[R-SIG-Mac] R 4.4 crashes loading dplyr
Carl Witthoft
ce||ocgw @end|ng |rom gm@||@com
Tue Apr 30 14:32:41 CEST 2024
Thanks, Peter! The funny thing is that I had kept R 4.2 around in the
Frameworks directory, but didn't expect a new installation of R4.4 to
choose that path for libs. I removed R4.2 , then reinstalled R4.4 and now
the correct libs are invoked. I guess some config macro file must have
remained in the list of startup items.
FWIW, after removing R4.2 but before reinstalling R4.4, I tried
'library(dplyr)' , which didn't crash but failed with the error msgs shown
here.
Error: package or namespace load failed for ‘dplyr’ in dyn.load(file,
DLLpath = DLLpath, ...):
unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/magrittr/libs/magrittr.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/magrittr/libs/magrittr.so,
0x0006): Library not loaded:
/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib
Referenced from: <B6E9C258-16F0-31E8-AF63-50207542C35F>
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/magrittr/libs/magrittr.so
Reason: tried:
'/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (no
such file),
'/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib'
(no such file),
'/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (no
such file), '/usr/local/lib/libR.dylib' (no such file),
'/usr/lib/libR.dylib' (no such file, not in dyld cac
regards,
Carl
On Tue, Apr 30, 2024 at 4:48 AM peter dalgaard <pdalgd using gmail.com> wrote:
> Hmm, worx4me. At least from a fresh source build.
>
> I am suspicious of the "4.2" in a number of entries in your log, e.g.
>
> {
> "source" : "P",
> "arch" : "x86_64",
> "base" : 5029900288,
> "size" : 3260416,
> "uuid" : "c3e6d895-7059-3865-aa61-a941ea1c4569",
> "path" :
>
> "\/Library\/Frameworks\/R.framework\/Versions\/4.2\/Resources\/lib\/libR.dylib",
>
> "name" : "libR.dylib"
> },
>
> which suggests that you may be mixing incompatible binaries. Do you have
> an older private library on your search path? That has bitten me at some
> point.
>
>
> - pd.
>
> > On 30 Apr 2024, at 00:55 , Carl Witthoft <cellocgw using gmail.com> wrote:
> >
> > I apologize if the file posted below is the wrong log.
> > I start up R 4.4.0 on my iMac 13.5.2 , type 'library(dplyr)' and r.app
> > gui crashes immediately. Same for ggplot2, gert, stringr, and others .
> >
> > I have verified that I've updated every R library in my system. I can
> > successfully load other libs, e.g., Rmpfr,knitr, MASS, so I doubt it's a
> > directory or permissions problem.
> >
> > From the command line:
> > library(dplyr)
> >
> > *** caught segfault ***
> > address 0x406e0, cause 'memory not mapped'
> >
> > Traceback:
> > 1: fun(libname, pkgname)
> > 2: doTryCatch(return(expr), name, parentenv, handler)
> > 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> > 4: tryCatchList(expr, classes, parentenv, handlers)
> > 5: tryCatch(fun(libname, pkgname), error = identity)
> > 6: runHook(".onLoad", env, package.lib, package)
> > 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
> > vI[[j]])
> > 8: asNamespace(ns)
> > 9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
> > .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
> > 10: loadNamespace(package, lib.loc)
> > 11: doTryCatch(return(expr), name, parentenv, handler)
> > 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> > 13: tryCatchList(expr, classes, parentenv, handlers)
> > 14: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <-
> > loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos,
> > deps, exclude, include.only)}, error = function(e) { P <- if
