annis@biostat.wisc.edu
2003-Oct-09 19:41 UTC
[Rd] R-1.8.0 on Sparc Solaris 8, gcc3.2.1, bus error and core dump (PR#4485)
Example run and stack trace: wazor /s/src/stat/R-1.8.0/tests/Examples $ ../../bin/R --no-save < base-Ex.R R : Copyright 2003, The R Development Core Team Version 1.8.0 (2003-10-08) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R.> ### * <HEADER> > ### > attach(NULL, name = "CheckExEnv") > assign(".CheckExEnv", as.environment(2), pos = length(search())) # base > ## This plot.new() patch has no effect yet for persp(); > ## layout() & filled.contour() are now ok > assign("plot.new",+ function() { + .Internal(plot.new()) + pp <- par(c("mfg","mfcol","oma","mar")) + if(all(pp$mfg[1:2] == c(1, pp$mfcol[2]))) { + outer <- (oma4 <- pp$oma[4]) > 0; mar4 <- pp$mar[4] + mtext(paste("help(", ..nameEx, ")"), side = 4, + line = if(outer)max(1, oma4 - 1) else min(1, mar4 - 1), + outer = outer, adj = 1, cex = .8, col = "orchid") + } + }, + env = environment(plot))> assign("cleanEx",+ function(env = .GlobalEnv) { + rm(list = ls(envir = env, all.names = TRUE), envir = env) + RNGkind("Wichmann-Hill", "default") + assign(".Random.seed", c(0, rep(7654, 3)), pos = 1) + assign("T", delay(stop("T used instead of TRUE")), + pos = .CheckExEnv) + assign("F", delay(stop("F used instead of FALSE")), + pos = .CheckExEnv) + }, + env = .CheckExEnv)> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now > assign("ptime", proc.time(), env = .CheckExEnv) > postscript("base-Examples.ps") > assign("par.postscript", par(no.readonly = TRUE), env = .CheckExEnv) > options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly")) > cleanEx(); ..nameEx <- "AIC" > > ### * AIC > > ### Name: AIC > ### Title: Akaike's An Information Criterion > ### Aliases: AIC AIC.default AIC.logLik > ### Keywords: models > > ### ** Examples > > data(swiss) > lm1 <- lm(Fertility ~ . , data = swiss) > AIC(lm1)[1] 326.0716> stopifnot(all.equal(AIC(lm1),+ AIC(logLik(lm1))))> ## a version of BIC or Schwarz' BC : > AIC(lm1, k = log(nrow(swiss)))[1] 339.0226> > > > cleanEx(); ..nameEx <- "Arithmetic" > > ### * Arithmetic > > ### Name: Arithmetic > ### Title: Arithmetic Operators > ### Aliases: + - * / ^ \%\% \%/\% Arithmetic > ### Keywords: arith > > ### ** Examples > > x <- -1:12 > x + 1[1] 0 1 2 3 4 5 6 7 8 9 10 11 12 13> 2 * x + 3[1] 1 3 5 7 9 11 13 15 17 19 21 23 25 27> x %% 2 #-- is periodic[1] 1 0 1 0 1 0 1 0 1 0 1 0 1 0> x %/% 5[1] -1 0 0 0 0 0 1 1 1 1 1 2 2 2> > > > cleanEx(); ..nameEx <- "Bessel" > > ### * Bessel > > ### Name: Bessel > ### Title: Bessel Functions > ### Aliases: bessel Bessel besselI besselJ besselK besselY gammaCody > ### Keywords: math > > ### ** Examples > > nus <- c(0:5,10,20) > > x <- seq(0,4, len= 501) > plot(x,x, ylim = c(0,6), ylab="",type='n', main = "Bessel Functions I_nu(x)")Bus Error(coredump) wazor /s/src/stat/R-1.8.0/tests/Examples $ gdb ../../bin/R.bin core GNU gdb 5.3 Copyright 2002 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "sparc-sun-solaris2.8"... Core was generated by `/s/src/stat/R-1.8.0/bin/R.bin --no-save'. Program terminated with signal 10, Bus error. Reading symbols from /usr/lib/libm.so.1...done. Loaded symbols for /usr/lib/libm.so.1 Reading symbols from /usr/lib/libbz2.so.1...done. Loaded symbols for /usr/lib/libbz2.so.1 Reading symbols from /usr/lib/libz.so...done. Loaded symbols for /usr/lib/libz.so Reading symbols from /usr/lib/libnsl.so.1...done. Loaded symbols for /usr/lib/libnsl.so.1 Reading