Re: [R-SIG-Mac] R 4.4 crashes loading dplyr

[Carl Witthoft]

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
> 

[R-SIG-Mac] R 4.4 crashes loading dplyr

[Carl Witthoft]

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-- 
Carl Witthoft

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Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 245, Issue 2

[Carl Witthoft]

That makes me wonder if something untoward is in your .login, .bashrc, 
or similar startup files invoked by Terminal.



On 8/1/23 6:00 AM, r-sig-mac-requ...@r-project.org wrote:

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Today's Topics:

1. Re:  Rcmdr (Sabrina Droussy)

--

Message: 1
Date: Tue, 1 Aug 2023 02:27:58 +0200
From: Sabrina Droussy 
To: John Fox 
Cc: Simon Urbanek , r-sig-mac R
, Steve Landers 
Subject: Re: [R-SIG-Mac] Rcmdr
Message-ID: <8d583d0a-e5c1-444f-a1c7-ce1aa4cc5...@gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello !

Many thanks for your answers. I found a way to open Rcmdr maybe it can help if 
someone has an issue with that. I had to open R with the Xquartz’s terminal 
it’s weird because it wasn’t like that some months ago …

Thanks again

Sabrina


Le 1 août 2023 à 01:27, John Fox  a écrit :

Hello Simon,

Actually the Rcmdr *does* import (and use) the tcltk2 package, but I've had no 
other report of this kind of problem and haven't observed it myself.

Best,
John

--
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://www.john-fox.ca/

On 2023-07-31 6:46 p.m., Simon Urbanek wrote:

Caution: External email.
Agreed, no problem here even with Rcmdr in older R 4.2.0. As Peter said, Rcmdr 
doesn't use tcltk2 so I'm sure there is a lot you're omitting here. If it 
doubt, make sure you don't load some old workspace and have the latest versions 
of all packages, e.g. via update.packages(ask=FALSE).
Cheers,
Simon

On 1/08/2023, at 1:18 AM, peter dalgaard  wrote:

Hum.. Not happening here with 4.3.1 from CRAN. Why are you getting errors 
relating to 4.2? Also puzzling is library/tcltk2, which I don't seem to have 
(only tcltk).

A hunch is that the tcltk2 package could be involved, but even installing that, 
I don't see a directory of that name under R.framework.

- pd


On 22 Jul 2023, at 14:20 , Sabrina Droussy  wrote:




Hello,
I have a big problem with R. I hope you can help me please.
I didn’t use R for some months and wanted to use it again to prepare an exam. I 
can’t open Rcmdr anymore. I tried several things : install packages, delete and 
reinstall R. It isn’t working.

Here is the message I get :
error reading package index file / Library/ Frameworks / R. Framework/ 
Versions/ 4.2/ Resources/ library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: 
can’t find package tile
error reading package index file / Library/ Frameworks / R. Framework/ 
Versions/ 4.2/ Resources/ 
library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested 
evaluations (infinite loop ? )

Best regards

Envoyé de mon iPhone


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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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End of R-SIG-Mac Digest, Vol 245, Issue 2
*


--
Carl Witthoft
personal: c...@witthoft.com
The Witthoft Group, Consulting
https://witthoftgroup.weebly.com/

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Re: [R-SIG-Mac] 4.3.1 fails to load

[Carl Witthoft]

Problem fixed but not solved.
On previous updates to R, I always copied all the packages (that aren't 
part of the base installation) from the previous version's Library 
folder to the new version's Library folder, and then updated when I 
actually use them.
The fix for my problem was to run "Update All" before trying to load any 
library.
The problem remains not-solved, because (prior to updating everything), 
any attempt to run


>>  library(any_package)

would cause  failure similar to those I posted previously.  So, while 
I'm reasonably confident that R 4.3.1 doesn't play nicely with 4.2 - 
level libraries, I most definitely cannot point to any particular 
library.  The deepest level of the traceback report for  ggplot2 was


1: dyn.load(file, DLLpath = DLLpath, ...)

but when trying to load gmp, get the traceback quoted below.


carl




On 7/22/23 8:09 PM, r-sig-mac-requ...@r-project.org wrote:

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Today's Topics:

1.  R 4.3.1 fails to load (Carl Witthoft)
2. Re:  R 4.3.1 fails to load (David Winsemius)
3. Re:  R 4.3.1 fails to load (David Winsemius)
4. Re:  R 4.3.1 fails to load (Carl Witthoft)
5. Re:  R 4.3.1 fails to load (Duncan Murdoch)

--

Message: 1
Date: Sat, 22 Jul 2023 16:29:59 -0400
From: Carl Witthoft 
To: "r-sig-mac@r-project.org" 
Subject: [R-SIG-Mac] R 4.3.1 fails to load
Message-ID: 
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Neither R.app Gui nor R from command line will work.
This is 4.3.1 ,  MacOS 13.4  on an x86 (and yes, that's the version I
installed).

   Heres the error traceback from the command line:

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
   1: as.bigz(NA)
   2: fun(libname, pkgname)
   3: doTryCatch(return(expr), name, parentenv, handler)
   4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5: tryCatchList(expr, classes, parentenv, handlers)
   6: tryCatch(fun(libname, pkgname), error = identity)
   7: runHook(".onLoad", env, package.lib, package)
   8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
vI[[j]])
   9: asNamespace(ns)
10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
11: loadNamespace(package, lib.loc)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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)})
16: library(cgwtools)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace




--
Carl Witthoft
personal: c...@witthoft.com
The Witthoft Group, Consulting
https://witthoftgroup.weebly.com/

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Re: [R-SIG-Mac] R 4.3.1 fails to load

[Carl Witthoft]

On 7/22/23 4:42 PM, David Winsemius wrote:

And I forgot to ask  what's in your .Rprofile file?

Nothing that ever caused trouble in the past, but FWIW, here it is:

setwd('~/Rgames')
#print('diagnostic: ~/.Rprofile ran')
#doubt this'l work... 'quartz' not recognized by startup sequence
#quartz(family='Times',points=24)
#I think fontsize is OK on the iMac -- needed par() on 10.4
#library(graphics)
#par(cex=0.7)
#I don't know what mechanism "stuffed" a value inside the 'function()" 
inside

# the definition of 'prev' , but putting in ellipsis cleaned it up
invisible(makeActiveBinding("prev", function(...) .Last.value, .GlobalEnv))

#change this list if other items desired
srclist<-c( 'mytoys.R')
for (dafile in srclist) {
source(dafile)
}
rm(dafile)
rm(srclist)
# load things I always want
if (length(find.package('cgwtools'))) library(cgwtools)


# will this fix history
#.Last <- function() if(interactive()) 
try(savehistory("~/Rgames/.Rhistory"))

# change prompt
options(prompt=paste(basename(getwd()),'> ',sep=""))

cat("Gosh, boss, it's great to see you again.\n\n")
print(fortunes::fortune())


On 7/22/23 13:29, Carl Witthoft wrote:

Neither R.app Gui nor R from command line will work.
This is 4.3.1 ,  MacOS 13.4  on an x86 (and yes, that's the version I 
installed).


 Heres the error traceback from the command line:

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: as.bigz(NA)
 2: fun(libname, pkgname)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(fun(libname, pkgname), error = identity)
 7: runHook(".onLoad", env, package.lib, package)
 8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck 
= vI[[j]])

 9: asNamespace(ns)
10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)

11: loadNamespace(package, lib.loc)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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)})

16: library(cgwtools)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace




--
Carl Witthoft
personal: c...@witthoft.com
The Witthoft Group, Consulting
https://witthoftgroup.weebly.com/

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[R-SIG-Mac] R 4.3.1 fails to load

[Carl Witthoft]

Neither R.app Gui nor R from command line will work.
This is 4.3.1 ,  MacOS 13.4  on an x86 (and yes, that's the version I 
installed).


 Heres the error traceback from the command line:

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: as.bigz(NA)
 2: fun(libname, pkgname)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(fun(libname, pkgname), error = identity)
 7: runHook(".onLoad", env, package.lib, package)
 8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = 
vI[[j]])

 9: asNamespace(ns)
10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)

11: loadNamespace(package, lib.loc)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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)})

16: library(cgwtools)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace


--
Carl Witthoft
personal: c...@witthoft.com
The Witthoft Group, Consulting
https://witthoftgroup.weebly.com/

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[R-SIG-Mac] problem with editor in R.app GUI

[Carl Witthoft]

Hi,
This is difficult to trigger consistently, which is why I'm not posting 
a file that causes it.  Here's the issue:


If I have a file with a function that has many bracket pairs , {  } , 
e.g., for-loops or if - else constructs,  and  there's a mismatch 
somewhere in the code,  I try to simplify the view by using the little 
triangles to "fold up" internal bracket pairs.
But every now and then this causes an immediate GUI crash. My suspicion 
is that the tool is trying to search past the beginning  -- or end -- of 
the file and never finds the matching bracket, but that's just a guess.


Here is, I think, the crash log contents

Process:   R [84853]
Path:  /Applications/R.app/Contents/MacOS/R
Identifier:org.R-project.R
Version:   R 4.2.2 GUI 1.79 High Sierra build (8160)
Code Type: X86-64 (Native)
Parent Process:??? [1]
Responsible:   R [84853]
User ID:   502

Date/Time: 2023-05-29 19:27:42.116 -0400
OS Version:macOS 11.7.4 (20G1120)
Report Version:12
Anonymous UUID:CD7A5AA1-F53E-DB32-2D97-4F4C0CC4EC41

Sleep/Wake UUID:   72994ECF-95D4-46A4-9280-4B345968CE0F

Time Awake Since Boot: 200 seconds
Time Since Wake:   7700 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Segmentation fault: 11
Termination Reason:Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [84853]

VM Regions Near 0:
-->
__TEXT  1078c-107948000[  544K] r-x/r-x 
SM=COW  /Applications/R.app/Contents/MacOS/R


Thread 0 Crashed:: Dispatch queue: com.apple.main-thread

Thread 1:: JavaScriptCore bmalloc scavenger
0   libsystem_kernel.dylib  0x7fff20647cce __psynch_cvwait + 10
1   libsystem_pthread.dylib   	0x7fff2067ae49 _pthread_cond_wait 
+ 1298
2   libc++.1.dylib	0x7fff205e3d72 
std::__1::condition_variable::wait(std::__1::unique_lock&) 
+ 18
3   com.apple.JavaScriptCore  	0x7fff3776f894 void 
std::__1::condition_variable_any::wait 
>(std::__1::unique_lock&) + 84
4   com.apple.JavaScriptCore  	0x7fff3777435b 
bmalloc::Scavenger::threadRunLoop() + 331
5   com.apple.JavaScriptCore  	0x7fff37773ee9 
bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 9
6   com.apple.JavaScriptCore  	0x7fff37776a77 void* 
std::__1::__thread_proxystd::__1::default_delete >, void 
(*)(bmalloc::Scavenger*), bmalloc::Scavenger*> >(void*) + 39

7   libsystem_pthread.dylib 0x7fff2067a8fc _pthread_start + 224
8   libsystem_pthread.dylib 0x7fff20676443 thread_start + 15

Thread 2:
0   libsystem_kernel.dylib  0x7fff2064d646 __select + 10
1   org.R-project.R   	0x0001078c5d42 -[RController 
readThread:] + 610
2   com.apple.Foundation  	0x7fff214fb497 
__NSThread__start__ + 1068

3   libsystem_pthread.dylib 0x7fff2067a8fc _pthread_start + 224
4   libsystem_pthread.dylib 0x7fff20676443 thread_start + 15

Thread 3:: com.apple.NSEventThread
0   libsystem_kernel.dylib  0x7fff206452aa mach_msg_trap + 10
1   libsystem_kernel.dylib  0x7fff2064561c mach_msg + 60
2   com.apple.CoreFoundation  	0x7fff20772f0f 
__CFRunLoopServiceMachPort + 316

3   com.apple.CoreFoundation0x7fff207715ef __CFRunLoopRun + 1328
4   com.apple.CoreFoundation  	0x7fff207709fc 
CFRunLoopRunSpecific + 563

5   com.apple.AppKit0x7fff230ffbba _NSEventThread + 124
6   libsystem_pthread.dylib 0x7fff2067a8fc _pthread_start + 224
7   libsystem_pthread.dylib 0x7fff20676443 thread_start + 15

Thread 4:: LocalStorage
0   libsystem_kernel.dylib  0x7fff20647cce __psynch_cvwait + 10
1   libsystem_pthread.dylib   	0x7fff2067ae49 _pthread_cond_wait 
+ 1298
2   com.apple.JavaScriptCore  	0x7fff376fae60 
WTF::ParkingLot::parkConditionallyImpl(void const*, 
WTF::ScopedLambda const&, WTF::ScopedLambda const&, 
WTF::TimeWithDynamicClockType const&) + 3760
3   com.apple.WebKitLegacy	0x7fff34ee33ea bool 
WTF::Condition::waitUntil(WTF::Lock&, 
WTF::TimeWithDynamicClockType const&) + 154
4   com.apple.WebKitLegacy	0x7fff34ee6443 
std::__1::unique_ptr, 
std::__1::default_delete > > 
WTF::MessageQueue 
>::waitForMessageFilteredWithTimeout >::waitForMessage()::'lambda'(WTF::Function const&)>(WTF::MessageQueueWaitResult&, WTF::MessageQueue >::waitForMessage()::'lambda'(WTF::Function const&)&&, WTF::Seconds) + 147
5   com.apple.WebKitLegacy	0x7fff34ee5ab6 
WebCore::StorageThread::threadEntryPoint() + 86
6   com.apple.JavaScriptCore   

[R-SIG-Mac] minor bugfix request in R Help window

[Carl Witthoft]

Hi,
Just a nit that annoys me.  If I do "?some_func"  and then, in the R 
Help window,  I do a word search,  the search box at the bottom of the 
window covers up the  footer containing the link to the package "Index" 
page.  I have to close the search box to see that link.
Any chance the Help page can be configured so opening the search box 
doesn't cover up this stuff?


