[R-sig-Debian] error installing/compiling kernlab
Dirk Eddelbuettel
edd at debian.org
Mon Oct 5 15:39:30 CEST 2009
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):
| >
| >
| > edd at 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 at 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]]
| > |
| > |
| > | ----------------------------------------------------------------------
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| >
| >
|
|
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