symbols from /usr/lib/libsocket.so.1...done. Loaded symbols for /usr/lib/libsocket.so.1 Reading symbols from /usr/lib/libdl.so.1...done. Loaded symbols for /usr/lib/libdl.so.1 Reading symbols from /usr/lib/libcurses.so.1...done. Loaded symbols for /usr/lib/libcurses.so.1 Reading symbols from /usr/lib/libc.so.1...done. Loaded symbols for /usr/lib/libc.so.1 Reading symbols from /usr/lib/libmp.so.2...done. Loaded symbols for /usr/lib/libmp.so.2 Reading symbols from /usr/platform/SUNW,Ultra-5_10/lib/libc_psr.so.1...done. Loaded symbols for /usr/platform/SUNW,Ultra-5_10/lib/libc_psr.so.1 Reading symbols from /usr/lib/locale/en_US.ISO8859-1/en_US.ISO8859-1.so.2... done. Loaded symbols for /usr/lib/locale/en_US.ISO8859-1/en_US.ISO8859-1.so.2 Reading symbols from /s/src/stat/R-1.8.0/library/ts/libs/ts.so...done. Loaded symbols for /s/src/stat/R-1.8.0/library/ts/libs/ts.so Reading symbols from /s/src/stat/R-1.8.0/library/nls/libs/nls.so...done. Loaded symbols for /s/src/stat/R-1.8.0/library/nls/libs/nls.so Reading symbols from /s/src/stat/R-1.8.0/library/modreg/libs/modreg.so...done. Loaded symbols for /s/src/stat/R-1.8.0/library/modreg/libs/modreg.so Reading symbols from /s/src/stat/R-1.8.0/library/mva/libs/mva.so...done. Loaded symbols for /s/src/stat/R-1.8.0/library/mva/libs/mva.so Reading symbols from /s/src/stat/R-1.8.0/library/ctest/libs/ctest.so...done. Loaded symbols for /s/src/stat/R-1.8.0/library/ctest/libs/ctest.so Reading symbols from /s/src/stat/R-1.8.0/library/methods/libs/methods.so... done. Loaded symbols for /s/src/stat/R-1.8.0/library/methods/libs/methods.so Reading symbols from /s/src/stat/R-1.8.0/library/tools/libs/tools.so...done. Loaded symbols for /s/src/stat/R-1.8.0/library/tools/libs/tools.so Reading symbols from /usr/lib/nss_files.so.1...done. Loaded symbols for /usr/lib/nss_files.so.1 Reading symbols from /usr/lib/nss_nis.so.1...done. Loaded symbols for /usr/lib/nss_nis.so.1 #0 Rf_gpptr (dd=0xd) at base.c:162 162 if (dd->newDevStruct) (gdb) bt #0 Rf_gpptr (dd=0xd) at base.c:162 #1 0x00092ff4 in setClipRect (x1=0xffbed0e0, y1=0xffbed0d8, x2=0xffbed0d0, y2=0xffbed0c8, coords=1298034561, dd=0xd) at graphics.c:2392 #2 0x0009524c in clipRectCode (x0=11.033191163604547, y0=6.0986887576552915, x1=11.232635608048993, y1=5.3139879049022003e-315, coords=873873659, dd=0xd) at graphics.c:3340 #3 0x00095dd8 in clipText (x=11.13291338582677, y=6.9477165354330692, str=0xdb8f18 "help( Bessel )", rot=90, clipToDevice=1, hadj=1, dd=0xd8e1a0) at graphics.c:3585 #4 0x00096240 in Rf_GText (x=11.13291338582677, y=6.9477165354330692, coords=1, str=0x0, xc=1, yc=0, rot=90, dd=0xd8e1a0) at graphics.c:3740 #5 0x000988d0 in Rf_GMtext (str=0xb400e0 "help( Bessel )", side=4, line=1.8, outer=0, at=1.04, las=0, dd=0xd8e1a0) at graphics.c:4366 #6 0x000c736c in do_mtext (call=0x80d818, op=0x224b90, args=0x0, env=0x1) at plot.c:2374 #7 0x000ac114 in do_internal (call=0x1bc688, op=0x1, args=0xec15a8, env=0xec328c) at names.c:1046 #8 0x0007d6cc in Rf_eval (e=0x80d78c, rho=0xec328c) at eval.c:375 #9 0x0007ed28 in do_begin (call=0x80cc6c, op=0x2163b8, args=0x80d770, rho=0xec328c) at eval.c:1034 #10 0x0007d6cc in Rf_eval (e=0x80cc6c, rho=0xec328c) at eval.c:375 #11 0x0007da54 in Rf_applyClosure (call=0xf6d5b4, op=0x80d690, arglist=0xec2fec, rho=0xec5468, suppliedenv=0x1fb768) at eval.c:558 #12 0x0007d4f8 in Rf_eval (e=0xf6d5b4, rho=0xec5468) at eval.c:410 #13 0x0007ed28 in do_begin (call=0xf6cea0, op=0x2163b8, args=0xf6d598, rho=0xec5468) at