From h@nne@ @end|ng |rom duckdb|@b@@com  Thu Apr  4 09:47:00 2024
From: h@nne@ @end|ng |rom duckdb|@b@@com (=?UTF-8?Q?Hannes_M=C3=BChleisen?=)
Date: Thu, 4 Apr 2024 09:47:00 +0200
Subject: [R-SIG-Mac] Debugging Symbols
Message-ID: <CAMf67Cs19rn2WUcOz5wyra12yqDKWBcJhAt2-Qjp4XhrJa+_sw@mail.gmail.com>

Hello List,

we would like to bring up the topic of debug symbols in the CRAN OSX
binaries again. I realize this has been discussed before [1] and
realize the symbols are there for a reason, but in the duckdb package
their inclusion is particularly problematic.

Currently, the CRAN binary for OSX Arm64 weighs in at a whopping 97 MB
[2]. Inside it lives a 311 MB (uncompressed) folder with the debugging
symbols. When I remove the debugging symbols and re-create the
compressed tarball, its compressed size goes down to 11 MB, a pretty
drastic difference.

We are getting feedback from users that the package is too large for
them to be useful, so we would really like to improve this situation.

Would it perhaps be possible to exclude the duckdb from the inclusion
of the debug symbols? Is there anything we as package authors can do
here? There also may be other packages where this is relevant, e.g.
arrow would go down from 82 MB to 12 MB.

Best and thanks

Hannes

[1] https://stat.ethz.ch/pipermail/r-sig-mac/2022-June/014500.html
[2] curl -I https://cran.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/duckdb_0.10.1.tgz


From jeroenoom@ @end|ng |rom gm@||@com  Thu Apr  4 10:41:55 2024
From: jeroenoom@ @end|ng |rom gm@||@com (Jeroen Ooms)
Date: Thu, 4 Apr 2024 10:41:55 +0200
Subject: [R-SIG-Mac] Debugging Symbols
In-Reply-To: <CAMf67Cs19rn2WUcOz5wyra12yqDKWBcJhAt2-Qjp4XhrJa+_sw@mail.gmail.com>
References: <CAMf67Cs19rn2WUcOz5wyra12yqDKWBcJhAt2-Qjp4XhrJa+_sw@mail.gmail.com>
Message-ID: <CABFfbXsr+PBa8Tb=UWn=cDvCjcrW72txQ_LHWv8Noc2dqHZ+jA@mail.gmail.com>

On Thu, Apr 4, 2024 at 9:47?AM Hannes M?hleisen <hannes at duckdblabs.com> wrote:
>
> Hello List,
>
> we would like to bring up the topic of debug symbols in the CRAN OSX
> binaries again. I realize this has been discussed before [1] and
> realize the symbols are there for a reason, but in the duckdb package
> their inclusion is particularly problematic.
>
> Currently, the CRAN binary for OSX Arm64 weighs in at a whopping 97 MB
> [2]. Inside it lives a 311 MB (uncompressed) folder with the debugging
> symbols. When I remove the debugging symbols and re-create the
> compressed tarball, its compressed size goes down to 11 MB, a pretty
> drastic difference.
>
> We are getting feedback from users that the package is too large for
> them to be useful, so we would really like to improve this situation.

FWIW, the binaries on https://duckdb.r-universe.dev/duckdb are built
with _R_SHLIB_STRIP_: TRUE and those are indeed around 10M (both for
Linux and MacOS).

For similar reasons p3m (formerly rspm) also strips debugging symbols
these days, e.g:
https://p3m.dev/cran/latest/bin/macosx/big-sur-x86_64/contrib/4.3/duckdb_0.10.1.tgz
See also this comment:
https://github.com/rocker-org/rocker-versioned2/issues/340#issuecomment-1301157428

I agree it would be nice for a package to be able to opt-out
altogether, including on CRAN. I don't think that is possible right
now.


From gp@ct @end|ng |rom proton@me  Thu Apr  4 15:13:24 2024
From: gp@ct @end|ng |rom proton@me (Gregory)
Date: Thu, 04 Apr 2024 13:13:24 +0000
Subject: [R-SIG-Mac] How to correct tcltk path?
Message-ID: <UdG4uAUUIpTgWoD0rA_4fTstBzyBqI2m5x79nk73fTshzpbBFwxsPianGRXLtouhK271ywHZHUrCMW834OnVxfJEohcE7UIAfDIjSiCRMeU=@proton.me>

Hello,

I'm having an issue with R looking for tcltk in the wrong place. Whenever I start R, I get a message: tcltk DLL is linked to '/opt/X11/lib/libX11.6.dylib'. However, there is no /opt/X11 on my system and tcltk is really in /opt/R/arm64, where the R binary installer put it. Where is R getting the /opt/X11 path and how do I correct that? So far I've tried exporting DYLD_LIBRARY_PATH=opt/R/arm64:$DYLD_LIBRARY_PATH to my environment in my zprofile, but that hasn't worked.

