[R-SIG-Mac] Problem (segfault) using surveillance package on Mac (not on FreeBSD)
Ben Madin
lists at remoteinformation.com.au
Tue Nov 9 01:13:50 CET 2010
G'day all,
I am having a problem with a function in surveillance package when trying to use one function on my mac (either GUI or commandline). It works fine on FreeBSD, and the contributor uses Linux or windows, so I thought I might ask here first - my apologies in advance. Many of the package functions work absolutely fine on all three.
Using the spatio-temporal cluster detection function stcd, and using the example in the help file, the final command takes about 1 second to return a result on FreeBSD (output of sessionInfo() first):
R version 2.11.1 (2010-05-31)
i386-portbld-freebsd7.0
locale:
[1] C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] splancs_2.01-27 surveillance_1.2-1 Matrix_0.999375-44 msm_0.9.7
[5] vcd_1.2-9 colorspace_1.0-1 MASS_7.3-7 maptools_0.7-38
[9] lattice_0.19-13 foreign_0.8-41 sp_0.9-72 spc_0.3
[13] xtable_1.5-6
loaded via a namespace (and not attached):
[1] mvtnorm_0.9-92 splines_2.11.1 survival_2.35-8 tools_2.11.1
Warning messages:
1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
3: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
library(surveillance)
library("splancs")
data(burkitt)
# order the times
burkitt <- burkitt[order(burkitt$t), ]
#Parameters for the SR detection
epsilon <- 0.5 # relative change within the cluster
radius <- 20 # radius
threshold <- 161 # threshold limit
res <- stcd(x=burkitt$x, y=burkitt$y, t=burkitt$t, radius=radius, epsilon=epsilon, areaA=1, areaAcapBk=1, threshold=threshold)
takes about 1 second
Using the R GUI - latest patches from r.research.att.com :
> sessionInfo()
R version 2.11.1 Patched (2010-09-30 r53084)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] splancs_2.01-27 surveillance_1.2-1 Matrix_0.999375-44 msm_0.9.7 vcd_1.2-9 colorspace_1.0-1
[7] MASS_7.3-7 maptools_0.7-38 lattice_0.19-13 foreign_0.8-41 sp_0.9-72 spc_0.3
[13] xtable_1.5-6
loaded via a namespace (and not attached):
[1] mvtnorm_0.9-92 splines_2.11.1 survival_2.35-8 tools_2.11.1
> library(surveillance)
Loading required package: xtable
Loading required package: spc
Loading required package: sp
Loading required package: maptools
Loading required package: foreign
Loading required package: lattice
Note: polygon geometry computations in maptools
depend on the package gpclib, which has a
restricted licence. It is disabled by default;
to enable gpclib, type gpclibPermit()
Checking rgeos availability as gpclib substitute:
FALSE
Loading required package: vcd
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
Loading required package: msm
Loading required package: Matrix
Attaching package: 'Matrix'
The following object(s) are masked from 'package:base':
det
> library("splancs")
Spatial Point Pattern Analysis Code in S-Plus
Version 2 - Spatial and Space-Time analysis
> data(burkitt)
> # order the times
> burkitt <- burkitt[order(burkitt$t), ]
> #Parameters for the SR detection
> epsilon <- 0.5 # relative change within the cluster
> radius <- 20 # radius
> threshold <- 161 # threshold limit
> res <- stcd(x=burkitt$x,
+ y=burkitt$y,
+ t=burkitt$t,
+ radius=radius,
+ epsilon=epsilon,
+ areaA=1,
+ areaAcapBk=1,
+ threshold=threshold)
*** caught segfault ***
address 0x11b115000, cause 'memory not mapped'
Traceback:
1: .C("SRspacetime", x = as.double(x), y = as.double(y), t = as.double(t), n = as.integer(n), radius = as.double(radius), epsilon = as.double(epsilon), areaA = as.double(areaA), areaAcapBk = as.double(areaAcapBk), cusum = as.integer(cusum), threshold = as.double(threshold), R = as.double(numeric(n)), idxFA = as.integer(-1), idxCC = as.integer(-1), PACKAGE = "surveillance")
2: stcd(x = burkitt$x, y = burkitt$y, t = burkitt$t, radius = radius, epsilon = epsilon, areaA = 1, areaAcapBk = 1, threshold = threshold)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Using the R program on the commandline :
R version 2.11.1 Patched (2010-09-30 r53084)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] splancs_2.01-27 surveillance_1.2-1 Matrix_0.999375-44 msm_0.9.7
[5] vcd_1.2-9 colorspace_1.0-1 MASS_7.3-7 maptools_0.7-38
[9] lattice_0.19-13 foreign_0.8-41 sp_0.9-72 spc_0.3
[13] xtable_1.5-6
loaded via a namespace (and not attached):
[1] mvtnorm_0.9-92 splines_2.11.1 survival_2.35-8 tools_2.11.1
All the commands run fine, except that the final one does not finish, and after an initial flash of enthusiasm, R ticks along between about 3 and 15% of CPU chewing up as much memory as it can. I have attached a sample at the very bottom of this email, taken before I killed it off.
