MacOSX 10.4.11 update breaks tests/lapack.R (R 2.6.0)? (PR#10454)
Ren?,
On Nov 23, 2007, at 6:00 AM, rjvbertin at gmail.com wrote:
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 .
this is almost certainly a problem with the complex ABI (i.e. the Fortran compiler and vecLib/ALTAS disagree). Normally R detects complex ABI mismatch and either enables a work-around (vecLib) or disables BLAS (others). If the ABI changed between versions, you'll have to re-compile R. If the problem still persists after a re- compile, please send me your config.log. Cheers, Simon
R
R version 2.6.0 (2007-10-03)
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ISBN 3-900051-07-0
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##> 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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