> > (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L])
> > else "" msg <- gettextf("package or namespace load failed for %s%s:\n
> > %s", sQuote(package), P, conditionMessage(e)) if
> (logical.return
> > && !quietly) message(paste("Error:", msg), domain = NA) else
> > stop(msg, call. = FALSE, domain = NA)})
> > 15: library(dplyr)
> >
> >
> >
> > ---- ~/library/logs/diagnosticreports file pasted below --
> >
> > {"app_name":"R","timestamp":"2024-04-29 11:11:39.00
> -0400","app_version":"R
> > 4.4.0 GUI 1.80 Big Sur Intel
> >
> build","slice_uuid":"8311af3a-aa38-355b-acef-bbecbdb69a11","build_version":"8376","platform":1,"bundleID":"org.R-project.R","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS
> > 13.5.2
> >
> (22G91)","roots_installed":0,"name":"R","incident_id":"059EF229-5343-4EE7-9843-B88A513B8019"}
> >
> > {
> > "uptime" : 260000,
> > "procRole" : "Foreground",
> > "version" : 2,
> > "userID" : 502,
> > "deployVersion" : 210,
> > "modelCode" : "iMac19,2",
> > "coalitionID" : 1308,
> > "osVersion" : {
> > "train" : "macOS 13.5.2",
> > "build" : "22G91",
> > "releaseType" : "User"
> > },
> > "captureTime" : "2024-04-29 11:11:38.8062 -0400",
> > "incident" : "059EF229-5343-4EE7-9843-B88A513B8019",
> > "pid" : 55298,
> > "cpuType" : "X86-64",
> > "roots_installed" : 0,
> > "bug_type" : "309",
> > "procLaunch" : "2024-04-29 11:10:04.6528 -0400",
> > "procStartAbsTime" : 261494660416425,
> > "procExitAbsTime" : 261588804970703,
> > "procName" : "R",
> > "procPath" : "\/Applications\/R.app\/Contents\/MacOS\/R",
> > "bundleInfo" : {"CFBundleShortVersionString":"R 4.4.0 GUI 1.80 Big Sur
> > Intel
> > build","CFBundleVersion":"8376","CFBundleIdentifier":"org.R-project.R"},
> > "storeInfo" :
> >
> {"deviceIdentifierForVendor":"415552B1-5065-5FAB-8DB9-7D60A9149E9E","thirdParty":true},
> >
> > "parentProc" : "launchd",
> > "parentPid" : 1,
> > "coalitionName" : "org.R-project.R",
> > "crashReporterKey" : "CD7A5AA1-F53E-DB32-2D97-4F4C0CC4EC41",
> > "codeSigningID" : "org.R-project.R",
> > "codeSigningTeamID" : "VZLD955F6P",
> > "codeSigningFlags" : 570491653,
> > "codeSigningValidationCategory" : 6,
> > "codeSigningTrustLevel" : 0,
> > "wakeTime" : 1661,
> > "sleepWakeUUID" : "3454232B-C5AA-4B88-A913-8D5DB632B8A8",
> > "sip" : "enabled",
> > "vmRegionInfo" : "0x406e0 is not in any region. Bytes before following
> > region: 4486408480\n REGION TYPE START -
> > END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE
> AT
> > START\n---> \n __TEXT 10b6d3000-10b763000 [ 576K] r-x\/r-x
> > SM=COW ...tents\/MacOS\/R",
> > "exception" : {"codes":"0x0000000000000001,
> >
> 0x00000000000406e0","rawCodes":[1,263904],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS
> > at 0x00000000000406e0"},
> > "termination" :
> > {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation
> fault:
> > 11","byProc":"exc handler","byPid":55298},
> > "vmregioninfo" : "0x406e0 is not in any region. Bytes before following
> > region: 4486408480\n REGION TYPE START -
> > END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE
> AT
> > START\n---> \n __TEXT 10b6d3000-10b763000 [ 576K] r-x\/r-x
> > SM=COW ...tents\/MacOS\/R",
> > "extMods" :
> >
> {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
> >
> > "faultingThread" : 0,
> > "threads" :
> >