I realise this could be a package function, but I know almost nothing about what goes on under the R hood, so if this helps to find a problem in the package I am very happy to switch to go back to the package authors with some help.
Thank you for your help,
cheers
Ben
Sampling process 7948 for 3 seconds with 1 millisecond of run time between samples
Sampling completed, processing symbols...
Analysis of sampling R (pid 7948) every 1 millisecond
Process: R [7948]
Path: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/exec/x86_64/R
Load Address: 0x100000000
Identifier: R
Version: ??? (???)
Code Type: X86-64 (Native)
Parent Process: bash [7944]
Date/Time: 2010-11-09 10:54:49.806 +1100
OS Version: Mac OS X 10.6.4 (10F569)
Report Version: 6
Call graph:
2113 Thread_47293 DispatchQueue_1: com.apple.main-thread (serial)
2113 start
2113 main
2113 run_Rmainloop
2113 R_ReplConsole
2113 Rf_ReplIteration
2113 Rf_eval
2113 do_set
2113 Rf_eval
2113 Rf_applyClosure
2113 Rf_eval
2113 do_begin
2113 Rf_eval
2113 do_set
2113 Rf_eval
2113 do_dotCode
2112 SRspacetime
2048 SRspacetime
60 operator new(unsigned long)
58 malloc
57 malloc_zone_malloc
54 szone_malloc_should_clear
23 allocate_pages
22 __mmap
1 munmap
20 tiny_malloc_from_free_list
11 szone_malloc_should_clear
2 malloc_zone_malloc
1 szone_malloc
1 malloc
2 operator new(unsigned long)
4 std::_List_node_base::hook(std::_List_node_base*)
1 dyld_stub_operator new(unsigned long)
Total number in stack (recursive counted multiple, when >=5):
5 Rf_eval
Sort by top of stack, same collapsed (when >= 5):
SRspacetime 2048
__mmap 22
tiny_malloc_from_free_list 20
szone_malloc_should_clear 11
Binary Images:
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0x7fff84d21000 - 0x7fff84d32ff7 libz.1.dylib 1.2.3 (compatibility 1.0.0) <FB5EE53A-0534-0FFA-B2ED-486609433717> /usr/lib/libz.1.dylib
0x7fff84d63000 - 0x7fff84d6eff7 com.apple.speech.recognition.framework 3.11.1 (3.11.1) <60484D84-BA63-13DD-50E9-ABDA402C3C45> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
0x7fff84d6f000 - 0x7fff84e88fef libGLProgrammability.dylib ??? (???) <0E55A58B-5B42-669F-2655-90893554CA21> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff8501e000 - 0x7fff8501fff7 com.apple.TrustEvaluationAgent 1.1 (1) <306FD9EE-A301-41D5-EBDE-2FC52F28229C> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff85022000 - 0x7fff851d8fef com.apple.ImageIO.framework 3.0.3 (3.0.3) <A32D0B5A-7149-7739-22D3-84D38B07E9E5> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO
0x7fff851fe000 - 0x7fff852adfff edu.mit.Kerberos 6.5.10 (6.5.10) <F3F76EDF-5660-78F0-FE6E-33B6174F55A4> /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
0x7fff852ae000 - 0x7fff852e9fff com.apple.AE 496.4 (496.4) <64C27EC8-FC7F-EA6B-9435-9A3452425915> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
0x7fff852ea000 - 0x7fff852eaff7 com.apple.ApplicationServices 38 (38) <10A0B9E9-4988-03D4-FC56-DDE231A02C63> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x7fff852eb000 - 0x7fff8533aff7 com.apple.DirectoryService.PasswordServerFramework 6.0 (6.0) <17EFD646-6F53-36E9-56BF-5A339E83EFFC> /System/Library/PrivateFrameworks/PasswordServer.framework/Versions/A/PasswordServer
0x7fff853e2000 - 0x7fff853e3ff7 com.apple.audio.units.AudioUnit 1.6.3 (1.6.3) <5264A680-010D-4DD6-911E-04AD0DA3D0B4> /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
