From simon.urbanek at r-project.org  Fri Nov 23 20:07:14 2007
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Fri, 23 Nov 2007 14:07:14 -0500
Subject: [Rd] MacOSX 10.4.11 update breaks tests/lapack.R (R 2.6.0)?
	(PR#10454)
In-Reply-To: <20071123110028.3F9082834156@mail.pubhealth.ku.dk>
References: <20071123110028.3F9082834156@mail.pubhealth.ku.dk>
Message-ID: <E77F7953-E208-43A2-AA14-4876391E52FC@r-project.org>

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)
> 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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> Frameworks/CarbonSound.framework/Versions/A/CarbonSound
> 0x93293000 - 0x935a1fff com.apple.HIToolbox 1.4.10
> (???)	/System/Library/Frameworks/Carbon.framework/Versions/A/ 
> Frameworks/HIToolbox.framework/Versions/A/HIToolbox
> 0x936f1000 - 0x936fdfff com.apple.opengl
> 1.4.7	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
> 0x93799000 - 0x93dccfff com.apple.AppKit 6.4.9
> (824.44)	/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
> 0x94159000 - 0x941cbfff com.apple.CoreData 91
> (92.1)	/System/Library/Frameworks/CoreData.framework/Versions/A/ 
> CoreData
> 0x94204000 - 0x942c9fff com.apple.audio.toolbox.AudioToolbox
> 1.4.7	/System/Library/Frameworks/AudioToolbox.framework/Versions/A/ 
> AudioToolbox
> 0x9431c000 - 0x9431cfff com.apple.audio.units.AudioUnit
> 1.4	/System/Library/Frameworks/AudioUnit.framework/Versions/A/ 
> AudioUnit
> 0x9431e000 - 0x944defff com.apple.QuartzCore
> 1.4.12	/System/Library/Frameworks/QuartzCore.framework/Versions/A/ 
> QuartzCore
> 0x94528000 - 0x94565fff libsqlite3.0.dylib 	/usr/lib/ 
> libsqlite3.0.dylib
> 0x9456d000 - 0x945bdfff libGLImage.dylib
> 	/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/ 
> libGLImage.dylib
> 0x945c6000 - 0x945e0fff com.apple.CoreVideo
> 1.4.2	/System/Library/Frameworks/CoreVideo.framework/Versions/A/ 
> 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
>
>



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