From rjvbertin at gmail.com  Fri Nov 23 12:00:28 2007
From: rjvbertin at gmail.com (rjvbertin at gmail.com)
Date: Fri, 23 Nov 2007 12:00:28 +0100 (CET)
Subject: [Rd] MacOSX 10.4.11 update breaks tests/lapack.R (R 2.6.0)?
	(PR#10454)
Message-ID: <20071123110028.3F9082834156@mail.pubhealth.ku.dk>

Hello,

It seems the recent Mac OS X 10.4.11 update installed a new
libBLAS.dylib in the Accelerate framework which either contains a bug
itself or exposes a bug somewhere in R's lapack code on the PowerPC G4
and G5.
My build of R 2.6.0 executed the tests/lapack.R code succesfully when
I upgraded when 2.6.0 was released. After the OS update, it now
crashes. This happens both with the version I built using Apple's gcc
4.0.1 and gfortran 4.2.2, and with the version built completely with
gcc 4.2.2 .

> R

R version 2.6.0 (2007-10-03)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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 and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

##> source("R-2.6.0/tests/lapack.R", echo=TRUE, verbose=TRUE)
'envir' chosen:<environment: R_GlobalEnv>
encoding = "native.enc" chosen
--> parsed 40 expressions; now eval(.)ing them:

>>>> eval(expression_nr. 1 )
                 =================

##> ## tests of R functions based on the lapack module
##>
##> options(digits=4)
curr.fun: symbol options
 .. after 'expression(options(digits=4))'

<SNIP>

##> sm[] <- as.complex(sm)
curr.fun: symbol <-
 .. after 'expression(sm[] <- as.complex(sm))'

>>>> eval(expression_nr. 35 )
                 =================

##> Ceigenok(sm, eigen(sm))

 *** caught bus error ***
address 0x1, cause 'invalid alignment'

Traceback:
 1: .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
 2: eigen(sm)
 3: apply(A, 2, function(x) x * sign(Re(x[1])))
 4: fixsign(E$vectors)
 5: print(fixsign(E$vectors))
 6: Ceigenok(sm, eigen(sm))
 7: eval.with.vis(expr, envir, enclos)
 8: eval.with.vis(ei, envir)
 9: source("~/cworks/new/R-2.6.0/tests/lapack.R", echo = TRUE, verbose = TRUE)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

*************** OS X Crash report:
Date/Time:      2007-11-23 11:19:19.135 +0100
OS Version:     10.4.11 (Build 8S165)
Report Version: 4

Command: R
Path:    /Library/Frameworks/R.framework/Resources/bin/exec/R
Parent:  tcsh [2437]

Version: ??? (???)

PID:    3167
Thread: 0

Exception:  EXC_BAD_ACCESS (0x0001)
Codes:      KERN_PROTECTION_FAILURE (0x0002) at 0x00000001

