
Hi dirk,

Thanks for the reply. I am using R version 2.9.2 (2009-08-24). I used to 
run it on a 32bit machine and everything worked fine. It's only after I 
switched to 64bit that I had this problem. Maybe it's something about 
64bit vs 32bit? So it'd be great if you could check if it works on a 
64bit machine.

Thanks again,
Mircea

Dirk Eddelbuettel said the following on 2009-10-04 10:29:
> On 4 October 2009 at 09:54, Mircea Trandafir wrote:
> | 
> | Hi everybody,
> | 
> | 
> | 
> | I'm using R on a 64-bit Ubuntu 9.04 (Jaunty). I prefer to install R
> | packages from source, even if they are available in Synaptic. The
> | problem is that I can't install/compile kernlab. Everything works fine
> | until it gets to the lazy loading part:
> | 
> | 
> | 
> | ** preparing package for lazy loading
> | 
> | Creating a new generic function for "terms" in "kernlab"
> | 
> | Creating a new generic function for "fitted" in "kernlab"
> | 
> | Creating a new generic function for "coef" in "kernlab"
> | 
> | Error in conformMethod(signature, mnames, fnames, f, fdef, definition)
> | : 
> | 
> |   In method for function "size": formal arguments omitted in the method
> | definition cannot be in the signature (obj = "specc")
> | 
> | Error : unable to load R code in package 'kernlab'
> | 
> | ERROR : lazy loading failed for the package �kernlab�
> | 
> | 
> | 
> | 
> | Does anybody have any idea what might cause this? And, more
> | importantly, how I can move forward?
>
> Works fine here (and 'install.r' is from the 'littler' package and I just
> create a symlink for it so that I can quickly install packages from the
> command-line):
>
>
> edd@ron:~$ install.r kernlab
> trying URL 'http://cran.us.r-project.org/src/contrib/kernlab_0.9-8.tar.gz'
> Content type 'application/x-gzip' length 1262166 bytes (1.2 Mb)           
> opened URL                                                                
> ==================================================                        
> downloaded 1.2 Mb                                                         
>
> * Installing *source* package ‘kernlab’ ...
> ** libs                                    
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c brweight.cpp -o brweight.o
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c ctable.cpp -o ctable.o    
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c cweight.cpp -o cweight.o  
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dbreakpt.c -o dbreakpt.o
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dcauchy.c -o dcauchy.o  
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dgpnrm.c -o dgpnrm.o    
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dgpstep.c -o dgpstep.o  
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dprecond.c -o dprecond.o
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dprsrch.c -o dprsrch.o  
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dspcg.c -o dspcg.o      
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dtron.c -o dtron.o      
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dtrpcg.c -o dtrpcg.o    
> dtrpcg.c: In function ‘dtrpcg’:                                                                 
> dtrpcg.c:157: warning: value computed is not used                                               
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c dtrqsol.c -o dtrqsol.o  
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c esa.cpp -o esa.o                   
> In file included from wmsufsort.h:46,                                                           
>                  from esa.cpp:68:                                                               
> msufsort.h: In member function ‘void MSufSort::ShowProgress()’:                                 
> msufsort.h:907: warning: unused variable ‘p’                                                    
> esa.cpp: In constructor ‘ESA::ESA(const UInt32&, SYMBOL*, int)’:                                
> esa.cpp:114: warning: comparison between signed and unsigned integer expressions                
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c expdecayweight.cpp -o expdecayweight.o
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c inductionsort.cpp -o inductionsort.o  
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c kspectrumweight.cpp -o kspectrumweight.o
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c lcp.cpp -o lcp.o                        
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c misc.c -o misc.o             
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c msufsort.cpp -o msufsort.o              
> In file included from msufsort.cpp:28:                                                               
> msufsort.h: In member function ‘void MSufSort::ShowProgress()’:                                      
> msufsort.h:907: warning: unused variable ‘p’                                                         
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c solvebqp.c -o solvebqp.o     
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c stringk.c -o stringk.o       
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c stringkernel.cpp -o stringkernel.o      
> stringkernel.cpp: In function ‘SEXPREC* stringtv(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
> stringkernel.cpp:506: warning: comparison between signed and unsigned integer expressions                               
> stringkernel.cpp:513: warning: comparison between signed and unsigned integer expressions                               
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c svm.cpp -o svm.o                                           