Thanks
Carl

--
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personal: c...@witthoft.com
The Witthoft Group, Consulting
https://witthoftgroup.weebly.com/

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Re: [R-SIG-Mac] making rattle run

[Carl Witthoft]

tes (6.1 MB)
==
downloaded 6.1 MB



library(rattle)

Loading required package: tibble
Loading required package: bitops
Rattle: A free graphical interface for data science with R.
Version 5.5.1 Copyright (c) 2006-2021 Togaware Pty Ltd.
Type 'rattle()' to shake, rattle, and roll your data.

rattle()

Loading required package: RGtk2
Error in dyn.load(file, DLLpath = DLLpath, ...)



For me just now R 4.2.2 successfully downloaded

trying URL
'
https://cran.wu.ac.at/bin/macosx/big-sur-arm64/contrib/4.2/rattle_5.5.1.tgz
'



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[R-SIG-Mac] spontaneous window switches?

[Carl Witthoft]

Just wondering if anyone else has observed the R-GUI spontaneously 
changing which window is in front & has keyboard focus?


I've even seen this happen when the gui is not the foreground application.
R 4.2.2 GUI 1.79 High Sierra build (8160)

MacOS  11.6.8 BigSur

regards,
Carl
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[R-SIG-Mac] another R crash issue

[Carl Witthoft]

This may be the fault of the `gmp` library, but posting to r-sig as well 
just in case.


Mac OS 11.6.8  , R 4.2.2


Consider the following work:

Rgames> foo <- NULL
Rgames> rbind(foo,c(1,3))
 [,1] [,2]
[1,]13
Rgames> foo <- NULL
Rgames> # rbind(foo,as.bigz(c(1,3)))  ## instant crash


Further playing around suggests that , given that  as.bigz(NULL) returns 
a  "bigz(0) " empty object,   gmp is really unhappy trying to do almost 
anything with said object.



regards,
Carl


Crash log follows
Process:   R [11657]
Path:  /Applications/R.app/Contents/MacOS/R
Identifier:org.R-project.R
Version:   R 4.2.2 GUI 1.79 High Sierra build (8160)
Code Type: X86-64 (Native)
Parent Process:??? [1]
Responsible:   R [11657]
User ID:   502

Date/Time: 2022-11-16 19:42:41.462 -0500
OS Version:macOS 11.6.8 (20G730)
Report Version:12
Anonymous UUID:B755C094-C366-46AB-8EEA-9D3B8E7B388D

Sleep/Wake UUID:   D725679E-AF7A-4203-8EA3-B313AA2846F5

Time Awake Since Boot: 98000 seconds
Time Since Wake:   2100 seconds

System Integrity Protection: enabled

Crashed Thread:0  Dispatch queue: com.apple.main-thread

Exception Type:EXC_ARITHMETIC (SIGFPE)
Exception Codes:   EXC_I386_DIV (divide by zero)
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Floating point exception: 8
Termination Reason:Namespace SIGNAL, Code 0x8
Terminating Process:   exc handler [11657]

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   gmp.so	0x0001149159c2 
math::Matrix::nCols() const + 34
1   gmp.so	0x00011491e5af 
matrixz::bigint_transpose(bigvec&) + 47

2   gmp.so  0x00011491f8be biginteger_rbind + 
158
3   libR.dylib	0x000104b3f8dc R_doDotCall + 1420 
(dotcode.c:601)
4   libR.dylib	0x000104b8b7ed bcEval + 104269 
(eval.c:7692)
5   libR.dylib	0x000104b71a01 Rf_eval + 385 
(eval.c:748)

6   libR.dylib  0x000104b91839 R_execClosure + 2169
7   libR.dylib	0x000104b90627 Rf_applyClosure + 
471 (eval.c:1844)
8   libR.dylib	0x000104af61db do_bind + 1051 
(bind.c:1118)
9   libR.dylib	0x000104bdbbfa do_internal + 362 
(names.c:1399)
10  libR.dylib	0x000104b7920d bcEval + 29037 
(eval.c:7156)
11  libR.dylib	0x000104b71a01 Rf_eval + 385 
(eval.c:748)

12  libR.dylib  0x000104b91839 R_execClosure + 2169
13  libR.dylib	0x000104b90627 Rf_applyClosure + 
471 (eval.c:1844)
14  libR.dylib	0x000104b71ebb Rf_eval + 1595 
(eval.c:871)
15  libR.dylib	0x000104b95821 do_eval + 625 
(eval.c:3366)
16  libR.dylib	0x000104b79035 bcEval + 28565 
(eval.c:7136)
17  libR.dylib	0x000104b71a01 Rf_eval + 385 
(eval.c:748)

18  libR.dylib  0x000104b91839 R_execClosure + 2169
19  libR.dylib	0x000104b90627 Rf_applyClosure + 
471 (eval.c:1844)
20  libR.dylib	0x000104b7892e bcEval + 26766 
(eval.c:7104)
21  libR.dylib	0x000104b71a01 Rf_eval + 385 
(eval.c:748)

22  libR.dylib  0x000104b91839 R_execClosure + 2169
23  libR.dylib	0x000104b90627 Rf_applyClosure + 
471 (eval.c:1844)
24  libR.dylib	0x000104b7892e bcEval + 26766 
(eval.c:7104)
25  libR.dylib	0x000104b71a01 Rf_eval + 385 
(eval.c:748)

26  libR.dylib  0x000104b91839 R_execClosure + 2169
27  libR.dylib	0x000104b90627 Rf_applyClosure + 
471 (eval.c:1844)
28  libR.dylib	0x000104b71ebb Rf_eval + 1595 
(eval.c:871)
29  libR.dylib	0x000104bc9351 R_ReplDLLdo1 + 449 
(main.c:396)
30  org.R-project.R   	0x0001049b2e15 
run_REngineRmainloop + 261
31  org.R-project.R   	0x0001049a798f -[REngine runREPL] 
+ 143

32  org.R-project.R 0x000104997288 main + 792
33  libdyld.dylib   0x7fff20913f3d start + 1

Thread 1:: JavaScriptCore bmalloc scavenger
0   libsystem_kernel.dylib  0x7fff208c5cce __psynch_cvwait + 10
1   libsystem_pthread.dylib   	0x7fff208f8e49 _pthread_cond_wait 
+ 1298
2   libc++.1.dylib	0x7fff20861d72 
std::__1::condition_variable::wait(std::__1::unique_lock&) 
+ 18
3   com.apple.JavaScriptCore  	0x7fff379ea894 void 
std::__1::condition_variable_any::wait 
>(std::__1::unique_lock&) + 84
4   com.apple.JavaScriptCore  	0x7fff379ef35b 
bmalloc::Scavenger::thr

Re: [R-SIG-Mac] [External] Re: problem with Rprof

[Carl Witthoft]

 by another 
thread. We could also report such situation to indicate that the 
interval is unreasonable. But it would be good first to know for sure 
what caused the problem.


How can you check anything if pthread functions fail? If a simple 
pthead_self() crashes then I don't see how you can do anything since 
we don't even know what thread we are, cannot call mutexes etc.


Cheers,
Simon



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[R-SIG-Mac] problem with Rprof

[Carl Witthoft]

Wondering if this is a hiccup in  R-mac 4.2.1 (running under 11.6.8 Big 
Sur), or a bug in Rprof:


If I try to set a very small time interval,

>>  Rprof(interval = 0.01)  ,
R crashes.

Crash report follows:

Process:   R [54439]
Path:  /Applications/R.app/Contents/MacOS/R
Identifier:org.R-project.R
Version:   R 4.2.1 GUI 1.79 High Sierra build (8095)
Code Type: X86-64 (Native)
Parent Process:??? [1]
Responsible:   R [54439]
User ID:   502

Date/Time: 2022-11-05 13:37:36.003 -0400
OS Version:macOS 11.6.8 (20G730)
Report Version:12
Anonymous UUID:B755C094-C366-46AB-8EEA-9D3B8E7B388D

Sleep/Wake UUID:   6135D492-FF9D-4ED1-AF9F-C0F790F64110

Time Awake Since Boot: 150 seconds
Time Since Wake:   7200 seconds

System Integrity Protection: enabled

Crashed Thread:6

Exception Type:EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:   KERN_INVALID_ADDRESS at 0x
Exception Note:EXC_CORPSE_NOTIFY

Termination Signal:Segmentation fault: 11
Termination Reason:Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [54439]

VM Regions Near 0:
-->
__TEXT  103034000-1030bc000[  544K] r-x/r-x 
SM=COW  /Applications/R.app/Contents/MacOS/R


Thread 0:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib  0x7fff208cdf4a __sigaction + 10
1   libsystem_platform.dylib  	0x7fff2094367c 
__platform_sigaction + 103

2   libsystem_c.dylib   0x7fff207fe689 signal__ + 66
3   libR.dylib	0x00010323a23c doprof + 1676 
(eval.c:345)

4   libsystem_platform.dylib0x7fff20943d7d _sigtramp + 29
5   ???   	0x8000 0 + 
9223372036854775808

6   libsystem_malloc.dylib  0x7fff207255ed nanov2_allocate + 367
7   libsystem_malloc.dylib  0x7fff2072754d nanov2_calloc + 123
8   libsystem_malloc.dylib	0x7fff2073fff4 
_malloc_zone_calloc + 59
9   libobjc.A.dylib   	0x7fff2079c5fa 
class_createInstance + 65
10  com.apple.CoreFoundation  	0x7fff2097a335 __CFAllocateObject 
+ 15
11  com.apple.CoreFoundation  	0x7fff20980f04 
__NSDictionaryI_new + 126
12  com.apple.CoreFoundation  	0x7fff20980d48 +[NSDictionary 
dictionaryWithObjects:forKeys:count:] + 49
13  com.apple.AppKit  	0x7fff23a5 
-[_NSToolbarButtonCell _symbolImageHints] + 213
14  com.apple.AppKit  	0x7fff2326659a -[NSButtonCell 
_currentImageInView:] + 401
15  com.apple.AppKit  	0x7fff232c0992 -[NSButtonCell 
_effectiveContentStyleForImageInView:] + 184
16  com.apple.AppKit  	0x7fff232646c4 -[NSButtonCell 
_updateImageViewImageInView:] + 93
17  com.apple.AppKit  	0x7fff232645a4 __60-[NSButtonCell 
_updateSubviewsInView:includeTitleTextField:]_block_invoke + 134
18  com.apple.AppKit  	0x7fff231ea835 +[NSAppearance 
_performWithCurrentAppearance:usingBlock:] + 66
19  com.apple.AppKit  	0x7fff23231321 -[NSButtonCell 
_updateSubviewsInView:includeTitleTextField:] + 131
20  com.apple.AppKit  	0x7fff232310eb -[NSButton 
updateCell:] + 87
21  com.apple.AppKit  	0x7fff23230a84 -[NSCell 
setEnabled:] + 156
22  com.apple.AppKit  	0x7fff23230d0f -[NSControl 
setEnabled:] + 120
23  com.apple.AppKit  	0x7fff2330af46 -[NSToolbarItem 
_reallySetEnabled:] + 124

24  org.R-project.R 0x00010304542b Re_RBusy + 59
25  libR.dylib	0x0001032694bf R_ReplDLLdo1 + 559 
(main.c:408)
26  org.R-project.R   	0x000103052e15 
run_REngineRmainloop + 261
27  org.R-project.R   	0x00010304798f -[REngine runREPL] 
+ 143

28  org.R-project.R 0x000103037288 main + 792
29  libdyld.dylib   0x7fff20919f3d start + 1

Thread 1:: JavaScriptCore bmalloc scavenger
0   libsystem_kernel.dylib  0x7fff208cf91e __pthread_kill + 10
1   libsystem_pthread.dylib 0x7fff208fe5bd pthread_kill + 263
2   libR.dylib	0x00010323a24d doprof + 1693 
(eval.c:231)

3   libsystem_platform.dylib0x7fff20943d7d _sigtramp + 29
4   ??? 00 0 + 0
5   libc++.1.dylib	0x7fff20867d72 
std::__1::condition_variable::wait(std::__1::unique_lock&) 
+ 18
6   com.apple.JavaScriptCore  	0x7fff379f0894 void 
std::__1::condition_variable_any::wait 
>(std::__1::unique_lock&) + 84
7   com.apple.JavaScriptCore  	0x7fff379f535b 
bmalloc::Scavenger::threadRunLoop() + 331
8   com.apple.JavaScriptCore  	0x7fff379f4ee9 
bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 9
9   com.apple.Java

[R-SIG-Mac] strange error message

[Carl Witthoft]

Hi,
this popped up in the middle of a long-running function. Is it anything 
to worry about?


date-string, followed by

R[56662:11921428] Error from CoreDragRequestrDrageCompleteMessage: -1850

regards,
Carl

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Re: [R-SIG-Mac] noob asked for help

[Carl Witthoft]

For those who haven't checked in a while, the sad state of affairs over 
at StackOverflow.com is that 99% of the R-tagged questions there are at 
this level of [non]understanding.   We should consider ourselves very 
lucky that r-sig-mac remains almost entirely devoid of such stuff.



