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

[Romain Francois]

Le 20/08/10 09:41, baptiste auguie a écrit :
> 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

Ok. It installs and loads fine for me on OSX too. I'll try later on 
fedora to see what happens.

Romain

> 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
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http://romainfrancois.blog.free.fr
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