Le 20/08/10 10:46, Romain Francois a écrit :
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.
Hmm. I get the same error now on fedora.
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/usr/local/lib/R/library/cda/libs/cda.so':
/usr/local/lib/R/library/cda/libs/cda.so: undefined symbol: zgetri_
ERROR: loading failed
* removing ‘/usr/local/lib/R/library/cda’
Is it possible that this is not included in R's lapack ?
$ cd R-devel/src
$ egrep -R [a-z]getri *
include/R_ext/.svn/text-base/Lapack.h.svn-base:F77_NAME(dgetri)(const
int* n, double* a, const int* lda,
include/R_ext/Lapack.h:F77_NAME(dgetri)(const int* n, double* a, const
int* lda,
Romain
On 20 August 2010 08:42, Romain Francois<rom...@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<ba...@stat.wisc.edu> wrote:
On Thu, Aug 19, 2010 at 3:06 PM, baptiste auguie
<baptiste.aug...@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
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