On Sep 6, 2020, at 4:31 PM, Mike Feher  wrote:

Greetings,

As I’m getting familiar with R, I have some basic questions that I thought
of to shoot to useRs:

[snip]

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Re: [R-SIG-Mac] svn location

[Carl Witthoft]

Well, I put this new svn in /usr/local, then checked around my Catalina 
system:



iMac:~ cgw$ which svn
/usr/bin/svn
iMac:local cgw$ cd /usr/bin
iMac:bin cgw$ ls -l svn
-rwxr-xr-x  1 root  wheel  31488 Aug 10 16:55 svn
iMac:bin cgw$ cd /usr/local
iMac:local cgw$ ls -l svn
-rwxr-xr-x@ 1 cgw  wheel  8767792 Aug 25 18:04 svn
iMac:local cgw$ what svn
svn
1.14.0 (r1876290)

That's a huge difference in file size!  Any idea what the /usr/bin one is?

Carl

On 8/26/20 1:00 PM, peter dalgaard wrote:

Not dumb.

Simon's usual style is that tarballs are installed at / and things end up under 
/usr/local, using the procedure outlined at the bottom of

https://mac.r-project.org/libs/

but you should probably check with "tar tvfz" first.

-pd

  


On 26 Aug 2020, at 18:43 , Carl Witthoft  wrote:

Dumb question from someone who hasn't done any building in quite a while: 
recommended director to place the svn executable?
thanks
Carl

On 8/26/20 6:00 AM, r-sig-mac-requ...@r-project.org wrote:


1.  svn now available from the tools (Simon Urbanek)
ntent-Type: text/plain; charset="us-ascii"
If you want to build R from the svn repository you need svn (subversion). Xcode 
10 has removed svn so it is no loner available from Apple, we are providing a 
binary (cmopatible with OS X 10.11 and higher) in
https://mac.r-project.org/tools/
(in "optional tools and libraries" at the bottom), direct link:
https://mac.r-project.org/tools/subversion-1.14.0-darwin15.6.tar.gz
It is a single-file signed, static build so has no dependencies and can be run 
from anywhere.
Cheers,


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Re: [R-SIG-Mac] svn tarball

[Carl Witthoft]

Dumb question from someone who hasn't done any building in quite a 
while: recommended director to place the svn executable?

thanks
Carl

On 8/26/20 6:00 AM, r-sig-mac-requ...@r-project.org wrote:



1.  svn now available from the tools (Simon Urbanek)

ntent-Type: text/plain; charset="us-ascii"

If you want to build R from the svn repository you need svn (subversion). Xcode 
10 has removed svn so it is no loner available from Apple, we are providing a 
binary (cmopatible with OS X 10.11 and higher) in
https://mac.r-project.org/tools/
(in "optional tools and libraries" at the bottom), direct link:
https://mac.r-project.org/tools/subversion-1.14.0-darwin15.6.tar.gz
It is a single-file signed, static build so has no dependencies and can be run 
from anywhere.

Cheers,


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[R-SIG-Mac] Editor beginning-of-line-chomp?

[Carl Witthoft]

Hi,
Not sure when I first noticed this.  When I open a file in the Rgui 
Editor,  the window opens with the text "shifted left" so the first char 
or two are invisible. I can click & "push" to get the proper left-hand 
margin viewable, but have to do this every time.


I've tried it with "show line numbers" preference set to ON and to OFF; 
same problem.
I'm running Catalina, R7849Debug but saw the same thing with previous 
release versions.



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Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Carl Witthoft]

Hi, I ran  7849 high sierra debug GUI,

and am happy to report that I had zero crashes or hangs.

I tried opening via the icon in the console window, from the File menu, 
and even by selecting a dozen "name.r" files in the Finder and hitting 
-O .  All files opened, no problems seen.


On 7/2/20 1:27 AM, Simon Urbanek wrote:

Thanks to all, much appreciated. Please try the latest GUI revision 7849 from 
https://mac.R-project.org
The issue I found so far seems to have to do with function folding in documents 
- which is why is actually depends on the document content - and a selector 
that is apparently missing in Catalina.

Thanks,
Simon



On 29/06/2020, at 11:22 AM, Brandon Hurr  wrote:

Simon.
Default changed, RGUI 7846 Debug downloaded and run on same scripts.

Crash report here;
https://gist.github.com/bhive01/fd844404ef3e1d295036e5abd127864b

Let me know if you need more reports or to try something else.

Brandon

On Sun, Jun 28, 2020 at 4:00 PM Simon Urbanek 
wrote:


Brandon,

Yes, this is of great help! It shows the the GUI spins in the segfault
handler (it segfaults while rendering text which calls the R segfault
handler which in turn tries to render more text etc. ...).
So first thing is to avoid the signal handler, run this command in
Terminal:

defaults write org.R-project.R 'Disable R signal handlers' YES

Then download the debug version of the R GUI from

https://mac.R-project.org/

where it says Mac OS X GUI ... high-sierra-Debug.dmg - pick the one
matching your R version (4.0 for release or 4.1 for R-devel). You don't
need to replace your regular one, you can run it simply from the image.
Note that it is signed, but not notarized, so right-click (=ctrl-click) on
it and select "Open".

That will avoid the "hang" but will give a proper segfault with an Apple
report so won't help immediately but will make it easier to pinpoint. Also
it should include debug symbols with line numbers and all that. Please post
the crash report.

Thank you for your help,
Simon




On Jun 29, 2020, at 4:25 AM, Brandon Hurr 

wrote:


Thanks Ben.

I fired up R did a 20 second sample as I loaded files and it went into a

hang.

https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727

Seems to have the symbols you describe. Is that more helpful?

Brandon





[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Carl Witthoft]

Hi, here's my sample R 10 dump:

Sampling process 16681 for 10 seconds with 1 millisecond of run time 
between samples

Sampling completed, processing symbols...
Sample analysis of process 16681 written to file 
/tmp/R_2020-06-28_170339_imcz.sample.txt


Analysis of sampling R (pid 16681) every 1 millisecond
Process: R [16681]
Path:/Applications/R.app/Contents/MacOS/R
Load Address:0x10e3dc000
Identifier:  org.R-project.R
Version: R for R 4.0.1 GUI 1.72 Catalina build (7845)
Code Type:   X86-64
Parent Process:  ??? [1]

Date/Time:   2020-06-28 17:03:39.436 -0400
Launch Time: 2020-06-28 17:02:38.458 -0400
OS Version:  Mac OS X 10.15.5 (19F101)
Report Version:  7
Analysis Tool:   /usr/bin/sample

Physical footprint: 190.6M
Physical footprint (peak):  233.4M


Call graph:
8617 Thread_2990078   DispatchQueue_1: com.apple.main-thread  (serial)
+ 8617 start  (in libdyld.dylib) + 1  [0x7fff735e3cc9]
+   8617 main  (in R) + 792  [0x10e3ddfa8]
+ 8617 -[REngine runREPL]  (in R) + 177  [0x10e3ee441]
+   8617 run_REngineRmainloop  (in R) + 263  [0x10e3f9837]
+ 8617 R_ReplDLLdo1  (in libR.dylib) + 148  [0x10e5ff1e4] 
main.c:371

+   8617 Re_ReadConsole  (in R) + 184  [0x10e3ebd38]
+ 8617 -[RController handleReadConsole:]  (in R) + 158 
[0x10e3e29be]
+   8617 -[RController doProcessEvents:]  (in R) + 190 
[0x10e3e836e]
+ 8617 -[NSApplication(NSEvent) 
_nextEventMatchingEventMask:untilDate:inMode:dequeue:]  (in AppKit) + 
1352  [0x7fff3685c070]
+   8617 _DPSNextEvent  (in AppKit) + 883 
[0x7fff3685d829]
+ 8617 
_BlockUntilNextEventMatchingListInModeWithFilter  (in HIToolbox) + 64 
[0x7fff38215579]
+   8617 ReceiveNextEventCommon  (in HIToolbox) 
+ 359  [0x7fff382156f4]
+ 8617 RunCurrentEventLoopInMode  (in 
HIToolbox) + 292  [0x7fff38215abd]
+   8617 CFRunLoopRunSpecific  (in 
CoreFoundation) + 462  [0x7fff395e6ece]
+ 8617 __CFRunLoopRun  (in 
CoreFoundation) + 874  [0x7fff395e7895]
+   8617 __CFRunLoopDoObservers  (in 
CoreFoundation) + 457  [0x7fff395e82f7]
+ 8617 
__CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__  (in 
CoreFoundation) + 23  [0x7fff395e83c5]
+   8617 
___NSRunLoopObserverCreateWithHandler_block_invoke  (in AppKit) + 41 
[0x7fff3711c850]
+ 8617 
__62+[CATransaction(NSCATransaction) 
NS_setFlushesWithDisplayLink]_block_invoke  (in AppKit) + 266 
[0x7fff369fd591]
+   8617 
CA::Transaction::commit()  (in QuartzCore) + 644  [0x7fff450ac0a0]
+ 8617 
CA::Context::commit_transaction(CA::Transaction*, double)  (in 
QuartzCore) + 334  [0x7fff450ad4b6]
+   8617 
CA::Layer::display_if_needed(CA::Transaction*)  (in QuartzCore) + 757 
[0x7fff450cf1fd]
+ 8617 
-[_NSViewBackingLayer display]  (in AppKit) + 800  [0x7fff36948977]
+   8617 
-[_NSBackingLayer display]  (in AppKit) + 537  [0x7fff369e6e8a]
+ 8617 -[CALayer 
_display]  (in QuartzCore) + 2103  [0x7fff450d0162]
+   8617 invocation 
function for block in CA::Layer::display_()  (in QuartzCore) + 53 
[0x7fff451307d9]
+ 8617 
CABackingStoreUpdate_  (in QuartzCore) + 595  [0x7fff450d0c5d]
+   8617 
-[NSView(NSLayerKitGlue) 
_drawViewBackingLayer:inContext:drawingHandler:]  (in AppKit) + 1271 
[0x7fff369e749a]
+ 8617 
-[NSView(NSInternal) 
_recursive:displayRectIgnoringOpacity:inContext:stopAtLayerBackedViews:] 
 (in AppKit) + 2170  [0x7fff369e809e]
+   8617 
_NSViewDrawRect  (in AppKit) + 139  [0x7fff369e8d8f]
+ 8617 
-[_NSRulerContentView drawRect:]  (in AppKit) + 157  [0x7fff36f6bd67]
+ 
8617 -[NSRulerView _drawContentRect:]  (in AppKit) + 233  [0x7fff36f6b02f]
+ 
8617 -[NoodleLineNumberView drawHashMarksAndLabelsInRect:]  (in R) + 345 
 [0x10e42e8e9]
+ 
8617 -[NSLayoutManager(NSPrivate) 
_glyphRangeForBoundingRect:inTextContainer:fast:okToFillHoles:]  (in 
UIFoundation) + 857  [0x7fff6a63611b]
+ 
  8617 -[NSLayoutManager(NSPrivate) 
_firstPassGlyphRangeForBoundingRect:inTextContainer:okToFillHoles:]  (in 
UIFoundation) + 1441  [0x7fff6a63765a]
+ 
8617 _NSF

Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Carl Witthoft]

sing BBEdit to open other
scripts,
 > but often forget and end up with a crash because I double-click
on a file.
 > I might try to get BBEdit to work with R more intimately as Carl
pointed
 > out.
 >
 > B
 >
 > On Sun, Jun 7, 2020 at 3:46 PM Simon Urbanek
mailto:simon.urba...@r-project.org>>
 > wrote:
 >
 >> Thanks for the reports. Unfortunately, I still cannot reproduce
it on
 >> Catalina - neither with 4.0.1 nor 4.0.0.
 >> Can someone post exactly how to replicate? (How do exactly you
open the
 >> file? - the Open dialog works fine for me...)
 >>
 >> Note that the GUI is independent of R and compatible up to the patch
 >> version, i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa.
You can also
 >> just download the GUI from
 >> https://mac.R-project.org
 >> and run it from the image, you don’t even have to install it.
 >>
 >> The only changes in the GUI for 4.0.1 were in the colours for
dark mode,
 >> so file handling behaviour didn’t really change.
 >>
 >> Some places to remove to try if it has any effect:
 >>
 >> rm -rf ~/Library/Caches/org.R-project.R
 >> rm ~/Library/Preferences/org.R-project.R.plist
 >>
 >> Thanks,
 >> Simon
 >>
 >>
 >>
 >>> On Jun 8, 2020, at 10:22 AM, Brandon Hurr
mailto:brandon.h...@gmail.com>>
 >> wrote:
 >>>
 >>> This sounds exactly like the issue I am still having when I run
to open
 >>> more than one R script file in R-GUI’s editor. Perhaps it has
got worse
 >>> with the newer builds?
 >>>
 >>> On Sun, Jun 7, 2020 at 15:16 Carl Witthoft mailto:c...@witthoft.com>> wrote:
 >>>
 >>>> I'm not sure what to look for in the Reports sections of
Console.app,
 >>>> but I did find this report of R exceeding a diagnostic limit
of CPU
 >>>> usage, which most likely is related to one of the hangs -
R.app always
 >>>> goes full throttle on one CPU core.
 >>>>
 >>>> Date/Time:        2020-06-05 18:58:36 -0400
 >>>> End time:         2020-06-05 19:00:16 -0400
 >>>> OS Version:       Mac OS X 10.15.5 (Build 19F101)
 >>>> Architecture:     x86_64h
 >>>> Report Version:   29
 >>>> Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B
 >>>>
 >>>> Data Source:      Microstackshots
 >>>> Shared Cache:     0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535
 >>>>
 >>>> Command:          R
 >>>> Path:             /Applications/R.app/Contents/MacOS/R
 >>>> Identifier:       org.R-project.R
 >>>> Version:          R 4.0.0 GUI 1.71 Catalina build (7827)
 >>>> PID:              21391
 >>>>
 >>>> Event:            cpu usage
 >>>> Action taken:     none
 >>>> CPU:              90 seconds cpu time over 100 seconds (90% cpu
 >>>> average), exceeding limit of 50% cpu over 180 seconds
 >>>> CPU limit:        90s
 >>>> Limit duration:   180s
 >>>> CPU used:         90s
 >>>> CPU duration:     100s
 >>>> Duration:         100.35s
 >>>> Duration Sampled: 87.74s
 >>>> Steps:            51
 >>>>
 >>>> Hardware model:   iMac19,2
 >>>> Active cpus:      4
 >>>>
 >>>> Fan speed:        1200 rpm
 >>>>
 >>>> Heaviest stack for the target process:
 >>>>  51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
 >>>>  51  main + 720 (R + 8032) [0x105c66f60]
 >>>>  51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
 >>>> [0x7fff2dc1c938]
 >>>>  51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
 >>>> 306403) [0x7fff2dc34ce3]
 >>>>  51  -[NSNotificationCenter
postNotificationName:object:userInfo:] +
 >>>> 59 (Foundation + 38790) [0x7fff32ff6786]
 >>>>  51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
 >>>> [0x7fff3097ba39]
 >>>>  51  -[_CFXNotificationRegistrar
find:object:observer:enumerator:] +
 >>>> 1554 (CoreFoundation + 300429) [0x7fff3097c58d]
 >>>>  51  ___CFXNotificati

