[R-sig-Debian] error installing/compiling kernlab
Dirk Eddelbuettel
edd at debian.org
Sun Oct 4 16:29:15 CEST 2009
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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