Re: [R-SIG-Mac] R 4.4 crashes loading dplyr
Carl, it shows that you apparently had some ancient version of magrittr installed way back from R 4.2.x. I have no idea why or how you got it, but update.packages(checkBuilt=TRUE) in R 4.4.0 should have fixed it. Cheers, Simon > On 1/05/2024, at 12:32 AM, Carl Witthoft wrote: > > 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: > /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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R 4.4 crashes loading dplyr
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:
/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 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 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.locns <-
> > 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" : 26,
> > "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" :
Re: [R-SIG-Mac] R 4.4 crashes loading dplyr
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 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.locns <-
> 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" : 26,
> "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 TYPESTART -
> 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":"0x0001,
> 0x000406e0","rawCodes":[1,263904],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS
> at 0x000406e0"},
> "termination" :
> {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault:
> 11","byProc":"exc
[R-SIG-Mac] R 4.4 crashes loading dplyr
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.locns <-
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" : 26,
"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 TYPESTART -
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":"0x0001,
0x000406e0","rawCodes":[1,263904],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS
at 0x000406e0"},
"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 TYPESTART -
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" :