[R-SIG-Mac] Strange "NOTE" when running R CMD CHECK

[Carl Witthoft]

Hi,
Has anyone seen this kind of NOTE when running R CMD CHECK --as-cran?

(quote)
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Carl Witthoft ’

New submission
(end quote)

I've seen this pop up since I switched to Catalina & R 4.X .  I don't 
understand what it means or what the implications are, other than that 
it puts my package submissions into limbo because these notes pop up 
when the win-builder site does its automatic checking of the package.



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Re: [R-SIG-Mac] labels on plots

[Carl Witthoft]

You sure you don't have a font or fontsize missing?  Or possibly a 
screen resolution-setting mismatch?


On 6/8/20 5:11 PM, r-sig-mac-requ...@r-project.org wrote:



1.  Labels not displaying in R plots (David Akin)

--

Message: 1
Date: Mon, 8 Jun 2020 14:37:46 -0400
From: David Akin 
To: r-sig-mac@r-project.org
Subject: [R-SIG-Mac] Labels not displaying in R plots
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hey listers --

I'm a journalist and an R newbie but do I know my way around a Mac.

Got a weird problem I'm trying to troubleshoot

Both my Macbook Air and my iMac are running the same OS: Mojave 10.14.6

But each one is running different versions of R.

The iMac is running v 4.0.0 "Arbor Day"

The Macbook is running 3.6.0 "Planting of a Tree"

*PROBLEM:* Labels do not display in plots run on the iMac. Labels do
display properly on the MacBook.

Example:
Here's the colour wheel example from demo(topic="graphics") on the iMac. No
labels.
[image: image.png]

And here's the same plot as it displays on the Macbook. With Labels.
[image: Image 2020-06-08 at 9.11 AM.jpg]

Looking a little closer at the fine print in the console when I fire up R,
there is this line on my iMac:

[R.app GUI 1.71 (7827) x86_64-apple-darwin17.0]

But we have different version numbers on my Macbook:

[R.app GUI 1.70 (7657) x86_64-apple-darwin15.6.0]

Attempted the following on the iMac:

1. Uninstalled R 4.0.0
2. Grab the R 3.6.3 from http://mac.r-project.org/
3. Installed R 3.6.3.
4. Ran demo(topics="Graphics") again -- and got the same result -- no
labels on any plots.

Help?





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Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Carl Witthoft]

In the meantime, there is a decent alternative.  I found some scripts 
for BBEdit which let you execute code or "source" code directly from 
BBEdit.  See  http://bearak.org/code/text/index.html


On 6/7/20 11:39 PM, John Helly wrote:

Fails for me 100%.  If you want to zoom to look at it, I can arrange.
Hard to explain how to replicate since it happens right away as soon as
I try to do anything.  Running Catalina on a brand-new Mac Pro.

J.

On 6/7/20 15:46, Simon Urbanek wrote:

Thanks for the reports. Unfortunately, I still cannot reproduce it on Catalina 
- neither with 4.0.1 nor 4.0.0.
Can someone post exactly how to replicate? (How do exactly you open the file? - 
the Open dialog works fine for me...)

Note that the GUI is independent of R and compatible up to the patch version, 
i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also just 
download the GUI from
https://urldefense.com/v3/__https://mac.R-project.org__;!!Mih3wA!ReiXSbqAjm6U4nbE1g9kiDWBjuTDcKsZfnp69eK0Ey0VZg4-UB24sxHHdM6_uVk$
and run it from the image, you don’t even have to install it.

The only changes in the GUI for 4.0.1 were in the colours for dark mode, so 
file handling behaviour didn’t really change.

Some places to remove to try if it has any effect:

rm -rf ~/Library/Caches/org.R-project.R
rm ~/Library/Preferences/org.R-project.R.plist

Thanks,
Simon




On Jun 8, 2020, at 10:22 AM, Brandon Hurr  wrote:

This sounds exactly like the issue I am still having when I run to open
more than one R script file in R-GUI’s editor. Perhaps it has got worse
with the newer builds?

On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:


I'm not sure what to look for in the Reports sections of Console.app,
but I did find this report of R exceeding a diagnostic limit of CPU
usage, which most likely is related to one of the hangs - R.app always
goes full throttle on one CPU core.

Date/Time:2020-06-05 18:58:36 -0400
End time: 2020-06-05 19:00:16 -0400
OS Version:   Mac OS X 10.15.5 (Build 19F101)
Architecture: x86_64h
Report Version:   29
Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B

Data Source:  Microstackshots
Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535

Command:  R
Path: /Applications/R.app/Contents/MacOS/R
Identifier:   org.R-project.R
Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
PID:  21391

Event:cpu usage
Action taken: none
CPU:  90 seconds cpu time over 100 seconds (90% cpu
average), exceeding limit of 50% cpu over 180 seconds
CPU limit:90s
Limit duration:   180s
CPU used: 90s
CPU duration: 100s
Duration: 100.35s
Duration Sampled: 87.74s
Steps:51

Hardware model:   iMac19,2
Active cpus:  4

Fan speed:1200 rpm

Heaviest stack for the target process:
   51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
   51  main + 720 (R + 8032) [0x105c66f60]
   51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
[0x7fff2dc1c938]
   51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
306403) [0x7fff2dc34ce3]
   51  -[NSNotificationCenter postNotificationName:object:userInfo:] +
59 (Foundation + 38790) [0x7fff32ff6786]
   51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
[0x7fff3097ba39]
   51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] +
1554 (CoreFoundation + 300429) [0x7fff3097c58d]
   51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation +
496660) [0x7fff309ac414]
   51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576)
[0x7fff309ac7a8]
   51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation +
497715) [0x7fff309ac833]
   51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
(CoreFoundation + 497823) [0x7fff309ac89f]
   51  -[RController applicationDidFinishLaunching:] + 1176 (R + 15960)
[0x105c68e58]
   51  -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e]
   51  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation +
393672) [0x7fff3304d1c8]
   51  CFRunLoopRunSpecific + 462 (CoreFoundation + 532174)
[0x7fff309b4ece]
   51  __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895]
   51  __CFRunLoopDoObservers + 457 (CoreFoundation + 537335)
[0x7fff309b62f7]
   51  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ +
23 (CoreFoundation + 537541) [0x7fff309b63c5]
   51  ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit +
9439312) [0x7fff2e4ea850]
   51  __62+[CATransaction(NSCATransaction)
NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601)
[0x7fff2ddcb591]
   51  CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0]
   51  CA::Context::commit_transaction(CA::Transaction*, double) + 334
(QuartzCore + 13494) [0x7fff3c47b4b6]
   51  CA::Layer::display_if_needed(CA::Transaction*) + 757 (QuartzCore
+ 152061) [0x7fff3c49d1fd]
   51  -[_NSViewBackingLayer display] + 800 (A

Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Carl Witthoft]

I tried removing those Pref and Cache items. No help
It doesn't matter how I try to open a file: double-click the file, 
drag&drop,  from the Rgui File menu or the icon in the header of the 
console window.  They all hang the same way.  I tried turning off 
DefaultFolder and QuickSilver; no help.
I'm happy to try other experiments -- about the only other "unusual" 
thing in my setup is  USBOverdrive.


Just in case:  10.15.5, 3.6 GHz quadcore i3, 16GB Apple-installed RAM , 
APFS, SATA hard drive (not SSD)


On 6/7/20 6:46 PM, Simon Urbanek wrote:

Thanks for the reports. Unfortunately, I still cannot reproduce it on Catalina 
- neither with 4.0.1 nor 4.0.0.
Can someone post exactly how to replicate? (How do exactly you open the file? - 
the Open dialog works fine for me...)

Note that the GUI is independent of R and compatible up to the patch version, 
i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also just 
download the GUI from
https://mac.R-project.org
and run it from the image, you don’t even have to install it.

The only changes in the GUI for 4.0.1 were in the colours for dark mode, so 
file handling behaviour didn’t really change.

Some places to remove to try if it has any effect:

rm -rf ~/Library/Caches/org.R-project.R
rm ~/Library/Preferences/org.R-project.R.plist

Thanks,
Simon




On Jun 8, 2020, at 10:22 AM, Brandon Hurr  wrote:

This sounds exactly like the issue I am still having when I run to open
more than one R script file in R-GUI’s editor. Perhaps it has got worse
with the newer builds?

On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:


I'm not sure what to look for in the Reports sections of Console.app,
but I did find this report of R exceeding a diagnostic limit of CPU
usage, which most likely is related to one of the hangs - R.app always
goes full throttle on one CPU core.

Date/Time:2020-06-05 18:58:36 -0400
End time: 2020-06-05 19:00:16 -0400
OS Version:   Mac OS X 10.15.5 (Build 19F101)
Architecture: x86_64h
Report Version:   29
Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B

Data Source:  Microstackshots
Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535

Command:  R
Path: /Applications/R.app/Contents/MacOS/R
Identifier:   org.R-project.R
Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
PID:  21391

Event:cpu usage
Action taken: none
CPU:  90 seconds cpu time over 100 seconds (90% cpu
average), exceeding limit of 50% cpu over 180 seconds
CPU limit:90s
Limit duration:   180s
CPU used: 90s
CPU duration: 100s
Duration: 100.35s
Duration Sampled: 87.74s
Steps:51

Hardware model:   iMac19,2
Active cpus:  4

Fan speed:1200 rpm

Heaviest stack for the target process:
   51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
   51  main + 720 (R + 8032) [0x105c66f60]
   51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
[0x7fff2dc1c938]
   51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
306403) [0x7fff2dc34ce3]
   51  -[NSNotificationCenter postNotificationName:object:userInfo:] +
59 (Foundation + 38790) [0x7fff32ff6786]
   51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
[0x7fff3097ba39]
   51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] +
1554 (CoreFoundation + 300429) [0x7fff3097c58d]
   51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation +
496660) [0x7fff309ac414]
   51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576)
[0x7fff309ac7a8]
   51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation +
497715) [0x7fff309ac833]
   51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
(CoreFoundation + 497823) [0x7fff309ac89f]
   51  -[RController applicationDidFinishLaunching:] + 1176 (R + 15960)
[0x105c68e58]
   51  -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e]
   51  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation +
393672) [0x7fff3304d1c8]
   51  CFRunLoopRunSpecific + 462 (CoreFoundation + 532174)
[0x7fff309b4ece]
   51  __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895]
   51  __CFRunLoopDoObservers + 457 (CoreFoundation + 537335)
[0x7fff309b62f7]
   51  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ +
23 (CoreFoundation + 537541) [0x7fff309b63c5]
   51  ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit +
9439312) [0x7fff2e4ea850]
   51  __62+[CATransaction(NSCATransaction)
NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601)
[0x7fff2ddcb591]
   51  CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0]
   51  CA::Context::commit_transaction(CA::Transaction*, double) + 334
(QuartzCore + 13494) [0x7fff3c47b4b6]
   51  CA::Layer::display_if_needed(CA::Transaction*) + 757 (QuartzCore
+ 152061) [0x7fff3c49d1fd]
   51  -[_NSViewBackingLayer display] + 800 (AppKit + 1231223)
[0x7fff2dd16

Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Carl Witthoft]

> 
/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
0x7fff30933000 - 0x7fff30db2fff  com.apple.CoreFoundation 
6.9 (1676.105)<6AF8B3CC-BC3F-3869-B9FB-1D881422364E> 
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff32fed000 - 0x7fff333b2fff  com.apple.Foundation 6.9 
(1676.105)<1FA28BAB-7296-3A09-8E1E-E62A7D233DB8> 
/System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
0x7fff3c478000 - 0x7fff3c6fafff  com.apple.QuartzCore 1.11 
(841.2)  <444E6F22-DFA6-391B-B51F-A96AE69E524D> 
/System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
0x7fff619b2000 - 0x7fff61c0afff  com.apple.UIFoundation 1.0 
(662)
/System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff6a997000 - 0x7fff6a9cdfff  libdyld.dylib (750.5) 
<7E711A46-5E4D-393C-AEA6-440E2A5CCD0C> 
/usr/lib/system/libdyld.dylib
0x7fff6aba7000 - 0x7fff6aba  libsystem_platform.dylib 
(220.100.1)   <736920EA-6AE0-3B1B-BBDA-7DCDF0C229DF> 
/usr/lib/system/libsystem_platform.dylib




On 6/7/20 5:51 PM, Bob Rudis wrote:

Are there any entries in Console.app that might help triage?