0x7fff853e4000 - 0x7fff85407fff com.apple.opencl 12.1 (12.1) <403E8F37-4348-B9BC-08E6-7693A995B7EC> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff8540b000 - 0x7fff8541ffff libGL.dylib ??? (???) <5AD69545-D1A3-C017-C7AF-B4AFD6F08FA2> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff854c7000 - 0x7fff85685fff libicucore.A.dylib 40.0.0 (compatibility 1.0.0) <0E53A4A6-AC06-1B61-2285-248F534EE356> /usr/lib/libicucore.A.dylib
0x7fff85686000 - 0x7fff8568aff7 libmathCommon.A.dylib 315.0.0 (compatibility 1.0.0) <95718673-FEEE-B6ED-B127-BCDBDB60D4E5> /usr/lib/system/libmathCommon.A.dylib
0x7fff8568b000 - 0x7fff85690fff libGFXShared.dylib ??? (???) <1B50D804-966B-30D2-D0FD-B090B6FEAC7E> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x7fff85691000 - 0x7fff85747fff libobjc.A.dylib 227.0.0 (compatibility 1.0.0) <B1F5CDC0-96BD-C7C0-BEAA-1E2259DDE067> /usr/lib/libobjc.A.dylib
0x7fff85764000 - 0x7fff85924fef libSystem.B.dylib 125.2.0 (compatibility 1.0.0) <95E02DD0-ADEA-745B-E7FA-ABA064E4658C> /usr/lib/libSystem.B.dylib
0x7fff85a30000 - 0x7fff85ad0fff com.apple.LaunchServices 362.1 (362.1) <4529EF9C-45C7-E2E3-6726-4A5AD382566D> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
0x7fff85ad1000 - 0x7fff85b12fff com.apple.SystemConfiguration 1.10.2 (1.10.2) <BC27BDD4-9CC8-9AF0-B4C2-DD50FD751CBF> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
0x7fff85b13000 - 0x7fff85bd3fff libFontParser.dylib ??? (???) <A4F8189D-1D5B-2F8D-E78E-6D934A8E8407> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
0x7fff85c47000 - 0x7fff85c4dff7 IOSurface ??? (???) <EB2019F6-7C5C-3D59-E11F-6119466C12A9> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
0x7fff85c4e000 - 0x7fff85c73ff7 com.apple.CoreVideo 1.6.1 (45.5) <BB098B75-BA61-50E6-FE8E-FFE285BDECE8> /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
0x7fff85cb1000 - 0x7fff85e26ff7 com.apple.CoreFoundation 6.6.3 (550.29) <48810602-63C3-994D-E563-DD02B16E76E1> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff862b6000 - 0x7fff86307fe7 com.apple.HIServices 1.8.0 (???) <A16322D3-8EEC-9928-4730-8916C21D8187> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
0x7fff866ea000 - 0x7fff867e2ff7 libiconv.2.dylib 7.0.0 (compatibility 7.0.0) <E0683DF0-8180-58A2-BA49-511111D4F36E> /usr/lib/libiconv.2.dylib
0x7fff867e3000 - 0x7fff867e3ff7 com.apple.Accelerate.vecLib 3.6 (vecLib 3.6) <DA9BFF01-40DF-EBD5-ABB7-787DAF2D77CF> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x7fff867e4000 - 0x7fff867f2ff7 libkxld.dylib ??? (???) <EE840168-1F67-6219-8BA3-C46039BCC8B3> /usr/lib/system/libkxld.dylib
0x7fff867f3000 - 0x7fff86819fe7 libJPEG.dylib ??? (???) <4060F3E2-BAD3-244F-D777-51BA16569DA4> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
0x7fff86827000 - 0x7fff86870fef libGLU.dylib ??? (???) <88F0E457-EE53-B5FF-6A1B-D0326D0C643D> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff86b0d000 - 0x7fff86b8cfef com.apple.audio.CoreAudio 3.2.2 (3.2.2) <243E456E-7A74-BE76-FF18-E589BDCAA785> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
0x7fff86b8d000 - 0x7fff86c19fef SecurityFoundation ??? (???) <6860DE26-0D42-D1E8-CD7C-5B42D78C1E1D> /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
0x7fff86e46000 - 0x7fff86e58fe7 libsasl2.2.dylib 3.15.0 (compatibility 3.0.0) <76B83C8D-8EFE-4467-0F75-275648AFED97> /usr/lib/libsasl2.2.dylib
0x7fff86e8a000 - 0x7fff86ec9fef libncurses.5.4.dylib 5.4.0 (compatibility 5.4.0) <E1F34D53-3D62-78C0-CAD8-8AD22C110A9E> /usr/lib/libncurses.5.4.dylib
