You are absolutely right. Could not figure out which package was causing problems, so I just deleted the local R lib folder and reinstalled the libraries, starting with kernlab. It all installed without a problem. Strange, though... I only had pmg installed (with its dependencies) and I was trying to install Synth and its dependencies - kernlab was the last package to be installed and the only one to give errors.
Thanks for the help, it all works out now - though I guess it would be good to figure out which package caused the problems and why. Best, Mircea Dirk Eddelbuettel said the following on 2009-10-05 09:39: > On 4 October 2009 at 10:43, Mircea Trandafir wrote: > | 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. > > It works just the same on amd64 on my Ubuntu 9.04. I suspect that you may > have either a) an problem with one of the packages loaded by kernlab or > b) an RData file that is loaded that gets in the way and provides a size() > method that triggers the error > > In method for function "size": formal arguments omitted in the method > definition cannot be in the signature (obj = "specc") > > you reported. > > In short, the error is not reproducible on either amd64 or i386 with current > R installations, and I double kernlab or R are at fault. > > Hope this helps, Dirk > > > | > | 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 HTML version deleted]] > |> | > |> | > |> | ---------------------------------------------------------------------- > |> | _______________________________________________ > |> | R-SIG-Debian mailing list > |> | R-SIG-Debian@r-project.org > |> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian > |> > |> > | > | > [[alternative HTML version deleted]]
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