Thread 0 Crashed:
0   libBLAS.dylib    	0x920fc374 atl_f77wrap_zdotc__ + 80
1   libBLAS.dylib    	0x920f7864 zdotc_ + 60
2   libRlapack.dylib 	0x013701a0 zhetd2_ + 960
3   libRlapack.dylib 	0x0136fcdc zhetrd_ + 1900
4   libRlapack.dylib 	0x01370ad8 zheev_ + 1016
5   lapack.so        	0x010a4038 modLa_rs_cmplx + 392
6   libR.dylib       	0x003c99e8 La_rs_cmplx + 72
7   libR.dylib       	0x00372380 do_dotcall + 16864
8   libR.dylib       	0x003a170c Rf_eval + 1804
9   libR.dylib       	0x003a14dc Rf_eval + 1244
10  libR.dylib       	0x003a45f4 do_set + 980
11  libR.dylib       	0x003a14dc Rf_eval + 1244
12  libR.dylib       	0x003a2b08 do_begin + 104
13  libR.dylib       	0x003a14dc Rf_eval + 1244
14  libR.dylib       	0x003a14dc Rf_eval + 1244
15  libR.dylib       	0x003a2b08 do_begin + 104
16  libR.dylib       	0x003a14dc Rf_eval + 1244
17  libR.dylib       	0x003a14dc Rf_eval + 1244
18  libR.dylib       	0x003a2b08 do_begin + 104
19  libR.dylib       	0x003a14dc Rf_eval + 1244
20  libR.dylib       	0x003a4f58 Rf_applyClosure + 728
21  libR.dylib       	0x003a13f0 Rf_eval + 1008
22  libR.dylib       	0x003a62c8 forcePromise + 184
23  libR.dylib       	0x003a12c8 Rf_eval + 712
24  libR.dylib       	0x003a1650 Rf_eval + 1616
25  libR.dylib       	0x003a2714 Rf_DispatchOrEval + 244
26  libR.dylib       	0x0049d190 do_subset3 + 384
27  libR.dylib       	0x003a14dc Rf_eval + 1244
28  libR.dylib       	0x003a62c8 forcePromise + 184
29  libR.dylib       	0x003a12c8 Rf_eval + 712
30  libR.dylib       	0x003a1650 Rf_eval + 1616
31  libR.dylib       	0x003a62c8 forcePromise + 184
32  libR.dylib       	0x003a12c8 Rf_eval + 712
33  libR.dylib       	0x003a1650 Rf_eval + 1616
34  libR.dylib       	0x003a2488 Rf_evalList + 168
35  libR.dylib       	0x003a15a8 Rf_eval + 1448
36  libR.dylib       	0x003a45f4 do_set + 980
37  libR.dylib       	0x003a14dc Rf_eval + 1244
38  libR.dylib       	0x003a2b08 do_begin + 104
39  libR.dylib       	0x003a14dc Rf_eval + 1244
40  libR.dylib       	0x003a4f58 Rf_applyClosure + 728
41  libR.dylib       	0x003a13f0 Rf_eval + 1008
42  libR.dylib       	0x003a3cdc applydefine + 60
43  libR.dylib       	0x003a14dc Rf_eval + 1244
44  libR.dylib       	0x003a2b08 do_begin + 104
45  libR.dylib       	0x003a14dc Rf_eval + 1244
46  libR.dylib       	0x003a4f58 Rf_applyClosure + 728
47  libR.dylib       	0x003a13f0 Rf_eval + 1008
48  libR.dylib       	0x003a62c8 forcePromise + 184
49  libR.dylib       	0x003a12c8 Rf_eval + 712
50  libR.dylib       	0x003eafac do_usemethod + 1228
51  libR.dylib       	0x003a14dc Rf_eval + 1244
52  libR.dylib       	0x003a4f58 Rf_applyClosure + 728
53  libR.dylib       	0x003a13f0 Rf_eval + 1008
54  libR.dylib       	0x003a2b08 do_begin + 104
55  libR.dylib       	0x003a14dc Rf_eval + 1244
56  libR.dylib       	0x003a4f58 Rf_applyClosure + 728
57  libR.dylib       	0x003a13f0 Rf_eval + 1008
58  libR.dylib       	0x003a1eac do_eval + 1868
59  libR.dylib       	0x003e7d2c do_internal + 636
60  libR.dylib       	0x003a14dc Rf_eval + 1244
61  libR.dylib       	0x003a4f58 Rf_applyClosure + 728
62  libR.dylib       	0x003a13f0 Rf_eval + 1008
63  libR.dylib       	0x003a45f4 do_set + 980
64  libR.dylib       	0x003a14dc Rf_eval + 1244
65  libR.dylib       	0x003a2b08 do_begin + 104
66  libR.dylib       	0x003a14dc Rf_eval + 1244
67  libR.dylib       	0x003a31ac do_for + 572
68  libR.dylib       	0x003a14dc Rf_eval + 1244
69  libR.dylib       	0x003a2b08 do_begin + 104
70  libR.dylib       	0x003a14dc Rf_eval + 1244
71  libR.dylib       	0x003a4f58 Rf_applyClosure + 728
72  libR.dylib       	0x003a13f0 Rf_eval + 1008
73  libR.dylib       	0x003cf7cc Rf_ReplIteration + 332
74  libR.dylib       	0x003cff04 run_Rmainloop + 212
75  R                	0x00001d80 main + 48
76  R                	0x00001a9c _start + 760
77  R                	0x000017a0 start + 48

Thread 0 crashed with PPC Thread State 64:
  srr0: 0x00000000920fc374 srr1: 0x000000000000f030
    vrsave: 0x0000000000000000
    cr: 0x28002224          xer: 0x0000000000000004   lr:
0x00000000920f7864  ctr: 0x00000000920f7828
    r0: 0x000000003fd60f2c   r1: 0x00000000bfff24c0   r2:
0x0000000001384074   r3: 0x0000000002afe818
    r4: 0x0000000001384074   r5: 0x000000003ff00000   r6:
0x0000000001384074   r7: 0x0000000000000001
    r8: 0x00000000bfff24f8   r9: 0x0000000000000005  r10:
0x0000000000000000  r11: 0x0000000001385110
   r12: 0x00000000920f7828  r13: 0x00000000bfff2570  r14:
0x0000000000000004  r15: 0x0000000001384074
   r16: 0x000000000137fde8  r17: 0x00000000bfff256c  r18:
0x0000000002b098e8  r19: 0x00000000bfff2839
   r20: 0x0000000001384074  r21: 0x00000000019c7db0  r22:
0x0000000000000006  r23: 0x00000000bfff283c
   r24: 0x0000000002afe818  r25: 0x00000000bfff2688  r26:
0x0000000000000005  r27: 0x00000000fffffffa
   r28: 0x0000000000000001  r29: 0x000000000113e708  r30:
0x00000000bfff256c  r31: 0x000000000136fde8

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Model: PowerBook5,4, BootROM 4.8.6f0, 1 processors, PowerPC G4  (1.1),
1.5 GHz, 1 GB
Graphics: ATI Mobility Radeon 9700, ATY,RV360M11, AGP, 128 MB
Memory Module: SODIMM0/J25LOWER, 512 MB, DDR SDRAM, PC2700U-25330
Memory Module: SODIMM1/J25UPPER, 512 MB, DDR SDRAM, PC2700U-25330
AirPort: AirPort Extreme, 405.1 (3.90.34.0.p18)
Modem: Jump, V.92, Version 1.0
Bluetooth: Version 1.9.5f4, 2 service, 0 devices, 1 incoming serial ports
Network Service: Built-in Ethernet, Ethernet, en0
PCI Card: TXN,PCIXXXX-00, cardbus, PC Card
Parallel ATA Device: MATSHITACD-RW  CW-8123
Parallel ATA Device: HTE721080G9AT00, 74.53 GB
USB Device: Bluetooth USB Host Controller, Apple, Inc., Up to 12 Mb/sec, 500 mA



[Rd] MacOSX 10.4.11 update breaks tests/lapack.R (R 2.6.0)? (PR#10454)
rjvbertin at gmail.com