Have you tried creating a new user on your Mac and seeing if that account has 
issues performing the same tasks your user account is having?

Having said that, I just grabbed "Mac OS X GUI rev. 7843 for R 4.0.x" from 
mac.r-project.org (I never use R.app nor do I keep it installed unless testing something) 
and am running R 4.0.1 on latest Catalina beta — 10.15.6 Beta (19G36e) — and it crashes 
every time I try to open a .R file (crashlog 
https://paste.sr.ht/~hrbrmstr/9899f3a7f3c1724cc952b935c3fc39a47cac88ac)


On Jun 7, 2020, at 16:22, Carl Witthoft  wrote:




Hi,
2 weeks ago I installed R 4.0 on my new Catalina machine. Things seemed to be 
working fine.
Today I installed R 4.01, and now I can't open any FILE.r - no matter what way 
I try, i.e. double-click the file, drag/drop, or open from the R GUI menu,  R 
hangs with the beachball.
I tried giving R full disk access and other privileges via Security settings; 
no help.

So I deleted R 4.01 and reinstalled R 4.0, and dang if I no longer can open 
files any more!  I've tried all the suggestions in the previous thread in this 
mailing group; no help.

What else can I do, or delete, or uninstall, to at least get back to where I 
was? Right now I'm basically DIW.
--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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c...@witthoft.com
resume: https://app.box.com/file/498153801347

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[R-SIG-Mac] Can't open files in 4.0 or 4.01

[Carl Witthoft]

Hi,
2 weeks ago I installed R 4.0 on my new Catalina machine. Things seemed 
to be working fine.
Today I installed R 4.01, and now I can't open any FILE.r - no matter 
what way I try, i.e. double-click the file, drag/drop, or open from the 
R GUI menu,  R hangs with the beachball.
I tried giving R full disk access and other privileges via Security 
settings; no help.


So I deleted R 4.01 and reinstalled R 4.0, and dang if I no longer can 
open files any more!  I've tried all the suggestions in the previous 
thread in this mailing group; no help.


What else can I do, or delete, or uninstall, to at least get back to 
where I was? Right now I'm basically DIW.

--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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Re: [R-SIG-Mac] Problem with CHECK --as-cran on Catalina

[Carl Witthoft]

Looks like I found a way to succeed.

If I type

R CMD CHECK --as-cran  mypackage.tar.gz

then I get a successful check executed.  So this is a bit different from 
the "good old days" under R 3.6.X  and my old 10.11 OSX, but now I know 
how to get it done.




On 6/6/20 4:29 PM, Jeff Newmiller wrote:

AFAIK tgz is one possible file name extension equivalent to .tar.gz, which 
implies gzip compression, so I think Bob was just being a bit sloppy when he 
wrote tar.tgz.

Key point is not that a particular compression makes a difference, but that the 
check needs to be run on a source archive rather than the in-place source you 
have been editing. He was confirming that you are making that file and 
specifying it when checking.

On June 6, 2020 11:59:24 AM PDT, Carl Witthoft  wrote:

I plead ignorance here: I don't see an option to create .tgz . The
R CMD BUILD --help just lists "gzip" (default), "none", "bzip2", "xz"
.Does one of those create the .tgz -type compression?

Carl

On 6/6/20 2:37 PM, Bob Rudis wrote:

Does it still do it if you build a tar.tgz archive and run it on

that?


I could not dup your problem, but when I tried to run it on a couple
of my packages that work fine with tar.gz (I use Authors@R) in dir

(`R

CMD check --as-cran .` or parent dir and specify the pkg dir) I get:

  Required field missing or empty:
‘Author’

(running last R 4.0.1 beta before the release of R 4.0.1, latest
Catalina beta AND R 4.0.0 on ubuntu)

So, def something strange going on.

On Sat, Jun 6, 2020 at 12:47 PM Carl Witthoft 

wrote:


Hi,
I recently upgraded to a new iMac w/ Catalina.  Something really

strange

is happening when I try to run "R CMD CHECK --as-cran  " .
If I run it on various older packages that have previously passed

the

check, all is well.

I am writing a new package, and here's the response I get:


* using log directory ‘/Users/cgw/Rgames/fitConic.Rcheck’
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘fitConic/DESCRIPTION’ ... OK
* this is package ‘fitConic’ version ‘1.0’
* checking CRAN incoming feasibility ...Error:  file './DESCRIPTION'
does not exist
Execution halted


This happens whether I run R CMD CHECK  from the parent dirctory
/Users/cgw/Rgames  or from the source directory

/Users/cgw/Rgames/fitConic .


I verified I can edit the DESCRIPTION file in my previous packages &
still pass the check.  I even took one of those old DESCRIPTION

files

and put it into the fitConic directory, and changed only the

"Package:"

line  .

I'm guessing that last error message is not telling me what actually
went wrong, but I'm at a loss as to why this new package fails.

I've

created a new directory and moved all my files (DESCRIPTION,

NAMESPACE,

and the R & man folders) over. No luck.

Is this a hangup somewhere in R 4.0 for OSX, or is there something

else

going on?   (do I need, for example to do something to give XQuartz

more

permissions, or some other called app? )

thanks
--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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resume: https://app.box.com/file/498153801347

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Re: [R-SIG-Mac] Problem with CHECK --as-cran on Catalina

[Carl Witthoft]

 I always run R CMD BUILD before R CMD CHECK.  I popped open the tar.gz 
file and the folder did include DESCRIPTION.  So it's there, all right. 
I notice the 'build' folder contains one file, 'partial.rdb' . I don't 
have anything requiring compilation, so I'm not sure why there's a 
'build' directory at all.




On 6/6/20 4:29 PM, Jeff Newmiller wrote:

AFAIK tgz is one possible file name extension equivalent to .tar.gz, which 
implies gzip compression, so I think Bob was just being a bit sloppy when he 
wrote tar.tgz.

Key point is not that a particular compression makes a difference, but that the 
check needs to be run on a source archive rather than the in-place source you 
have been editing. He was confirming that you are making that file and 
specifying it when checking.

On June 6, 2020 11:59:24 AM PDT, Carl Witthoft  wrote:

I plead ignorance here: I don't see an option to create .tgz . The
R CMD BUILD --help just lists "gzip" (default), "none", "bzip2", "xz"
.Does one of those create the .tgz -type compression?

Carl

On 6/6/20 2:37 PM, Bob Rudis wrote:

Does it still do it if you build a tar.tgz archive and run it on

that?


I could not dup your problem, but when I tried to run it on a couple
of my packages that work fine with tar.gz (I use Authors@R) in dir

(`R

CMD check --as-cran .` or parent dir and specify the pkg dir) I get:

  Required field missing or empty:
‘Author’

(running last R 4.0.1 beta before the release of R 4.0.1, latest
Catalina beta AND R 4.0.0 on ubuntu)

So, def something strange going on.

On Sat, Jun 6, 2020 at 12:47 PM Carl Witthoft 

wrote:


Hi,
I recently upgraded to a new iMac w/ Catalina.  Something really

strange

is happening when I try to run "R CMD CHECK --as-cran  " .
If I run it on various older packages that have previously passed

the

check, all is well.

I am writing a new package, and here's the response I get:


* using log directory ‘/Users/cgw/Rgames/fitConic.Rcheck’
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘fitConic/DESCRIPTION’ ... OK
* this is package ‘fitConic’ version ‘1.0’
* checking CRAN incoming feasibility ...Error:  file './DESCRIPTION'
does not exist
Execution halted


This happens whether I run R CMD CHECK  from the parent dirctory
/Users/cgw/Rgames  or from the source directory

/Users/cgw/Rgames/fitConic .


I verified I can edit the DESCRIPTION file in my previous packages &
still pass the check.  I even took one of those old DESCRIPTION

files

and put it into the fitConic directory, and changed only the

"Package:"

line  .

I'm guessing that last error message is not telling me what actually
went wrong, but I'm at a loss as to why this new package fails.

I've

created a new directory and moved all my files (DESCRIPTION,

NAMESPACE,

and the R & man folders) over. No luck.

Is this a hangup somewhere in R 4.0 for OSX, or is there something

else

going on?   (do I need, for example to do something to give XQuartz

more

permissions, or some other called app? )

thanks
--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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c...@witthoft.com
resume: https://app.box.com/file/498153801347

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Re: [R-SIG-Mac] Problem with CHECK --as-cran on Catalina

[Carl Witthoft]

I plead ignorance here: I don't see an option to create .tgz . The
R CMD BUILD --help just lists "gzip" (default), "none", "bzip2", "xz" 
.Does one of those create the .tgz -type compression?


Carl

On 6/6/20 2:37 PM, Bob Rudis wrote:

Does it still do it if you build a tar.tgz archive and run it on that?

I could not dup your problem, but when I tried to run it on a couple
of my packages that work fine with tar.gz (I use Authors@R) in dir (`R
CMD check --as-cran .` or parent dir and specify the pkg dir) I get:

 Required field missing or empty:
   ‘Author’

(running last R 4.0.1 beta before the release of R 4.0.1, latest
Catalina beta AND R 4.0.0 on ubuntu)

So, def something strange going on.

On Sat, Jun 6, 2020 at 12:47 PM Carl Witthoft  wrote:


Hi,
I recently upgraded to a new iMac w/ Catalina.  Something really strange
is happening when I try to run "R CMD CHECK --as-cran  " .
If I run it on various older packages that have previously passed the
check, all is well.

I am writing a new package, and here's the response I get:


* using log directory ‘/Users/cgw/Rgames/fitConic.Rcheck’
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘fitConic/DESCRIPTION’ ... OK
* this is package ‘fitConic’ version ‘1.0’
* checking CRAN incoming feasibility ...Error:  file './DESCRIPTION'
does not exist
Execution halted


This happens whether I run R CMD CHECK  from the parent dirctory
/Users/cgw/Rgames  or from the source directory /Users/cgw/Rgames/fitConic .

I verified I can edit the DESCRIPTION file in my previous packages &
still pass the check.  I even took one of those old DESCRIPTION files
and put it into the fitConic directory, and changed only the "Package: "
line  .

I'm guessing that last error message is not telling me what actually
went wrong, but I'm at a loss as to why this new package fails.  I've
created a new directory and moved all my files (DESCRIPTION, NAMESPACE,
and the R & man folders) over. No luck.

Is this a hangup somewhere in R 4.0 for OSX, or is there something else
going on?   (do I need, for example to do something to give XQuartz more
permissions, or some other called app? )

thanks
--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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[R-SIG-Mac] Problem with CHECK --as-cran on Catalina

[Carl Witthoft]

Hi,
I recently upgraded to a new iMac w/ Catalina.  Something really strange 
is happening when I try to run "R CMD CHECK --as-cran  " .
If I run it on various older packages that have previously passed the 
check, all is well.


I am writing a new package, and here's the response I get:


* using log directory ‘/Users/cgw/Rgames/fitConic.Rcheck’
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘fitConic/DESCRIPTION’ ... OK
* this is package ‘fitConic’ version ‘1.0’
* checking CRAN incoming feasibility ...Error:  file './DESCRIPTION' 
does not exist

Execution halted


This happens whether I run R CMD CHECK  from the parent dirctory 
/Users/cgw/Rgames  or from the source directory /Users/cgw/Rgames/fitConic .


I verified I can edit the DESCRIPTION file in my previous packages & 
still pass the check.  I even took one of those old DESCRIPTION files 
and put it into the fitConic directory, and changed only the "Package: " 
line  .


I'm guessing that last error message is not telling me what actually 
went wrong, but I'm at a loss as to why this new package fails.  I've 
created a new directory and moved all my files (DESCRIPTION, NAMESPACE, 
and the R & man folders) over. No luck.


Is this a hangup somewhere in R 4.0 for OSX, or is there something else 
going on?   (do I need, for example to do something to give XQuartz more 
permissions, or some other called app? )


thanks
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[R-SIG-Mac] Transitioning from Mac to LInux?

[Carl Witthoft]

 If I should ask over at r-sig-debian instead of here, please tell me. 
I don't wish to clog r-sig-mac with off-topic stuff.



I've been watching the massive headaches people are dealing with trying 
to keep R fully compatible with each MacOS X upgrade,  I'm wondering 
whether replacing my iMac (2009) with a new Mac really makes sense from 
an R - user point of view, as opposed to getting some inexpensive 
desktop and installing Linux.  I know I can run R and RStudio under 
Linux, for example,  but don't know what limitations, if any there are 
when it comes to building packages from source, getting compatible 
compilers,  and so on.


What have some of you 'power R users' discovered when/if you tried to 
build , or incorporate Bioconductor or other repository's packages under 
Linux?



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[R-SIG-Mac] R vs. Microsoft R-Open updates?