> [{"triggered":true,"id":2202695,"instructionState":{"instructionStream":{"bytes":[22,0,232,224,92,255,255,72,141,61,137,99,23,0,232,228,217,14,0,15,31,64,0,85,72,137,229,65,87,65,86,65,85,65,84,83,80,73,137,254,232,154,237,247,255,76,99,248,73,105,199,129,28,83,85,72,137,193,72,193,233,63,72,193,248,46,1,200,105,192,5,192,0,0,68,137,249,41,193,72,141,5,161,179,52,0,72,139,0,72,99,201,72,137,77,208,76,139,36,200,72,141,5,196,178,52,0,76,139,40,77,57,236,116,56,15,31,64,0,102,65,131,124,36,6,0,15,133,177,0,0,0,73,139,92,36,32,72,139,115,32,72,131,198,48,76,137,247,232,242,91,22,0,133,192,15,132,130,0,0,0,77,139,100,36,40,77,57,236,117,204,65,128,62,0,15,132,142,0,0,0,76,137,247,232,248,91,22,0,72,61,17],"offset":96}},"threadState":{"r13":{"value":18446744073709551608},"rax":{"value":0},"rflags":{"value":66050},"cpu":{"value":3},"r14":{"value":4937277186},"rsi":{"value":208},"r8":{"value":0},"cr2":{"value":263904},"rdx":{"value":3489660928},"r10":{"value":140468889627856},"r9":{"value":
> >
> 0},"r15":{"value":38277134},"rbx":{"value":1},"trap":{"value":14,"description":"(no
> > mapping for user data
> >
> read)"},"err":{"value":4},"r11":{"value":4499443912,"symbolLocation":0,"symbol":"R_BCProtTop"},"rip":{"value":5031094489,"matchesCrashFrame":1},"rbp":{"value":140701862106416},"rsp":{"value":140701862106368},"r12":{"sourceLine":418,"value":4937274544,"sourceFile":"pipe.c","symbol":"magrittr_init","symbolLocation":0},"rcx":{"value":32988},"flavor":"x86_THREAD_STATE","rdi":{"value":4937277200}},"queue":"com.apple.main-thread","frames":[{"imageOffset":1194201,"sourceFile":"names.c","symbol":"Rf_install","symbolLocation":73,"imageIndex":23},{"imageOffset":10802,"sourceLine":117,"sourceFile":"utils.c","symbol":"magrittr_init_utils","imageIndex":22,"symbolLocation":18},{"imageOffset":9411,"sourceLine":420,"sourceFile":"pipe.c","symbol":"magrittr_init","imageIndex":22,"symbolLocation":19},{"imageOffset":601270,"sourceLine":754,"sourceFile":"dotcode.c","symbol":"R_doDotCall","imageIndex":1,"symbolLocation":5686},{"imageOffset":1033939,"sourceLine":8691,"sourceFile":"eval.c","symbol":"bcEval_
> >
> loop","imageIndex":1,"symbolLocation":146643},{"imageOffset":828276,"sourceLine":7524,"sourceFile":"eval.c","symbol":"bcEval","imageIndex":1,"symbolLocation":628},{"imageOffset":825978,"sourceLine":1167,"sourceFile":"eval.c","symbol":"Rf_eval","imageIndex":1,"symbolLocation":506},{"imageOffset":837049,"sourceLine":2398,"sourceFile":"eval.c","symbol":"R_execClosure","imageIndex":1,"symbolLocation":761},{"imageOffset":833216,"sourceLine":2311,"sourceFile":"eval.c","symbol":"applyClosure_core","imageIndex":1,"symbolLocation":128},{"symbol":"Rf_applyClosure","inline":true,"imageIndex":1,"imageOffset":826661,"symbolLocation":24,"sourceLine":2333,"sourceFile":"eval.c"},{"imageOffset":826661,"sourceLine":1285,"sourceFile":"eval.c","symbol":"Rf_eval","imageIndex":1,"symbolLocation":1189},{"imageOffset":1262209,"sourceLine":398,"sourceFile":"main.c","symbol":"R_ReplDLLdo1","imageIndex":1,"symbolLocation":449},{"imageOffset":125943,"symbol":"run_REngineRmainloop","symbolLocation":263,"imageIn
> > dex":0},{"imageOffset":79712,"symbol":"-[REngine
> >
> runREPL]","symbolLocation":144,"imageIndex":0},{"imageOffset":12040,"symbol":"main","symbolLocation":792,"imageIndex":0},{"imageOffset":25631,"symbol":"start","symbolLocation":1903,"imageIndex":28}]},{"id":2202741,"frames":[{"imageOffset":41618,"symbol":"__select","symbolLocation":10,"imageIndex":29},{"imageOffset":22914,"symbol":"-[RController
> >