Possibly relevant details:
M2 MacBook Pro, MacOS Sonoma 14.4.1
R.version 4.3.3 installed with binary installer from CRAN.

Thanks in advance,
Gregory

Sent with [Proton Mail](https://proton.me/) secure email.
	[[alternative HTML version deleted]]


From k@@perd@n|e|h@n@en @end|ng |rom gm@||@com  Thu Apr  4 18:46:38 2024
From: k@@perd@n|e|h@n@en @end|ng |rom gm@||@com (Kasper Daniel Hansen)
Date: Thu, 4 Apr 2024 12:46:38 -0400
Subject: [R-SIG-Mac] How to correct tcltk path?
In-Reply-To: <UdG4uAUUIpTgWoD0rA_4fTstBzyBqI2m5x79nk73fTshzpbBFwxsPianGRXLtouhK271ywHZHUrCMW834OnVxfJEohcE7UIAfDIjSiCRMeU=@proton.me>
References: <UdG4uAUUIpTgWoD0rA_4fTstBzyBqI2m5x79nk73fTshzpbBFwxsPianGRXLtouhK271ywHZHUrCMW834OnVxfJEohcE7UIAfDIjSiCRMeU=@proton.me>
Message-ID: <CAC2h7us4-r3ROmCtQhqora_HTGwdf0BUT-YqFKvKL-NM2Uq47A@mail.gmail.com>

You need to install XQuartz. This is IMO stated somewhat clearly at
  https://cran.r-project.org/bin/macosx/
("somewhat", because - as always - it seems pretty clear when you know what
its trying to say)

Kasper

On Thu, Apr 4, 2024 at 9:13?AM Gregory via R-SIG-Mac <
r-sig-mac at r-project.org> wrote:

> Hello,
>
> I'm having an issue with R looking for tcltk in the wrong place. Whenever
> I start R, I get a message: tcltk DLL is linked to
> '/opt/X11/lib/libX11.6.dylib'. However, there is no /opt/X11 on my system
> and tcltk is really in /opt/R/arm64, where the R binary installer put it.
> Where is R getting the /opt/X11 path and how do I correct that? So far I've
> tried exporting DYLD_LIBRARY_PATH=opt/R/arm64:$DYLD_LIBRARY_PATH to my
> environment in my zprofile, but that hasn't worked.
>
> Possibly relevant details:
> M2 MacBook Pro, MacOS Sonoma 14.4.1
> R.version 4.3.3 installed with binary installer from CRAN.
>
> Thanks in advance,
> Gregory
>
> Sent with [Proton Mail](https://proton.me/) secure email.
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>


-- 
Best,
Kasper

	[[alternative HTML version deleted]]


From r|p|ey @end|ng |rom @t@t@@ox@@c@uk  Thu Apr  4 19:26:20 2024
From: r|p|ey @end|ng |rom @t@t@@ox@@c@uk (Prof Brian Ripley)
Date: Thu, 4 Apr 2024 18:26:20 +0100
Subject: [R-SIG-Mac] How to correct tcltk path?
In-Reply-To: <CAC2h7us4-r3ROmCtQhqora_HTGwdf0BUT-YqFKvKL-NM2Uq47A@mail.gmail.com>
References: <UdG4uAUUIpTgWoD0rA_4fTstBzyBqI2m5x79nk73fTshzpbBFwxsPianGRXLtouhK271ywHZHUrCMW834OnVxfJEohcE7UIAfDIjSiCRMeU=@proton.me>
 <CAC2h7us4-r3ROmCtQhqora_HTGwdf0BUT-YqFKvKL-NM2Uq47A@mail.gmail.com>
Message-ID: <efb06032-8a7e-428d-aba2-9b2b3eb6eef6@stats.ox.ac.uk>

On 04/04/2024 17:46, Kasper Daniel Hansen wrote:
> You need to install XQuartz. This is IMO stated somewhat clearly at
>    https://cran.r-project.org/bin/macosx/
> ("somewhat", because - as always - it seems pretty clear when you know what
> its trying to say)

And definitely clear in the R-admin manual:

"Various parts of the build require XQuartz to be installed: see 
https://www.xquartz.org/releases/.20 These include the tcltk package and 
the X11 graphics device: attempting to use these without XQuartz will 
remind you."