[Carl Witthoft]

Hi.
I D/L'd the 3.3.1 version of R for MacOSX and ran the installer. After 
getting some "can't load" error messages, I discovered that the 
installer had updated the MicrosoftROpen.app, not the "vanilla"  R.app . 
Is this expected behavior, or am I making a hash of my apps and 
libraries by trying to keep both R and MRO available on my (Yosemite) 
machine?


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Re: [R-SIG-Mac] Help page key bindings

[Carl Witthoft]

May I suggest an alternative?   Since MacOS allows you to bind the 
keystroke of your choice to any menu item (on an app-specific basis), 
if the "help/forwards" and "help/backwards" were added to a menu, then 
everyone could set whatever bindings they prefer.



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[R-SIG-Mac] hangs under Yosemite redux

[Carl Witthoft]

Back to that question of the gui hanging at commands like "Save As" I 
brought up a few weeks back.   Someone posted a similar question to SO 
and someone else posted the following claim:


"Apparently, this is a bug in R's GUI. Some OS X features/libraries that 
used to be in place in earlier versions of OS X have been removed in 
Yosemite.


You can work around this bug by running R from the terminal / command 
line. Fire up the terminal app (quickest way is to use Spotlight search: 
cmd+space -> terminal), and type the following command:


/Applications/R.app/Contents/MacOS/R
"

Is this possible? rational?  I don't know how Yosemite cranks up an 
executable, so have no idea how booting the R-executable directly might 
differ from a Finder double-click.


What I did find is that the Terminal window gives me the following warnings:

"

2015-01-26 15:48:55.319 R[57903:2792043] Failed to connect 
(cancelButton) outlet from (SelectList) to (NSButton): missing setter or 
instance variable
2015-01-26 15:48:55.319 R[57903:2792043] Failed to connect (okButton) 
outlet from (SelectList) to (NSButton): missing setter or instance variable

"



Carl

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Re: [R-SIG-Mac] hangs on Open Dialog

[Carl Witthoft]

Hmmm.. you sure that deleting ~/Library/Saved Application 
State/org.R-project.R.savedState  won't kill off that "history" ?


BTW, possibly coincidence, but since installing R version 3.1.2 Patched 
(2015-01-11 r67421)  I've gone 24 hrs without the OpenDialog hanging.

Carl

On 1/12/15 6:03 PM, Simon Urbanek wrote:

Carl,


On Jan 12, 2015, at 5:43 PM, Carl Witthoft  wrote:

Updated info:  I installed the latest patch version of R from research.att.com ,
and there are several things behaving differently.  Now I do not get any files 
opened when I open R, whereas previously all files open when I quit R re-opened 
(even if I'd used quit() and had a normal end of session).
In addition, the Window menu no longer displays windows (such as files being 
edited) which had been closed earlier in my R session.

BUT: I torture-tested by opening about 50 files inside R.  I then force-quit R, 
and then on restart,  R tries to re-open all the files again! I'm guessing this 
is desired behavior, to recover any lost work, but it's a bit unnerving.  At 
the very least, can you advise if there's a config file somewhere that I could 
delete to avoid this recovery mode?



Send all thanks to Apple - this is how the OS behave now - I find it extremely 
annoying, but AFAIK the app has no control over it, because they come as 
regular open request to the app.

That said, nothing really changed on the R side - we didn't touch the R.app for 
almost a year, so whatever you may be seeing has to do wither with your OS or 
the build you picked.

Cheers,
Simon







--

Message: 4
Date: Mon, 12 Jan 2015 17:20:03 -0500
From: Carl Witthoft 
To: "r-sig-mac@r-project.org" 
Subject: [R-SIG-Mac] Still have hangs on Open Dialog Box
Message-ID: <54b44893.9040...@witthoft.com>
Content-Type: text/plain; charset=utf-8; format=flowed

I thought this problem had gone away, but it's still hitting me.

Yosemite on a dual-core iMac, R 3.1.2 GUI 1.65 Mavericks build (6833).
I've verified Permissions and Disk, using DiskUtility.

What happens is: I select "Open" from the menu to try to open a new file
inside R, and I get the OpenDialog window, but the contents of the
current directory never fill the window; just spinning beachball of
death.  I thought turning off DefaultFolder helped, but it didn't.  I
have to force-quit R and delete  the file "com.apple.finder.plist" from
my Library/Preferences directory to be able to successfully open a file
from inside R (as opposed to double-clicking on a Finder window's file
icon) the next time I open R.app GUI .

The only other thing I noticed is that, when R starts up,  a whole pile
of previously-opened files are displayed and then disappear.  WHen I hit
the  Mac OSX "F10" function key  to display all current windows
belonging to R, I got a strange (at least to me) display.  All the
current windows are displayed but ALSO a long row of mini-icons
representing previously open (and closed) document windows.  I posted a
screen shot at  https://app.box.com/s/qutc86rujitb49geur8c  ; this
appears to match my "Recent" doc list in the File Menu.
I don't know what causes that -- Microsoft Office apps don't do this,
but TextWrangler and GraphicConverter(for two examples) do.  I  don't
know  whether it is related to  R's misbehavior on my machine.  All I
know for certain is that no other application I've tried ever hangs on
Open dialog boxes.



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Re: [R-SIG-Mac] hangs on Open Dialog

[Carl Witthoft]

Updated info:  I installed the latest patch version of R from 
research.att.com ,
and there are several things behaving differently.  Now I do not get any 
files opened when I open R, whereas previously all files open when I 
quit R re-opened (even if I'd used quit() and had a normal end of session).
In addition, the Window menu no longer displays windows (such as files 
being edited) which had been closed earlier in my R session.


BUT: I torture-tested by opening about 50 files inside R.  I then 
force-quit R, and then on restart,  R tries to re-open all the files 
again! I'm guessing this is desired behavior, to recover any lost work, 
but it's a bit unnerving.  At the very least, can you advise if there's 
a config file somewhere that I could delete to avoid this recovery mode?




--

Message: 4
Date: Mon, 12 Jan 2015 17:20:03 -0500
From: Carl Witthoft 
To: "r-sig-mac@r-project.org" 
Subject: [R-SIG-Mac] Still have hangs on Open Dialog Box
Message-ID: <54b44893.9040...@witthoft.com>
Content-Type: text/plain; charset=utf-8; format=flowed

I thought this problem had gone away, but it's still hitting me.

Yosemite on a dual-core iMac, R 3.1.2 GUI 1.65 Mavericks build (6833).
I've verified Permissions and Disk, using DiskUtility.

What happens is: I select "Open" from the menu to try to open a new file
inside R, and I get the OpenDialog window, but the contents of the
current directory never fill the window; just spinning beachball of
death.  I thought turning off DefaultFolder helped, but it didn't.  I
have to force-quit R and delete  the file "com.apple.finder.plist" from
my Library/Preferences directory to be able to successfully open a file
from inside R (as opposed to double-clicking on a Finder window's file
icon) the next time I open R.app GUI .

The only other thing I noticed is that, when R starts up,  a whole pile
of previously-opened files are displayed and then disappear.  WHen I hit
the  Mac OSX "F10" function key  to display all current windows
belonging to R, I got a strange (at least to me) display.  All the
current windows are displayed but ALSO a long row of mini-icons
representing previously open (and closed) document windows.  I posted a
screen shot at  https://app.box.com/s/qutc86rujitb49geur8c  ; this
appears to match my "Recent" doc list in the File Menu.
I don't know what causes that -- Microsoft Office apps don't do this,
but TextWrangler and GraphicConverter(for two examples) do.  I  don't
know  whether it is related to  R's misbehavior on my machine.  All I
know for certain is that no other application I've tried ever hangs on
Open dialog boxes.

Any ideas?

Carl



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[R-SIG-Mac] Still have hangs on Open Dialog Box

[Carl Witthoft]

I thought this problem had gone away, but it's still hitting me.

Yosemite on a dual-core iMac, R 3.1.2 GUI 1.65 Mavericks build (6833).
I've verified Permissions and Disk, using DiskUtility.

What happens is: I select "Open" from the menu to try to open a new file 
inside R, and I get the OpenDialog window, but the contents of the 
current directory never fill the window; just spinning beachball of 
death.  I thought turning off DefaultFolder helped, but it didn't.  I 
have to force-quit R and delete  the file "com.apple.finder.plist" from 
my Library/Preferences directory to be able to successfully open a file 
from inside R (as opposed to double-clicking on a Finder window's file 
icon) the next time I open R.app GUI .


The only other thing I noticed is that, when R starts up,  a whole pile 
of previously-opened files are displayed and then disappear.  WHen I hit 
the  Mac OSX "F10" function key  to display all current windows 
belonging to R, I got a strange (at least to me) display.  All the 
current windows are displayed but ALSO a long row of mini-icons 
representing previously open (and closed) document windows.  I posted a 
screen shot at  https://app.box.com/s/qutc86rujitb49geur8c  ; this 
appears to match my "Recent" doc list in the File Menu.
I don't know what causes that -- Microsoft Office apps don't do this, 
but TextWrangler and GraphicConverter(for two examples) do.  I  don't 
know  whether it is related to  R's misbehavior on my machine.  All I 
know for certain is that no other application I've tried ever hangs on 
Open dialog boxes.


Any ideas?

Carl

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[R-SIG-Mac] apparently solved: hang on Open Dialog box

[Carl Witthoft]

I think I've solved the problem.  I have been using FinderPop for ages 
sans problems, but the R.app-specific problem described previously went 
away as soon as I added R.app to the list of excluded applications for 
FinderPop.


Dunno why this is, but hardly worth asking anyone to dive into the R.app 
source code (or FinderPop ) to fix.


Thanks to Simon for running some tests at his end.

Carl

On 12/23/14 11:36 AM, Simon Urbanek wrote:

Carl,

I cannot replicate it even with your file. "Hang" in open dialog are
typically caused by the system - e.g. waiting for disks mounted etc.
- R is simply waiting for the system (LS/Finder) to gather
information about all disks. I suspect you may be accessing some disk
(virtual or real) that has issues. The plist only has recent files,
so I don't think it's directly involved - the only thing I can think
of is that it may be directing the UI to the bad location. Is there
anything you can think of that would cause volume access issues on
your system? (network mounts, virutal disks, etc.)

Cheers, Simon







On Dec 23, 2014, at 10:07 AM, Carl Witthoft 
wrote:

Hi, I got the same corruption problem again that causes a spinning

beachball hang when I try to open a file via the "Open" dialog window.


This time I traced it down to a specific plist file, and have posted

the bad file to my GitHub account:




https://github.com/cellocgw/Rgoodies/blob/master/BADorg.R-project.R.LSSharedFileList.plist


If someone could take a look and see what happened to that file (or
if

a "bad" file name somehow is causing the problem, e.g.), I'd be very
greatful.


thanks Carl


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Re: [R-SIG-Mac] corrupted plist file again

[Carl Witthoft]

Hmm... The reason I suspected the file is that every time I delete this 
plist file, everything is OK again. However:


Other than some mystery "Shared" volume called "8e40280" which my 
OSX desktop tells me "connection failed," I don't have any oddball 
mounts.   I'm unable to collect any info on that volume, and I can't 
eject, unmount, or connect to it, so I dunno what it is, but it is true 
that when I run "GetInfo", the FinderInfo window goes into a spin while 
"Fetching more info" so possibly that is the headache.


Any idea how I can remove that alleged volume from my Network list?  It 
doesn't show up as ejectable.


Terminal % ls -a /Volumes doesn't show any other entries,btw.




On 12/23/14 11:36 AM, Simon Urbanek wrote:

Carl,

I cannot replicate it even with your file. "Hang" in open dialog are typically 
caused by the system - e.g. waiting for disks mounted etc. - R is simply waiting for the 
system (LS/Finder) to gather information about all disks. I suspect you may be accessing 
some disk (virtual or real) that has issues. The plist only has recent files, so I don't 
think it's directly involved - the only thing I can think of is that it may be directing 
the UI to the bad location. Is there anything you can think of that would cause volume 
access issues on your system? (network mounts, virutal disks, etc.)

Cheers,
Simon




On Dec 23, 2014, at 10:07 AM, Carl Witthoft  wrote:

Hi,
I got the same corruption problem again that causes a spinning beachball hang when I try 
to open a file via the "Open" dialog window.

This time I traced it down to a specific plist file, and have posted the bad 
file to my GitHub account:

https://github.com/cellocgw/Rgoodies/blob/master/BADorg.R-project.R.LSSharedFileList.plist

If someone could take a look and see what happened to that file (or if a "bad" 
file name somehow is causing the problem, e.g.), I'd be very greatful.

thanks
Carl

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[R-SIG-Mac] corrupted plist file again

[Carl Witthoft]

Hi,
I got the same corruption problem again that causes a spinning beachball 
hang when I try to open a file via the "Open" dialog window.


This time I traced it down to a specific plist file, and have posted the 
bad file to my GitHub account:


https://github.com/cellocgw/Rgoodies/blob/master/BADorg.R-project.R.LSSharedFileList.plist

If someone could take a look and see what happened to that file (or if a 
"bad" file name somehow is causing the problem, e.g.), I'd be very greatful.


thanks
Carl

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Re: [R-SIG-Mac] OpenFile hang; fixed not solved

[Carl Witthoft]

Pursuant to my last post:

I tracked down and deleted all the following support files, all of which 
are in  "~/Library/Preferences"


org.R-project.R copy.plist
org.R-project.R.LSSharedFileList.plist
org.R-project.R.plist
org.R-project.R.savedState

R now works correctly.  I don't know which of these files was corrupted, 
so if anyone has some suggestions as to the forensic studies :-) I could 
do, I'd appreciate it.


