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

From: <rjvbertin_at_gmail.com>
Date: Fri, 23 Nov 2007 12:00:28 +0100 (CET)


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.

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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))

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

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