Without the actual messages, I cannot check if that corresponds to what 
the OP saw.  But it probably was from

                 message("tcltk DLL is linked to ", shQuote(this))
                 stop("X11 library is missing: install XQuartz from 
www.xquartz.org",

and he omitted the second line ....



> 
> Kasper
> 
> On Thu, Apr 4, 2024 at 9:13?AM Gregory via R-SIG-Mac <
> r-sig-mac at r-project.org> wrote:
> 
>> Hello,
>>
>> I'm having an issue with R looking for tcltk in the wrong place. Whenever
>> I start R, I get a message: tcltk DLL is linked to
>> '/opt/X11/lib/libX11.6.dylib'. However, there is no /opt/X11 on my system
>> and tcltk is really in /opt/R/arm64, where the R binary installer put it.
>> Where is R getting the /opt/X11 path and how do I correct that? So far I've
>> tried exporting DYLD_LIBRARY_PATH=opt/R/arm64:$DYLD_LIBRARY_PATH to my
>> environment in my zprofile, but that hasn't worked.
>>
>> Possibly relevant details:
>> M2 MacBook Pro, MacOS Sonoma 14.4.1
>> R.version 4.3.3 installed with binary installer from CRAN.
>>
>> Thanks in advance,
>> Gregory
>>
>> Sent with [Proton Mail](https://proton.me/) secure email.
>>          [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
> 
> 

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford


From ce||ocgw @end|ng |rom gm@||@com  Tue Apr 30 00:55:38 2024
From: ce||ocgw @end|ng |rom gm@||@com (Carl Witthoft)
Date: Mon, 29 Apr 2024 18:55:38 -0400
Subject: [R-SIG-Mac] R 4.4 crashes loading dplyr
Message-ID: <CANkkNcg20E9Qj+W8jf=sPkE+v2zG8UJWq4kb8A517TeHAUS2vQ@mail.gmail.com>

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 --

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4.4.0 GUI 1.80 Big Sur Intel
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-- 
Carl Witthoft

	[[alternative HTML version deleted]]


From pd@|gd @end|ng |rom gm@||@com  Tue Apr 30 10:48:07 2024
From: pd@|gd @end|ng |rom gm@||@com (peter dalgaard)
Date: Tue, 30 Apr 2024 10:48:07 +0200
Subject: [R-SIG-Mac] R 4.4 crashes loading dplyr
In-Reply-To: <CANkkNcg20E9Qj+W8jf=sPkE+v2zG8UJWq4kb8A517TeHAUS2vQ@mail.gmail.com>
References: <CANkkNcg20E9Qj+W8jf=sPkE+v2zG8UJWq4kb8A517TeHAUS2vQ@mail.gmail.com>
Message-ID: <02808911-83F7-4106-8FEA-E74C6CE0DCB2@gmail.com>

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 at 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
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> Total=6.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%)
> 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" : {
>  "rollouts" : [
>    {
>      "rolloutId" : "5ffde50ce2aacd000d47a95f",
>      "factorPackIds" : {
> 
>      },
>      "deploymentId" : 240000372
>    },
>    {
>      "rolloutId" : "61675b89201f677a9a4cbd65",
>      "factorPackIds" : {
>        "HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
>      },
>      "deploymentId" : 240000112
>    }
>  ],
>  "experiments" : [
> 
>  ]
> }
> }
> 
> -- 
> Carl Witthoft
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at 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 at cbs.dk  Priv: PDalgd at gmail.com


From ce||ocgw @end|ng |rom gm@||@com  Tue Apr 30 14:32:41 2024
From: ce||ocgw @end|ng |rom gm@||@com (Carl Witthoft)
Date: Tue, 30 Apr 2024 08:32:41 -0400
Subject: [R-SIG-Mac] R 4.4 crashes loading dplyr
In-Reply-To: <02808911-83F7-4106-8FEA-E74C6CE0DCB2@gmail.com>
References: <CANkkNcg20E9Qj+W8jf=sPkE+v2zG8UJWq4kb8A517TeHAUS2vQ@mail.gmail.com>
 <02808911-83F7-4106-8FEA-E74C6CE0DCB2@gmail.com>
Message-ID: <CANkkNcgC2K3Hq4UYktAFf9uFDDobWdcZ1S7mdrVZA3QXBobEkA@mail.gmail.com>

