From annis at biostat.wisc.edu  Thu Oct  9 20:42:13 2003
From: annis at biostat.wisc.edu (annis@biostat.wisc.edu)
Date: Thu Oct  9 19:41:22 2003
Subject: [Rd] R-1.8.0 on Sparc Solaris 8, gcc3.2.1,
	bus error and core dump (PR#4485)
Message-ID: <200310091742.h99HgD0P008094@pubhealth.ku.dk>


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


[Rd] R-1.8.0 on Sparc Solaris 8, gcc3.2.1, bus error and core dump (PR#4485)
annis@biostat.wisc.edu