworks/R.framework/Resources/library/cda/libs/i386
> *** arch - x86_64
> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/x86_64
> -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> -I"/Library/Frameworks/R.framework/Resources/library/RcppArmadillo/include"
>   -fPIC  -g -O3 -Wall -pipe -c cda.cpp -o cda.o
> cda.cpp: In function ‘int progress_bar(double, double)’:
> cda.cpp:36: warning: no return statement in function returning non-void
> cda.cpp: In function ‘Rcpp::List linearExtinction(const arma::mat&, const
> arma::cx_mat&, double)’:
> cda.cpp:285: warning: unused variable ‘pi’
> cda.cpp: In function ‘int progress_bar(double, double)’:
> cda.cpp:36: warning: control reaches end of non-void function
> g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o
> cda.so cda.o
> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/lib/x86_64/libRcpp.a
> -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
> installation dans
> /Library/Frameworks/R.framework/Resources/library/cda/libs/x86_64
> ** R
> Error in .install_package_code_files(".", instdir) :
> les fichiers dans '/Users/romain/svn/photonics/pkg/cda/R' sont manquants
> dans le champ 'Collate' :
>  povray.r
> ERROR: unable to collate files for package ‘cda’
> * removing ‘/Library/Frameworks/R.framework/Resources/library/cda’
> * restoring previous ‘/Library/Frameworks/R.framework/Resources/library/cda’
>
>
>> which I obviously took from somewhere, perhaps automatically generated
>> from package.skeleton, I don't remember.
>
> Probably from RcppArmadillo.package.skeleton
>
>> It's worked for me on two
>> different machines (both Macs, though).
>>
>> Best regards,
>>
>> baptiste
>>
>>
>> On 19 August 2010 23:50, Douglas Bates<bates at stat.wisc.edu>  wrote:
>>>
>>> On Thu, Aug 19, 2010 at 3:06 PM, baptiste auguie
>>> <baptiste.auguie at googlemail.com>  wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I'm stumped by this error for my cda package on r-forge:
>>>>
>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>  unable to load shared library '/tmp/Rinst2710053821/cda/libs/cda.so':
>>>>  /tmp/Rinst2710053821/cda/libs/cda.so: undefined symbol: zgetri_
>>>>
>>>>
>>>> https://r-forge.r-project.org/R/?group_id=160&log=build_src&pkg=cda&flavor=patched
>>>>
>>>>
>>>> I don't have a clue what this means --- is this an incorrect
>>>> dependency, an error in my C++ code, a known problem with r-forge,
>>>> something I should have read in a vignette / manual ... ? It compiles
>>>> fine on my machine (Mac OS 10.6). The package uses RcppArmadillo.
>>>
>>> The error means that there is a reference to one of the Lapack
>>> functions, zgetri, which forms the inverse of a complex matrix using
>>> its triangular factorization, and the symbol could not be found.  What
>>> does your cda/src/Makevars file contain?
>
> --
> Romain Francois
> Professional R Enthusiast
> +33(0) 6 28 91 30 30
> http://romainfrancois.blog.free.fr
> |- http://bit.ly/bzoWrs : Rcpp svn revision 2000
> |- http://bit.ly/b8VNE2 : Rcpp at LondonR, oct 5th
> `- http://bit.ly/aAyra4 : highlight 0.2-2
>
>



-- 
____________________

Dr. Baptiste Auguié

Departamento de Química Física,
Universidade de Vigo,
Campus Universitario, 36310, Vigo, Spain

tel: +34 9868 18617
http://webs.uvigo.es/coloides
____________________