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

[baptiste auguie]

On 20 August 2010 22:33, Douglas Bates <bates at stat.wisc.edu> wrote:
> On Fri, Aug 20, 2010 at 12:35 PM, baptiste auguie
> <baptiste.auguie at googlemail.com> wrote:
>> Hi,
>>
>> On 20 August 2010 19:09, Romain Francois <romain at r-enthusiasts.com> wrote:
>>> Le 20/08/10 16:07, Dirk Eddelbuettel a écrit :
>>>>
>>>> On 20 August 2010 at 09:41, baptiste auguie wrote:
>>>> | 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
>>>>
>>>> This works for me on Ubuntu 10.4 / amd64 once I drop the Depends: on
>>>> the package constants which is not on CRAN:
>>>>
>>>> edd at max:/tmp/cda$ R CMD INSTALL .
>>>> * installing to library ‘/usr/local/lib/R/site-library’
>>>> * installing *source* package ‘cda’ ...
>>>> ** libs
>>>> g++ -I/usr/share/R/include
>>>> -I"/usr/local/lib/R/site-library/Rcpp/include"
>>>> -I"/usr/local/lib/R/site-library/RcppArmadillo/include"   -fpic  -O3 -g0
>>>> -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’
>>>> g++ -shared -o cda.so cda.o -L/usr/local/lib/R/site-library/Rcpp/lib
>>>> -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -llapack -lblas
>>>> -lgfortran -lm -L/usr/lib64/R/lib -lR
>>>> installing to /usr/local/lib/R/site-library/cda/libs
>>>> ** R
>>>> ** inst
>>>> ** preparing package for lazy loading
>>>> Loading required package: reshape
>>>> Loading required package: plyr
>>>> Loading required package: grid
>>>> Loading required package: proto
>>>> ** help
>>>> *** installing help indices
>>>> ** building package indices ...
>>>> ** testing if installed package can be loaded
>>>>
>>>> * DONE (cda)
>>>> edd at max:/tmp/cda$ r -lcda -e'cat("Hello cda world\n")'
>>>> Hello cda world
>>>> edd at max:/tmp/cda$
>>>>
>>>> FWIW on Debian and Ubuntu R uses external lapack and blas libraries.
>>>>
>>>> Dirk
>>>
>>> That is also why it works on OSX, because here we are using the vecLib
>>> framework for blas and lapack.
>>>
>>
>> Thank you all for investigating the matter.
>>
>>>
>>> So you are left with a few options :
>>> - don't call inv on your complex matrix
>>
>> i do need this, I feel it would be a waste to convert the matrix back
>> to R format, invert it with R facilities, and then convert it back for
>> Armadillo...
>
> On many occasions where people think that they need to calculate a
> matrix inverse they don't really need to do so.  For example you don't
> need to calculate the inverse explicitly if all you are going to do is
> to solve a linear system of equations.


True, on many occasions. In this particular case, I have to solve many
times (typically more than 400 times) the system Ax = b, with
different right-hand side b. I haven't checked objectively, but my
guess was that calculating the inverse once was to be more efficient
than solving the 400 linear systems. It may depend on the size of the
matrix, etc.

Best,

baptiste

>
>>> - negociate with R-core that they include missing lapack bits
>>
>> I wouldn't even know what's missing and where.
>>
>>> - write a package that supplies these bits
>>
>> Same here.
>>>
>>> I'm afraid there is nothing we can really do.
>>
>> That's OK, thankfully it works on the only platform(s) I use. A shame
>> that I can't easily share this work with others though.
>>
>> Thanks,
>>
>> baptiste
>>>
>>> Romain
>>>
>>> --
>>> 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
>> ____________________
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>>
>



-- 
____________________

Dr. Baptiste Auguié

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

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