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 at 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 at 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" : [
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64",
> >    "base" : 4486672384,
> >    "CFBundleShortVersionString" : "R 4.4.0 GUI 1.80 Big Sur Intel build",
> >    "CFBundleIdentifier" : "org.R-project.R",
> >    "size" : 589824,
> >    "uuid" : "8311af3a-aa38-355b-acef-bbecbdb69a11",
> >    "path" : "\/Applications\/R.app\/Contents\/MacOS\/R",
> >    "name" : "R",
> >    "CFBundleVersion" : "8376"
> >  },
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64",
> >    "base" : 4493672448,
> >    "size" : 4472832,
> >    "uuid" : "55f59695-e07b-358e-9273-5927a1204110",
> >    "path" :
> >
> "\/Library\/Frameworks\/R.framework\/Versions\/4.4-x86_64\/Resources\/lib\/libR.dylib",
> >
> >    "name" : "libR.dylib"
> >  },
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64",
> >    "base" : 4488380416,
> >    "size" : 180224,
> >    "uuid" : "4b8cfff6-611d-3cfa-ac4a-9f5de50f9039",
> >    "path" :
> >
> "\/Library\/Frameworks\/R.framework\/Versions\/4.4-x86_64\/Resources\/lib\/libRblas.0.dylib",
> >
> >    "name" : "libRblas.0.dylib"
> >  },
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64",
> >    "base" : 4500307968,
> >    "size" : 2883584,
> >    "uuid" : "1199fc6b-be2f-3ae9-abd5-eca4d24bc45d",
> >    "path" :
> >
> "\/Library\/Frameworks\/R.framework\/Versions\/4.4-x86_64\/Resources\/lib\/libgfortran.5.dylib",
> >
> >    "name" : "libgfortran.5.dylib"
> >  },
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64",
> >    "base" : 4489015296,
> >    "size" : 278528,
> >    "uuid" : "fa785330-1a6a-3c4f-a00a-d048a122de07",
> >    "path" :
> >
> "\/Library\/Frameworks\/R.framework\/Versions\/4.4-x86_64\/Resources\/lib\/libquadmath.0.dylib",
> >
> >    "name" : "libquadmath.0.dylib"
> >  },
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64",
> >    "base" : 4488626176,
> >    "size" : 98304,
> >    "uuid" : "da9b09fe-e0a8-3193-a338-1eb9a68c9fe2",
> >    "path" :
> >
> "\/Library\/Frameworks\/R.framework\/Versions\/4.4-x86_64\/Resources\/lib\/libgcc_s.1.1.dylib",
> >
> >    "name" : "libgcc_s.1.1.dylib"
> >  },
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64h",
> >    "base" : 4562251776,
> >    "size" : 65536,
> >    "uuid" : "2dd94238-d463-3bba-bb4e-e65afabe8a76",
> >    "path" : "\/usr\/lib\/libobjc-trampolines.dylib",
> >    "name" : "libobjc-trampolines.dylib"
> >  },
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64",
> >    "base" : 4912177152,
> >    "CFBundleShortVersionString" : "1.0",
> >    "CFBundleIdentifier" : "com.apple.CloudDocsFileProvider",
> >    "size" : 32768,
> >    "uuid" : "ff555cb2-b4f8-36d7-a136-7079179a10ef",
> >    "path" :
> >
> "\/System\/Library\/Frameworks\/FileProvider.framework\/OverrideBundles\/CloudDocsFileProvider.bundle\/Contents\/MacOS\/CloudDocsFileProvider",
> >
> >    "name" : "CloudDocsFileProvider",
> >    "CFBundleVersion" : "1553.141.1"
> >  },
> >  {
> >    "source" : "P",
> >    "arch" : "x86_64",
> >    "base" : 4914155520,
> >    "CFBundleShortVersionString" : "855.140.6",
> >    "CFBundleIdentifier" : "com.apple.FileProviderOverride",
> >    "size" : 32768,
> >    "uuid" : "dfea2018-d344-371c-979c-bceb40d6fa63",
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> > 824K       26 \n===========                     ======= =======
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> > }
> > }
> >
> > --
> > Carl Witthoft
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at 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 at cbs.dk  Priv: PDalgd at gmail.com
>
>

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