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): > > > e...@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 âkernlabâ ... > ** 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 âdtrpcgâ: > > 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 âvoid MSufSort::ShowProgress()â: > > msufsort.h:907: warning: unused variable âpâ > > esa.cpp: In constructor âESA::ESA(const UInt32&, SYMBOL*, int)â: > > 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 âvoid MSufSort::ShowProgress()â: > > msufsort.h:907: warning: unused variable âpâ > > 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 âSEXPREC* stringtv(SEXPREC*, SEXPREC*, > SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)â: > 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 âvoid MSufSort::ShowProgress()â: > > msufsort.h:907: warning: unused variable âpâ > > 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 > â/tmp/downloaded_packagesâ > e...@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 > | > | > | > | > | [[alternative 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