0x7fff872fa000 - 0x7fff87693ff7 com.apple.QuartzCore 1.6.2 (227.22) <76EE0A32-B20B-F316-ADDD-4230329253D5> /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
0x7fff87966000 - 0x7fff87a1bfe7 com.apple.ink.framework 1.3.3 (107) <D76C7591-B060-E2DE-6634-968FDABD87EF> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
0x7fff87a1c000 - 0x7fff87a3afff libPng.dylib ??? (???) <F6932C8D-E6B1-0871-B698-15180AA948F7> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
0x7fff87a3b000 - 0x7fff87af0fe7 com.apple.ColorSync 4.6.3 (4.6.3) <AA93AD96-6974-9104-BF55-AF7A813C8A1B> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
0x7fff87b48000 - 0x7fff87b4bff7 libCoreVMClient.dylib ??? (???) <CE19A78F-B76D-244A-1C04-0544B914F728> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff87b9f000 - 0x7fff87bb3ff7 com.apple.speech.synthesis.framework 3.10.35 (3.10.35) <63C87CF7-56B3-4038-8136-8C26E96AD42F> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
0x7fff87bb4000 - 0x7fff883befe7 libBLAS.dylib 219.0.0 (compatibility 1.0.0) <EEE5CE62-9155-6559-2AEA-05CED0F5B0F1> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x7fff883ef000 - 0x7fff8843efef libTIFF.dylib ??? (???) <A66CBA9C-A38D-5EDB-BFB5-CB398F033D6F> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
0x7fff8843f000 - 0x7fff8857dfff com.apple.CoreData 102.1 (251) <782F29CA-ACC7-4A77-5772-52FBE2CEFB5E> /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
0x7fff88587000 - 0x7fff8858cfff libGIF.dylib ??? (???) <21FC6B02-6AC3-C4DB-0B50-98144802274C> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
0x7fff88600000 - 0x7fff88601fff liblangid.dylib ??? (???) <EA4D1607-2BD5-2EE2-2A3B-632EEE5A444D> /usr/lib/liblangid.dylib
0x7fff88724000 - 0x7fff88770fff libauto.dylib ??? (???) <205CE82B-3DE0-4A9D-CEB9-F6A3DDA22ED4> /usr/lib/libauto.dylib
0x7fff88836000 - 0x7fff8884bff7 com.apple.LangAnalysis 1.6.6 (1.6.6) <DC999B32-BF41-94C8-0583-27D9AB463E8B> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
0x7fff8884f000 - 0x7fff88c93fef libLAPACK.dylib 219.0.0 (compatibility 1.0.0) <E14EC4C6-B055-A4AC-B971-42AB644E4A7C> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x7fff88c94000 - 0x7fff88da3fe7 libcrypto.0.9.8.dylib 0.9.8 (compatibility 0.9.8) <36DA89A6-3AF5-86F2-BDD5-B94C7C0844D4> /usr/lib/libcrypto.0.9.8.dylib
0x7fff88dc7000 - 0x7fff88ea1ff7 com.apple.vImage 4.0 (4.0) <354F34BF-B221-A3C9-2CA7-9BE5E14AD5AD> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x7fff88eb9000 - 0x7fff88fdefef com.apple.audio.toolbox.AudioToolbox 1.6.3 (1.6.3) <4931DCF6-072F-A4FA-0989-4C4B83BDF98A> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
0x7fff8905c000 - 0x7fff89072fe7 com.apple.MultitouchSupport.framework 205.34 (205.34) <01AAE66D-C2DF-4EF5-FC7B-E89E08C02A01> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
0x7fff89091000 - 0x7fff890a0fff com.apple.NetFS 3.2.1 (3.2.1) <3FC302C9-A5C6-A9CA-08CE-435AD05499F1> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
0x7fff890a1000 - 0x7fff890a8fff com.apple.OpenDirectory 10.6 (10.6) <72A65D76-7831-D31E-F1B3-9E48BF26A98B> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
0x7fffffe00000 - 0x7fffffe01fff libSystem.B.dylib ??? (???) <95E02DD0-ADEA-745B-E7FA-ABA064E4658C> /usr/lib/libSystem.B.dylib
Sample analysis of process 7948 written to file /dev/stdout
More information about the R-SIG-Mac
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