Rubén Gómez Antolí
2011-Dec-05 21:07 UTC
[R-sig-Debian] Illegal operation with lm on Debian Sid, PowerPC architecture
Hello all:
(First of all, sorry for my very bad english)
I came from R-help-es with this problem, they say me this is a better
place to find a solution, I hope that.
I try to use lm function, then R exploit. After I cleaned my code
without success I try the basic: open R (try on console and Rkward) and
run lm examples, this is the output:
---------- console cut -------------------
R version 2.14.0 (2011-10-31)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: powerpc-unknown-linux-gnu (32-bit)
R es un software libre y viene sin GARANTIA ALGUNA.
Usted puede redistribuirlo bajo ciertas circunstancias.
Escriba 'license()' o 'licence()' para detalles de distribucion.
R es un proyecto colaborativo con muchos contribuyentes.
Escriba 'contributors()' para obtener m?s informaci?n y
'citation()' para saber c?mo citar R o paquetes de R en publicaciones.
Escriba 'demo()' para demostraciones, 'help()' para el sistema
on-line
de ayuda,
o 'help.start()' para abrir el sistema de ayuda HTML con su navegador.
Escriba 'q()' para salir de R.
> example(lm)
lm> require(graphics)
lm> ## Annette Dobson (1990) "An Introduction to Generalized Linear
Models".
lm> ## Page 9: Plant Weight Data.
lm> ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
lm> trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
lm> group <- gl(2,10,20, labels=c("Ctl","Trt"))
lm> weight <- c(ctl, trt)
lm> lm.D9 <- lm(weight ~ group)
*** caught illegal operation ***
address 0xf759c60, cause 'illegal opcode'
Traceback:
1: lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...)
2: lm(weight ~ group)
3: eval.with.vis(expr, envir, enclos)
4: eval.with.vis(ei, envir)
5: source(tf, local, echo = echo, prompt.echo = paste(prompt.prefix,
getOption("prompt"), sep = ""), continue.echo =
paste(prompt.prefix,
getOption("continue"), sep = ""), verbose = verbose,
max.deparse.length = Inf, encoding = "UTF-8", skip.echo = skips,
keep.source = TRUE)
6: example(lm)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
aborting ...
Instrucci?n ilegal
----------------- end of console cut ---------------------------
The address is ever the same in all of test, I think is a important point.
Session info:
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: powerpc-unknown-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
My machine is a PowerBook G4 and I'm in Debian Sid, last upgrade run
now, yesterday was the n-1 upgrade.
Related R packages on my system:
$ dpkg -l |grep r- |grep GNU |awk '{print $2 $3}'
r-base-core2.14.0-1
r-base-html2.14.0-1
r-cran-boot1.3-3-1
r-cran-car2.0-11-1
r-cran-chron2.3-42-1
r-cran-class7.3-3-1
r-cran-cluster1.14.1-1
r-cran-codetools0.2-8-1
r-cran-date1.2.31-1
r-cran-fbasics2110.79-1
r-cran-foreign0.8.47-1
r-cran-gdata2.8.2-1
r-cran-getopt1.17-1
r-cran-gtools2.6.2-1
r-cran-kernsmooth2.23-7-1
r-cran-lattice0.20-0-1
r-cran-mass7.3-16-1
r-cran-matrix1.0-2-1
r-cran-mgcv1.7-11-1
r-cran-nlme3.1.102-1
r-cran-nnet7.3-1-2
r-cran-plotrix3.2-6-1
r-cran-quadprog1.5-4-1
r-cran-rcpp0.9.7-1
r-cran-rpart3.1.50-1
r-cran-spatial7.3-3-1
r-cran-survival2.36-10-1
r-cran-timedate2131.00-1
r-cran-timeseries2130.92-1
r-cran-tseries0.10-27-1
r-cran-xtable1:1.5-6-1
r-cran-zoo1.7-6-1
r-doc-html2.14.0-1
r-recommended2.14.0-1
And from sources, installed with "R CMD Install package" (root user):
akima_0.5-4.tar.gz
cacheSweave_0.6.tar.gz
climatol_2.0.tar.gz
digest_0.4.2.tar.gz
filehash_2.1-1.tar.gz
formatR_0.2-1.tar.gz
highlight_0.2-5.tar.gz
iterators_1.0.4.tar.gz
itertools_0.1-1.tar.gz
leaps_2.9.tar.gz
locfit_1.5-6.tar.gz
optparse_0.9.1.tar.gz
parser_0.0-13.tar.gz
pastecs_1.3-11.tar.gz
pgfSweave_1.2.1.tar.gz
plyr_1.5.2.tar.gz
reshape_0.8.4.tar.gz
reshape2_1.1.tar.gz
stashR_0.3-3.tar.gz
stringr_0.4.tar.gz
tikzDevice_0.6.2.tar.gz
TSA_0.98.tar.gz
TSAgg_0.2-1.tar.gz
Anyone can reproduce this fail? Is a bug? Can I do some more test? Try
with a debugger?
Thanks in advance.
Best regards.
Salud y Revoluci?n.
Lobo.
--
Libertad es poder elegir en cualquier momento. Ahora yo elijo GNU/Linux,
para no atar mis manos con las cadenas del soft propietario.
---------
Desde El Ejido, en Almer?a, usuario registrado Linux #294013
http://www.counter.li.org
Rubén Gómez Antolí
2011-Dec-05 21:46 UTC
[R-sig-Debian] Illegal operation with lm on Debian Sid, PowerPC architecture [solved]
Ok. Forget that message. I can solve it. I remember that last february I fall in troubles with lm function too. Search on my old e-mail, I found a thread with Debian maintainer of r-base-core. He say me that remove a package: ------------------ | Here are the installed packages on my system: | | libblas-dev 1.2-8 | libblas3gf 1.2-8 | liblash2 0.5.4.0-2+b1 | liblastfm0 0.4.0~git20090710-1 | libatlas3gf-base 3.8.3-28 Try removing libatlas3gf-base and see if that helps. -------------------------- El 05/12/11 22:07, Rub?n G?mez Antol? escribi?:> [...]> ---------- console cut ------------------- > R version 2.14.0 (2011-10-31) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: powerpc-unknown-linux-gnu (32-bit) > > [...]> lm> lm.D9 <- lm(weight ~ group) > > *** caught illegal operation *** > address 0xf759c60, cause 'illegal opcode' >Now, removing the ?offending? package, lm runs well. (I'll send a bug report against this on Debian bug db). Thanks for all. Best regards. Salud y Revoluci?n. Lobo. -- Libertad es poder elegir en cualquier momento. Ahora yo elijo GNU/Linux, para no atar mis manos con las cadenas del soft propietario. --------- Desde El Ejido, en Almer?a, usuario registrado Linux #294013 http://www.counter.li.org