> readThread:]","symbolLocation":642,"imageIndex":0},{"imageOffset":361987,"symbol":"__NSThread__start__","symbolLocation":1009,"imageIndex":30},{"imageOffset":25043,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":31},{"imageOffset":7123,"symbol":"thread_start","symbolLocation":15,"imageIndex":31}]},{"id":2202791,"name":"com.apple.NSEventThread","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":29},{"imageOffset":63293,"symbol":"mach_msg2_internal","symbolLocation":78,"imageIndex":29},{"imageOffset":34292,"symbol":"mach_msg_overwrite","symbolLocation":692,"imageIndex":29},{"imageOffset":6314,"symbol":"mach_msg","symbolLocation":19,"imageIndex":29},{"imageOffset":512111,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":145,"imageIndex":32},{"imageOffset":506608,"symbol":"__CFRunLoopRun","symbolLocation":1365,"imageIndex":32},{"imageOffset":503601,"symbol":"CFRunLoopRunSpecific","symbolLocation":560,"imageIndex":32},{"imageOffset":1
> >
> 696757,"symbol":"_NSEventThread","symbolLocation":132,"imageIndex":33},{"imageOffset":25043,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":31},{"imageOffset":7123,"symbol":"thread_start","symbolLocation":15,"imageIndex":31}]},{"id":2203120,"frames":[{"imageOffset":7088,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":31}]},{"id":2203475,"frames":[{"imageOffset":7088,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":31}]},{"id":2203476,"frames":[{"imageOffset":16334,"symbol":"__semwait_signal","symbolLocation":10,"imageIndex":29},{"imageOffset":62853,"symbol":"nanosleep","symbolLocation":196,"imageIndex":34},{"imageOffset":62858,"sourceLine":37,"sourceFile":"thread.c","symbol":"clic_thread_func","imageIndex":19,"symbolLocation":74},{"imageOffset":25043,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":31},{"imageOffset":7123,"symbol":"thread_start","symbolLocation":15,"imageIndex":31}]}],
> >
> > "usedImages" : [
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> > "path" : "\/Applications\/R.app\/Contents\/MacOS\/R",
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> > "path" :
> >
> "\/Library\/Frameworks\/R.framework\/Versions\/4.4-x86_64\/Resources\/lib\/libR.dylib",
> >
> > "name" : "libR.dylib"
> > },
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> >
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> >
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> >
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> >
> > "name" : "rlang.so"
> > },
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> > "size" : 163840,
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> >
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> >
> > "name" : "vctrs.so"
> > },
> > {
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> > "size" : 16384,
> > "uuid" : "d8a9a2f8-098d-327b-a9e3-3d3dad680ddb",
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> "\/Library\/Frameworks\/R.framework\/Versions\/4.4-x86_64\/Resources\/library\/glue\/libs\/glue.so",
> >
> > "name" : "glue.so"
> > },
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> "\/Library\/Frameworks\/R.framework\/Versions\/4.4-x86_64\/Resources\/library\/magrittr\/libs\/magrittr.so",
> >
> > "name" : "magrittr.so"
> > },
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> "\/Library\/Frameworks\/R.framework\/Versions\/4.2\/Resources\/lib\/libR.dylib",
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> > },
> > {
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> > "uuid" : "9f1750d9-e1bf-3a0a-95d8-8c28952d0cf9",
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> "\/Library\/Frameworks\/R.framework\/Versions\/4.2\/Resources\/lib\/libRblas.0.dylib",
> >
> > "name" : "libRblas.0.dylib"
> > },
> > {
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> > "base" : 4948615168,
> > "size" : 2301952,
> > "uuid" : "5b0f7278-9d16-3b60-a413-59eef538e568",
> > "path" :
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> >
