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 ‘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’ 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 -- Three out of two people have difficulties with fractions.
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