eval.c:1034 #14 0x0007d6cc in Rf_eval (e=0xf6cea0, rho=0xec5468) at eval.c:375 #15 0x0007d6cc in Rf_eval (e=0xf6d544, rho=0xec5468) at eval.c:375 #16 0x0007ed28 in do_begin (call=0xf6c834, op=0x2163b8, args=0xf6d528, rho=0xec5468) at eval.c:1034 #17 0x0007d6cc in Rf_eval (e=0xf6c834, rho=0xec5468) at eval.c:375 #18 0x0007da54 in Rf_applyClosure (call=0x8d5db4, op=0xf6e0b8, arglist=0x1fb768, rho=0xec9910, suppliedenv=0x1fb768) at eval.c:558 #19 0x0007d4f8 in Rf_eval (e=0x8d5db4, rho=0xec9910) at eval.c:410 #20 0x0007ed28 in do_begin (call=0x8d4760, op=0x2163b8, args=0x8d5d98, rho=0xec9910) at eval.c:1034 #21 0x0007d6cc in Rf_eval (e=0x8d4760, rho=0xec9910) at eval.c:375 #22 0x0007da54 in Rf_applyClosure (call=0xec945c, op=0x8d7004, arglist=0xeca770, rho=0xeca968, suppliedenv=0xec9424) at eval.c:558 #23 0x000ac484 in applyMethod (call=0xec945c, op=0x8d7004, args=0xeca770, rho=0xeca968, newrho=0xec9424) at objects.c:119 #24 0x000acad8 in Rf_usemethod (generic=0x8cf918 "plot", obj=0x8d7004, call=0xffbee300, args=0xec9424, rho=0xeca968, callrho=0x227480, defrho=0x229388, ans=0xffbee57c) at objects.c:326 #25 0x000acf7c in do_usemethod (call=0x8d3bd8, op=0x2251a8, args=0x8d3bf4, env=0xeca968) at objects.c:389 #26 0x0007d6cc in Rf_eval (e=0x8d3bd8, rho=0xeca968) at eval.c:375 #27 0x0007d6cc in Rf_eval (e=0x8d3b68, rho=0xeca968) at eval.c:375 #28 0x0007ed28 in do_begin (call=0x8d3b4c, op=0x2163b8, args=0x8d3b30, rho=0xeca968) at eval.c:1034 #29 0x0007d6cc in Rf_eval (e=0x8d3b4c, rho=0xeca968) at eval.c:375 #30 0x0007da54 in Rf_applyClosure (call=0xeca71c, op=0x8d3a50, arglist=0xeca770, rho=0x227480, suppliedenv=0x1fb768) at eval.c:558 #31 0x0007d4f8 in Rf_eval (e=0xeca71c, rho=0x227480) at eval.c:410 #32 0x0009e1ac in Rf_ReplIteration (rho=0x227480, savestack=0, browselevel=0, state=0xffbeec08) at main.c:245 #33 0x0009e350 in R_ReplConsole (rho=0x227480, savestack=0, browselevel=0) at main.c:293 #34 0x0009ebdc in run_Rmainloop () at main.c:643 #35 0x0010bfac in main (ac=0, av=0xffbef174) at system.c:99 (gdb) q -- William Annis - System Administrator - Biomedical Computing Group "No man forgets his original trade: the rights of nations and of kings sink into questions of grammar, if grammarians discuss them." Samuel Johnson
Prof Brian Ripley
2003-Oct-09 20:31 UTC
(PR#4485) Re: [Rd] R-1.8.0 on Sparc Solaris 8, gcc3.2.1, bus error and core dump (PR#4485)
That's an obselete and broken compiler, and the R-admin manual says
@command{gcc} 3.2.1 and 3.2.2 generate incorrect code on 32-bit Solaris
builds with optimization, but versions 3.1, 3.2, 3.2.3 and 3.3 work
correctly.
Please do pay attention to the documentation, as the INSTALL file asks!
You probably haven't read that either, so please note it says:
The main source of information on installation is the `R Installation
and Administration Manual', an HTML copy of which is available as file
`doc/html/R-admin.html'. Please read that before installing R. But
if you are impatient, read on but please refer to the manual to
resolve any problems.
--
Brian D. Ripley, ripley@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
Peter Dalgaard BSA
2003-Oct-09 20:50 UTC
[Rd] R-1.8.0 on Sparc Solaris 8, gcc3.2.1, bus error and core dump (PR#4485)
annis@biostat.wisc.edu writes:> Example run and stack trace:...> Bus Error(coredump)Bug, but not in R. See http://cran.r-project.org/doc/manuals/R-admin.pdf, sec. B.7.2 -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk) FAX: (+45) 35327907