> > "name" : "libgfortran.5.dylib"
> > },
> > {
> > "source" : "P",
> > "arch" : "x86_64",
> > "base" : 4940275712,
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> > "uuid" : "856f3e97-eecb-3dde-af45-56aea7758a1e",
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> >
> > "name" : "libquadmath.0.dylib"
> > },
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> > "uuid" : "c1f47ca1-564e-36b8-be6f-7a5fdd88e2c6",
> > "path" :
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> >
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> > "uuid" : "642737ce-21cf-3d87-a7b6-7eea2c080a7e",
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> > },
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> > "path" :
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> > },
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> > "uuid" : "3a3fa85c-f1fe-336c-bf68-924fc947ade3",
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> > },
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> > "size" : 4837360,
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> > "path" :
> >
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> >
> > "name" : "CoreFoundation",
> > "CFBundleVersion" : "1979"
> > },
> > {
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> > "path" :
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> > },
> > {
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> > "uuid" : "d5b303ad-54f4-323b-bbe2-2d0f34c45649",
> > "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
> > "name" : "libsystem_c.dylib"
> > },
> > {
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> > }
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> > },
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> > unallocated=6.0G(100%)\n\n VIRTUAL REGION
> > \nREGION TYPE SIZE COUNT (non-coalesced)
> > \n=========== ======= ======= \nAccelerate
> > framework 256K 2 \nActivity Tracing
> > 256K 1 \nCG backing stores 3072K 4 \nCG
> > image 1800K 46 \nCG raster
> > data 8K 1 \nColorSync 272K 32
> > \nCoreAnimation 184.4M 130
> > \nCoreGraphics 12K 2 \nCoreImage
> > 432K 18 \nCoreUI image data 4588K
> > 36 \nFoundation 56K 2 \nImage IO
> > 484K 16 \nJS JIT generated code
> > 1.0G 3 \nKernel Alloc Once 8K 1
> > \nMALLOC 266.8M 97 \nMALLOC guard page
> > 32K 8 \nMALLOC_NANO (reserved) 384.0M
> > 1 reserved VM address space (unallocated)\nSTACK GUARD
> > 56.0M 6 \nStack 10.5M 6
> > \nVM_ALLOCATE 131.3M 13 \nVM_ALLOCATE
> > (reserved) 3.9G 1 reserved VM address space
> > (unallocated)\nWebKit Malloc 192.0M 5
> > \n__CTF 824 1 \n__DATA
> > 35.2M 594 \n__DATA_CONST 37.3M 379
> > \n__DATA_DIRTY 1712K 209
> > \n__FONT_DATA 2352 1 \n__INFO_FILTER
> > 8 1 \n__LINKEDIT 175.4M
> > 30 \n__OBJC_RO 66.3M 1 \n__OBJC_RW
> > 2013K 1 \n__TEXT 617.8M 611 \ndyld
> > private memory 260K 2 \nmapped
> > file 239.4M 72 \nshared memory
> > 824K 26 \n=========== ======= =======
> > \nTOTAL 7.2G 2359 \nTOTAL, minus
> reserved
> > VM space 3.0G 2359 \n",
> > "legacyInfo" : {
> > "threadTriggered" : {
> > "queue" : "com.apple.main-thread"
> > }
> > },
> > "logWritingSignature" : "6cdfbb491c38e1280753887de64693565d8a493d",
> > "trialInfo" : {
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> > "rolloutId" : "5ffde50ce2aacd000d47a95f",
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> > }
> > ],
> > "experiments" : [
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> > ]
> > }
> > }
> >
> > --
> > Carl Witthoft
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd.mes using cbs.dk Priv: PDalgd using gmail.com
>
>
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