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

From: Simon Urbanek <simon.urbanek_at_r-project.org>
Date: Fri, 23 Nov 2007 14:07:14 -0500

René,

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)
> 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
>
> Binary Images Description:
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> CoreVideo
> 0x945f1000 - 0x94611fff libmx.A.dylib /usr/lib/libmx.A.dylib
> 0x97093000 - 0x970c1fff libncurses.5.4.dylib /usr/lib/libncurses.
> 5.4.dylib
> 0x97b13000 - 0x97b32fff com.apple.vecLib 3.2.2 (vecLib
> 3.2.2) /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
>
> 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
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri 23 Nov 2007 - 19:11:52 GMT

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