In any case, I'm functional again.

Carl


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[R-SIG-Mac] OpenFile Dialog hangs

[Carl Witthoft]

This just started out of the blue:  If I select, say, "Open Recent" and 
pick a file from the list, the file opens just fine.


But if I select "Open,"  then the dialog box opens, but the file list 
never gets filled in, I get the spinning beach ball, and never recover.


I took the precaution of turning off DefaultFolder; same problem.

I can execute "SaveAs" without any problem.

I am running Yosemite 10.10.1, R 3.1.2, and as I said up until 2 hours 
ago all was just fine.I even rebooted the machine and reinstalled R; 
no change.


The entire "hang" file (from /Library/Logs/DiagnosticReports) is huge so 
here's the top portion. PLease let me know if there is some specific 
section that could help diagnose this problem . -- or if someone would 
like me to email the zipped file.


thanks
Carl




Date/Time:   2014-12-21 13:07:11 -0500
OS Version:  10.10.1 (Build 14B25)
Architecture:x86_64
Report Version:  21

Command: R
Path:/Applications/R.app/Contents/MacOS/R
Version: R 3.1.2 GUI 1.65 Mavericks build (6833)
Parent:  launchd [1]
PID: 1010

Event:   hang
Duration:1.80s (process was unresponsive for 144 seconds before 
sampling)

Steps:   19 (100ms sampling interval)

Hardware model:  iMac9,1
Active cpus: 2

Fan speed:   1350 rpm

--
Timeline format: stacks are sorted chronologically
Use -i and -heavy to re-report with count sorting
--

Heaviest stack for the main thread of the target process:
  19  start + 1 (libdyld.dylib + 13769) [0x7fff9501b5c9]
  19  main + 819 (R + 6547) [0x10a477993]
  19  -[REngine runREPL] + 138 (R + 75898) [0x10a48887a]
  19  run_REngineRmainloop + 295 (R + 123703) [0x10a494337]
  19  ??? ( + 897903) [0x10a66236f]
  19  Re_ReadConsole + 185 (R + 65753) [0x10a4860d9]
  19  -[RController handleReadConsole:] + 186 (R + 26922) [0x10a47c92a]
  19  -[RController doProcessEvents:] + 221 (R + 50381) [0x10a4824cd]
  19  -[NSApplication sendEvent:] + 4035 (AppKit + 1619867) 
[0x7fff92afa79b]
  19  -[NSApplication _handleKeyEquivalent:] + 920 (AppKit + 2132165) 
[0x7fff92b778c5]
  19  -[NSMenu performKeyEquivalent:] + 359 (AppKit + 2147119) 
[0x7fff92b7b32f]
  19  _os_activity_initiate + 75 (libsystem_trace.dylib + 3287) 
[0x7fff961e3cd7]
  19  -[NSCarbonMenuImpl performActionWithHighlightingForItemAtIndex:] 
+ 114 (AppKit + 2151159) [0x7fff92b7c2f7]
  19  -[NSMenuItem _corePerformAction] + 382 (AppKit + 2151898) 
[0x7fff92b7c5da]
  19  -[NSApplication sendAction:to:from:] + 410 (AppKit + 2045079) 
[0x7fff92b62497]
  19  _os_activity_initiate + 75 (libsystem_trace.dylib + 3287) 
[0x7fff961e3cd7]

  19  -[RController openDocument:] + 194 (R + 47954) [0x10a481b52]
  19  -[NSSavePanel runModal] + 282 (AppKit + 681) [0x7fff92f42fcd]
  19  -[NSApplication runModalForWindow:] + 119 (AppKit + 3305862) 
[0x7fff92c96186]
  19  -[NSApplication _realDoModalLoop:peek:] + 666 (AppKit + 3312599) 
[0x7fff92c97bd7]
  19  -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] 
+ 194 (AppKit + 147072) [0x7fff92992e80]

  19  _DPSNextEvent + 964 (AppKit + 149201) [0x7fff929936d1]
  19  _BlockUntilNextEventMatchingListInModeWithFilter + 71 (HIToolbox 
+ 188411) [0x7fff97952ffb]

  19  ReceiveNextEventCommon + 179 (HIToolbox + 188606) [0x7fff979530be]
  19  RunCurrentEventLoopInMode + 235 (HIToolbox + 189503) [0x7fff9795343f]
  19  CFRunLoopRunSpecific + 296 (CoreFoundation + 464952) [0x7fff8e9ca838]
  19  __CFRunLoopRun + 872 (CoreFoundation + 466408) [0x7fff8e9cade8]
  19  __CFRunLoopDoObservers + 368 (CoreFoundation + 523488) 
[0x7fff8e9d8ce0]
  19  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 
23 (CoreFoundation + 523655) [0x7fff8e9d8d87]
  19  __38-[NSApplication setWindowsNeedUpdate:]_block_invoke2508 + 76 
(AppKit + 3556895) [0x7fff92cd361f]
  19  -[NSApplication updateWindows] + 86 (AppKit + 160649) 
[0x7fff92996389]
  19  +[NSTextInputContext currentInputContext] + 140 (AppKit + 162532) 
[0x7fff92996ae4]
  19  -[FI_TListView inputContext] + 29 (FinderKit + 1312876) 
[0x7fff8b09786c]
  19  +[FI_TFloatingInputWindowController singleton] + 80 (FinderKit + 
664266) [0x7fff8aff92ca]
  19  -[FI_TFloatingInputWindow init] + 668 (FinderKit + 665781) 
[0x7fff8aff98b5]
  19  -[NSWindow _setFrameCommon:display:stashSize:] + 2801 (AppKit + 
1132460) [0x7fff92a837ac]
  19  -[NSNotificationCenter postNotificationName:object:userInfo:] + 
66 (Foundation + 11937) [0x7fff8f920ea1]

  19  _CFXNotificationPost + 3140 (CoreFoundation + 65972) [0x7fff8e9691b4]
  19  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12 
(CoreFoundation + 1174716) [0x7fff8ea77cbc]
  19  -[RDocumentWinCtrl setStatusLineText:] + 430 (R + 208030) 
[0x10a4a8c9e]
  19  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 278 (Foundation + 
436921) [0x7fff8f988ab9]

  19  CFRunLoopRunSpecific + 296 (CoreFoundation + 464952) [0x

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 141, Issue 6

[Carl Witthoft]

On 11/13/14, 6:00 AM, r-sig-mac-requ...@r-project.org wrote:

>Duncan Murdoch wrote:

>"Yes, most people like to use a version that doesn't crash."

Well,  it looks like  we have another entry for the R-fortunes file!

:-)



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Re: [R-SIG-Mac] feature request: editor match brackets

[Carl Witthoft]

On 2/11/14 8:59 AM, Simon Urbanek wrote:


On Feb 10, 2014, at 5:40 PM, Carl Witthoft 
wrote:


Yes, I know about --B but that's ugly-ish.

What I'd like to request is a automatic paired-bracket color
highlighting in a manner similar to what Notepad++ does (which, if
you haven't used it, colors a bracket next to the cursor and its
matching pair).  While it's nice to get that quickie highlighting
while typing a line of code, in general it's a lot more useful to
get a highlighting while eding code blocks.



Just to understand - we do already highlight the matching bracket
when you move the cursor over/next to a bracket/paren. So is your
suggestion to make that highlighting longer/permanent as opposed to
flashing?

Thanks, Simon


Well, actually,   on R 3.0.2 GUI 1.62 Snow Leopard build (6558) I don't
get any response to a hovering pointer!  I get a very brief highlight if 
I pass the cursor "across" a bracket using the arrow keys.  If I move 
the mouse pointer and click at a location to place the cursor there, no 
highlighting.


But, yes,  what I'm requesting is for the bracket pair to stay 
highlighted as long as the cursor (not the mouse pointer) is situated 
next to a bracket.


ciao,
Carl


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[R-SIG-Mac] feature request: editor match brackets

[Carl Witthoft]

Yes, I know about --B but that's ugly-ish.

What I'd like to request is a automatic paired-bracket color 
highlighting in a manner similar to what Notepad++ does (which, if you 
haven't used it, colors a bracket next to the cursor and its matching 
pair).  While it's nice to get that quickie highlighting while typing a 
line of code, in general it's a lot more useful to get a highlighting 
while eding code blocks.


Just a request -- I can live without it :-)
Carl

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[R-SIG-Mac] arguments to dev.new()

[Carl Witthoft]

Hi,
the WindowsOS - specific command "windows()"  accepts an argument 
"restoreConsole" , which, when set to TRUE, returns focus to the console 
window after opening a new graphics device.
The help file for "dev.new()"  only says '...	arguments to be passed to 
the device selected.'


Is there an argument that will return focus to the R.app console window?

thanks
Carl
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[R-SIG-Mac] OT Re:haxies and injection

[Carl Witthoft]

While I can understand the frustration and confusion caused by 
DefaultFolderX not playing nice with R and MountainLion,  I would like 
to point out that many if not all of us use an awful lot of OSX apps 
that are not R.   Default Folder is, and has been since its inception, a 
spectacularly useful tool.  Add to that the fact that there is an 
options dialog to list apps that DFX does NOT load into, and you should 
be fine to go.


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Re: [R-SIG-Mac] "?" in scripteditor

[Carl Witthoft]

Well, first of all,  it appears the character got converted to '?' in 
the email.


Next,  I strongly suspect it's a NewLine character, not a tilde, which 
is not the "not" char in R anyway.  If I'm right,this happens when text 
files (sometimes) when text files get moved from WindowsOS to OSX and 
"end of line" is CR-LF or just LF, etc. and the editor gets confused.

HTH




I've been noticing lately some weirdness in the editor when copying and 
pasting code. Last night when I was trying to run some code from the 
ggplot2 mailing list I pasted the code in from gmail. As usual, there 
were extra line breaks that caused the code to fail. I pasted the code 
into the script editor to fix the line breaks and then copy/pasted it 
into R-GUI. I then got a lot more errors than I did previously, all of 
which were caused by the insertion of an invisible "?" symbol (a logical 
not). Here: 
https://plus.google.com/116319893425910717496/posts/5Yxkk7GFwts is a 
screen shot. The code in question is from this question: 
https://groups.google.com/forum/?fromgroups=#!topic/ggplot2/BxSDoDjJgSA 
... but this has happened before a few times (I cannot recall when it 
started, recently... perhaps since installing ML, but maybe before 
that). If I hit up to input the previous previous command the "?" are 
not there and when I search in the editor for this symbol nothing is 
found. Is there something going on with the editor or the clipboard or 
...? Where should I be looking? Brandons-MacBook-Air:~ bhurr$ 
system_profiler SPSoftwareDataType Software: System Software Overview: 
System Version: OS X 10.8.1 (12B19) Kernel Version: Darwin 12.1.0 Boot 
Volume: AIR Boot Mode: Normal Time since boot: 54 minutes

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid  stats graphics  grDevices utils datasets
methods   base

other attached packages:
 [1] gplots_2.11.0 MASS_7.3-18   KernSmooth_2.23-7
caTools_1.13  bitops_1.0-4.1
 [6] gdata_2.11.0  gtools_2.7.0  lattice_0.20-6
gridBase_0.4-5TeachingDemos_2.8
[11] plyr_1.7.1reshape2_1.2.1ggplot2_0.9.1

loaded via a namespace (and not attached):
 [1] colorspace_1.1-1   dichromat_1.2-4digest_0.5.2
labeling_0.1   memoise_0.1
 [6] munsell_0.3proto_0.3-9.2  RColorBrewer_1.0-5
scales_0.2.1   stringr_0.6
[11] tools_2.15.1

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Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 111, Issue 6

[Carl Witthoft]

Simon's response may have misled some folks:

Naive Windows users (redundant?)  don't understand either icon 
relationships or how to display full file names.  Those "bad" zip files 
are actually "sneakyname.zip.exe" .


AFAIK none of the more common unzipping utilities will launch an 
executable after unpacking the archive.  It may well be that some idiot 
(at Microsoft) set things up so that a new, say, .img file gets 
automounted sort of like what Windows does with an inserted audio CD. 
Otherwise, unpacking a true zip, or gzip, or tar.gz file will not lead 
to any autoexec.


On 5/3/12 11:56 AM, r-sig-mac-requ...@r-project.org wrote:
-- DWin wrote:


So I'm now wondering if there are two components to my misunderstanding:

1) My experience with Windows is that zip files are sometimes delivery
vehicles for executable files and htat the OS can be configure to auto-
execute such files on decompression without further intervention. I
worried that MacOS might have the same potential.


Simon wrote:
On Windows, yes, executables can be masqueraded as zip files with 
interesting consequences if the tools on the machine are broken enough


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Re: [R-SIG-Mac] Block commenting - I found it

[Carl Witthoft]

Many thanks for this explanation.

And, yes, I feel like an idiot for not having investigated the Edit Menu.

Carl

On 2/2/12 9:42 AM, Hans-Jörg Bibiko wrote:


On 2 Feb 2012, at 15:29, Carl Witthoft wrote:


A little hacking later:

CMD-'   will apply "#" to each line,
CMD-OPT-'  will remove them.

But I'm still interested in knowing what other undocumented keystrokes are out 
there.


Do you wonder why a selection will be wrapped by `` after pressing ` well then 
I can help you.

