rjvbertin at gmail.com
2007-Nov-23 11:00 UTC
[Rd] MacOSX 10.4.11 update breaks tests/lapack.R (R 2.6.0)? (PR#10454)
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 .> RR 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: 0x1000 - 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Simon Urbanek
2007-Nov-23 19:07 UTC
[Rd] 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) > 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: > 0x1000 - 0x1fff R /Library/Frameworks/R.framework/ > Resources/bin/exec/R > 0x4000 - 0x5fff libRblas.dylib > /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib > 0x3c000 - 0x48fff libgcc_s.1.dylib > /usr/local/gnu/gcc/4.2.2/lib/libgcc_s.1.dylib > 0xb5000 - 0xecfff libreadline.5.1.dylib > /usr/local/lib/libreadline.5.1.dylib > 0x24a000 - 0x24ffff methods.so > /Library/Frameworks/R.framework/Resources/library/methods/libs/ > methods.so > 0x2e9000 - 0x551fff libR.dylib > /Library/Frameworks/R.framework/Resources/lib/libR.dylib > 0x5d2000 - 0x65dfff libgfortran.2.dylib > /usr/local/gnu/gcc/4.2.2/lib/libgfortran.2.dylib > 0x1008000 - 0x102dfff grDevices.so > /Library/Frameworks/R.framework/Resources/library/grDevices/libs/ > grDevices.so > 0x10a2000 - 0x10a8fff lapack.so > /Library/Frameworks/R.framework/Resources/modules/lapack.so > 0x1205000 - 0x125dfff stats.so > /Library/Frameworks/R.framework/Resources/library/stats/libs/stats.so > 0x1266000 - 0x1384fff libRlapack.dylib > /Library/Frameworks/R.framework/Resources/lib/libRlapack.dylib > 0x8fe00000 - 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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 > >