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c wkasailcp.cpp -o wkasailcp.o                               
> g++ -I/usr/share/R/include      -fpic  -g -O3 -Wall -pipe -c wmsufsort.cpp -o wmsufsort.o                               
> In file included from wmsufsort.h:46,                                                                                   
>                  from wmsufsort.cpp:48:                                                                                 
> msufsort.h: In member function ‘void MSufSort::ShowProgress()’:                                                         
> msufsort.h:907: warning: unused variable ‘p’                                                                            
> g++ -shared -o kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -lblas -lgfortran -lm -llapack -L/usr/lib/R/lib -lR
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Creating a new generic function for "terms" in "kernlab"   
> Creating a new generic function for "fitted" in "kernlab"  
> Creating a new generic function for "coef" in "kernlab"    
> Creating a new generic function for "predict" in "kernlab" 
> Creating a new generic function for "plot" in "kernlab"    
> ** help                                                    
> *** installing help indices                                
> >>> Building/Updating help pages for package 'kernlab'    
>      Formats: text html latex example                      
>   as.kernelMatrix                   text    html    latex   example
>   couple                            text    html    latex   example
>   csi-class                         text    html    latex   example
>   csi                               text    html    latex   example
>   dots                              text    html    latex   example
>   gausspr-class                     text    html    latex   example
>   gausspr                           text    html    latex   example
>   inchol-class                      text    html    latex   example
>   inchol                            text    html    latex   example
>   income                            text    html    latex
>   inlearn                           text    html    latex   example
>   ipop-class                        text    html    latex   example
>   ipop                              text    html    latex   example
>   kcca-class                        text    html    latex   example
>   kcca                              text    html    latex   example
>   kernel-class                      text    html    latex   example
>   kernelMatrix                      text    html    latex   example
>   kfa-class                         text    html    latex   example
>   kfa                               text    html    latex   example
>   kha-class                         text    html    latex   example
>   kha                               text    html    latex   example
>   kkmeans                           text    html    latex   example
>   kmmd-class                        text    html    latex   example
>   kmmd                              text    html    latex   example
>   kpca-class                        text    html    latex   example
>   kpca                              text    html    latex   example
>   kqr-class                         text    html    latex   example
>   kqr                               text    html    latex   example
>   ksvm-class                        text    html    latex   example
>   ksvm                              text    html    latex   example
>   lssvm-class                       text    html    latex   example
>   lssvm                             text    html    latex   example
>   musk                              text    html    latex   example
>   onlearn-class                     text    html    latex   example
>   onlearn                           text    html    latex   example
>   plot                              text    html    latex   example
>   prc-class                         text    html    latex
>   predict.gausspr                   text    html    latex   example
>   predict.kqr                       text    html    latex   example
>   predict.ksvm                      text    html    latex   example
>   promotergene                      text    html    latex   example
>   ranking-class                     text    html    latex   example
>   ranking                           text    html    latex   example
>   reuters                           text    html    latex
>   rvm-class                         text    html    latex   example
>   rvm                               text    html    latex   example
>   sigest                            text    html    latex   example
>   spam                              text    html    latex
>   specc-class                       text    html    latex   example
>   specc                             text    html    latex   example
>   spirals                           text    html    latex   example
>   stringdot                         text    html    latex   example
>   ticdata                           text    html    latex
>   vm-class                          text    html    latex
> ** building package indices ...
> * DONE (kernlab)
>
> The downloaded packages are in
>         ‘/tmp/downloaded_packages’
> edd@ron:~$
>
> That's on i386 but if you insist I could try on one of the amd64 machines at
> work.  
>
> What version of R are you running?
>
> Dirk
>
>
> | Thanks,
> | 
> | Mircea
> | 
> | 
> | 
> |  		 	   		  
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