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? Thanks, Mircea [[alternative HTML version deleted]]
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]]
|
|
| ----------------------------------------------------------------------
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
Three out of two people have difficulties with fractions.
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): > > > edd@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@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]]
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): > |> > |> > |> edd@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@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]]