If you select something in the R script editor or in the RConsole and you will then 
press ( or { or [ or " or ' or ` then the selection will be wrapped by these 
characters; of course for parentheses by the corresponding closing variant.

Since ⌥⌘+` is not assigned to any command this short-cut will simply wrap the 
selection by ``.

Cheers,
--Hans


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[R-SIG-Mac] Block commenting - I found it

[Carl Witthoft]

A little hacking later:

CMD-'   will apply "#" to each line,
CMD-OPT-'  will remove them.

But I'm still interested in knowing what other undocumented keystrokes 
are out there.



Carl

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[R-SIG-Mac] Shortcut to apply comment character to a block of code in editor?

[Carl Witthoft]

Hi,
Someone claimed in this StackOverflow thread 
http://stackoverflow.com/questions/9107695/r-comment-out-block-of-code 
that the sequence "CMD-OPT-`"  would comment the selected block.  What 
it does, on my machine, is to place the "`" at the start and end of the 
selection, which of course just makes a mess.


So-- is there actually a  keystroke to apply "#" to all selected rows in 
the editor?  And while I'm at it,  does "CMD-OPT-`" have an intended 
use, or is it something "leftover" in the R.app editor code?


Many thanks
Carl

My R:  R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)


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Re: [R-SIG-Mac] quartz.save tilde

[Carl Witthoft]

Just to help him out,  here's the error message I get, which pretty
clearly indicates that one of the subfunctions does not parse a tilde 
(my working directory is /users/cgw/rgames) .


Rgames> quartz.save('~/downloads/foo.png')
Error in dev.off(eval.parent(oc)) :
  QuartzBitmap_Output - unable to open file '~/downloads/foo.png'
ImageIO: could not open '/Users/cgw/Rgames/~/downloads/.foo.png-zY8H'
 error = 2
Sat Nov 19 09:35:05 TheiMac.local R[2951] :
CGImageDestinationCreate destination parameter is nil


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Message: 2 Date: Wed, 2 Nov 2011 22:21:42 -0400 From: Denis
Chabot To: r-sig-mac@r-project.org Subject:
[R-SIG-Mac] saving files using quartz engine
Message-ID:<30dbf0c5-722e-4d65-85a0-87292ba89...@gmail.com>
Content-Type: text/plain; charset=us-ascii

Hi,

is there a reason that the quartz device does not like the "~" in
file names, whereas most functions handling files (including pdf() )
have no problem with it?

Thus

pdf(file="/Users/dchabot/Documents/Programmes R/test.pdf",
type="pdf", width=6, height=5) # works
pdf(file=~/Documents/Programmes R/test.pdf", type="pdf", width=6,
height=5) # works

quartz(file="~/Documents/Programmes R/test.pdf", type="pdf", width=6,
height=5) # does not work
quartz(file="/Users/dchabot/Documents/Programmes R/test.pdf",
type="pdf", width=6, height=5) # works


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Re: [R-SIG-Mac] incomplete final line?

[Carl Witthoft]

Yeah, I got that part :-).  The question is why R2.14 is suddenly 
complaining about files which have been fine for the last 4 years.  What 
changed, and is there a way I can fix it?
(other than adding a final 'return' in R.app GUI editor so there's a 
blank line in each file)



On 11/1/11 9:41 PM, Duncan Murdoch wrote:

On 11-11-01 6:27 PM, Carl Witthoft wrote:

Just installed R2.14.0 . Sourcing just about any existing .r file
gives me
Warning message:
In readLines(file) :
incomplete final line found on [file name]

Any ideas?


That means that the final line has no line terminator (LF on
Unix-alikes, or CR LF on Windows).

Duncan Murdoch



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[R-SIG-Mac] incomplete final line?

[Carl Witthoft]

Just installed R2.14.0 .  Sourcing just about any existing .r file gives me
Warning message:
In readLines(file) :
  incomplete final line found on [file name]

Any ideas?

thanks
Carl

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[R-SIG-Mac] saving a graph changes active quartz window?

[Carl Witthoft]

Setup:
   OSX 10.6.7,
R version 2.13.0 Patched (2011-05-25 r55988)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

Dumb question, maybe:
If I use --S to "save as" a quartz window, the graph is 
saved very nicely as a pdf, but the window in question is made inactive 
(and some other quartz window is set to active).


Is this intentional, or just some artifact of the save function closing 
a connection or something?


thanks
Carl

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Re: [R-SIG-Mac] packages failed to load

[Carl Witthoft]

Just wanted to mention that I saw the same behavior with a package or 
two, and found the same workaround (copying libs to the 2.12 tree).


Carl


Message: 4
Date: Tue, 24 May 2011 16:32:41 +1000
From: Ian Reeve 
To: "r-sig-mac@r-project.org" 
Subject: [R-SIG-Mac] Packages deldir,   class and gpclib fail to load in
R 2.13.0
Message-ID: <23292b0b-0329-454c-9a17-5bb1ccb45...@une.edu.au>
Content-Type: text/plain; charset="us-ascii"

Hi,

I've been running rgdal, RColorBrewer, maptools, classInt, spdep, 
gpclib, raster, zoo, cluster and lattice in R2.12 on Mac OSX 10.6.7 for 
the last 6 months with no problems.  Today I installed R 2.13.0, and 
downloaded the latest versions of the above packages.  Most of them load 
without problems, but class (a depend of classInt), and deldir (a depend 
of spdep) failed to load.  The error message is of the form:


---
Loading required package: class
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object 
'/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so':


dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so, 
6): Library not loaded: 
/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib
  Referenced from: 
/Library/Frameworks/R.framework/Versions/2.13/Resources/library/class/libs/x86_64/class.so

  Reason: image not found
Error: package 'class' could not be loaded
---

The problem seems to be either the package is looking in the wrong place 
(a subdirectory of 2.12 instead of a subdirectory of 2.13) for the file 
libR.dylib, or the install of R failed to put the files that package 
class needs in the 2.12 directory.  In the case of deldir, the errant 
file is libgfortran.2.dylib.


I can get  package class to load without error by taking a copy of 
libR.dylib from the subdirectory of 2.13 and putting it in the 
subdirectory of 2.12 where class  expects it to be.


I'm concerned this might be a stupid short-term fix, as calls to the 
functions in class might also fail due to other files not being in the 
expected places.


Can anyone suggest any leads to other approaches I could take to get 
these previously trouble-free packages to behave themselves in R 2.13?


Thank you.

Ian Reeve

Institute for Rural Futures
University of New England
Armidale, NSW 2351

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Re: [R-SIG-Mac] How to free up system memory?

[Carl Witthoft]

Excellent --  gc() is exactly what i was looking for.

thanks
Carl

On 5/2/11 7:36 PM, Ben Haller wrote:



   Call gc() if you want.  Or just relax.  :->


Thanks for your help -- I'm not the least put out if someone wants to point out 
what a dummy I'm being.


   No worries, it confused me when I started, too.

Ben Haller
McGill University

http://biology.mcgill.ca/grad/ben/






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Re: [R-SIG-Mac] How to free up system memory?

[Carl Witthoft]

One more test: quite by accident, after typing

rm(foo)

I invoked the help function, i.e.

?matrix  (or ?anything_valid)

and R freed up most of the memory allocated to foo.   Hope this helps.


 Original Message 
Subject: How to free up system memory?
Date: Mon, 02 May 2011 19:28:32 -0400
From: Carl Witthoft 
To: r-sig-mac@r-project.org 

I'm not sure exactly what's happening, so I'll try to describe the steps
in detail.  I get the same behavior with R 2.12.1 and R 2.13, OSX 10.6.6
or 10.6.4 .

First, I boot up Activity Monitor and set it to show memory usage.

I create a large object (in the R Console of R.app GUI) , such as

foo<-runif(1e8)

and the "real memory" in the table and "active memory" in the pie chart
go up.  No surprise.

Then I get rid of foo,

rm(foo)

But the memory allocations don't change.   Looks like a memory leak?

Two other things I found:

1) If I write a function that does nothing but create some big objects
like that, and then deletes them,  ActivityMonitor shows memory
allocated to R and then freed up.  This is what I'd expect from the
R.app GUI as well.

2) If I boot several other applications, using up all my RAM, at some
point the operating system moves some of R's active memory into virtual
memory.  Now the funny thing:  if I make R the foreground app, or if I
simply quit all the other apps,  R does not get its active memory
allocation back.  The 'pie chart' shows memory has been freed, not just
"inactive" .

Did I set some bad parameter in one of my config files?  Is there some
way within R to force all that memory to be freed up (other than
quitting and restarting R)?

Thanks for your help -- I'm not the least put out if someone wants to
point out what a dummy I'm being.

Carl

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[R-SIG-Mac] How to free up system memory?

[Carl Witthoft]

I'm not sure exactly what's happening, so I'll try to describe the steps 
in detail.  I get the same behavior with R 2.12.1 and R 2.13, OSX 10.6.6 
or 10.6.4 .


First, I boot up Activity Monitor and set it to show memory usage.

I create a large object (in the R Console of R.app GUI) , such as

foo<-runif(1e8)

and the "real memory" in the table and "active memory" in the pie chart 
go up.  No surprise.


Then I get rid of foo,

rm(foo)

But the memory allocations don't change.   Looks like a memory leak?

Two other things I found:

1) If I write a function that does nothing but create some big objects 
like that, and then deletes them,  ActivityMonitor shows memory 
allocated to R and then freed up.  This is what I'd expect from the 
R.app GUI as well.


2) If I boot several other applications, using up all my RAM, at some 
point the operating system moves some of R's active memory into virtual 
memory.  Now the funny thing:  if I make R the foreground app, or if I 
simply quit all the other apps,  R does not get its active memory 
allocation back.  The 'pie chart' shows memory has been freed, not just 
"inactive" .


Did I set some bad parameter in one of my config files?  Is there some 
way within R to force all that memory to be freed up (other than 
quitting and restarting R)?


Thanks for your help -- I'm not the least put out if someone wants to 
point out what a dummy I'm being.


Carl

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[R-SIG-Mac] biOps and fftw3

[Carl Witthoft]

I have successfully installed biOps, at least in the sense that the 
package loads and many of the functions work.  The question I have now 
is how to get biOps to recognize fftw3 during compilation.


I installed fftw3 from a Terminal session, and "make check" passed 
successfully.  The files residing in /usr/local/lib are


libfftw3.a  libfftw3.la

I checked for the existence of a certain item(?) as:

% grep fftw_plan_dft libff*
Binary file libfftw3.a matches

But then, when I ask the Package Installer in Rgui.app to install biOps 
from the localsource tarball, I get:


* installing *source* package ‘biOps’ ...
checking for gcc... gcc -arch i386 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none 
needed

checking for TIFFOpen in -ltiff... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking for fftw_plan_dft in -lfftw3... no
checking how to run the C preprocessor... gcc -arch i386 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E

(and more)

So, my question is: how come the checker doesn't "see" fftw_plan_dft ?

biOps library will load, and other functions like,say imgBlur run fine, 
and in case it helps, the error message I get if I try to run one of the 
fft routines is:


Error in .C("fft_image", image = as.complex(imgmatrix), width = 
as.integer(width),  :

  C symbol name "fft_image" not in DLL for package "biOps"

Thanks

Carl

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[R-SIG-Mac] followup: my problems with gmp and gnu MP

[Carl Witthoft]

Well, I finally found a version of gnuMP library that plays nicely with 
the R-gmp package and with my OSX 10.5.8 iMac. I loaded the gmp-4.3.1 
tarball from att.com, per Simon's suggestion and all is well.
 I have to admit I'm not sure what exactly solved the problems I'd been 
having, but now my modified gmp library loads and runs just fine.


Thanks again for the help.

Carl

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Re: [R-SIG-Mac] odd problem building gmp from source, addendum

[Carl Witthoft]

It occurs to me I should post the mods I made to the source matrixz.R, 
just in case I managed to do something really bad :-(.


Here is my code snippet:
apply <- function(X, MARGIN,FUN,...)
  UseMethod("apply")

apply.default <- function(X, MARGIN,FUN,...)
  base::apply(X, MARGIN,FUN,...)


apply.bigz <- function(X, MARGIN,FUN)

That differs from the original source only in the addition of the '...' 
argument to apply and apply.default.


Carl


On 1/11/11 9:01 PM, Simon Urbanek wrote:

On Jan 11, 2011, at 6:06 PM, Carl Witthoft wrote:


Hi,
I chose to make a minor edit to the R-source  matrixz.R in the gmp package (not 
to be confused with the GNU gmp library which it calls).

On my Intel iMac at work, running OSX 10.6.4,  it compiled just fine.

for reference, that Mac has:
%gcc -version
i686-apple-darwin10-gcc-4.2.1: no input files

and I honestly forget which version of gmplib I installed.

So, I took the R-gmp source home, where I have an Intel iMac w/ 10.5.8, and I 
get the following foulup:

TheiMac:~/downloads/gmpmod:cgw-507$ ./configure
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... no
configure: error: GNU MP not found, or not 4.1.4 or up, see http://swox.com.gmp

I've tried installing both GNU gmp 4.3.2 and 5.0.1, same problem.  And the 
libraries are in /usr/local/lib, just as they are on my work iMac.



If you have doubt about your builds of gmp you can always pick the one used on 
CRAN if you wish at
http://r.research.att.com/libs/



I thought it might be the compiler, so I checked:

TheiMac:~/downloads/gmpmod:cgw-508$ gcc -version
i686-apple-darwin9-gcc-4.2.1: no input files



You really meant to use --version I presume:

ginaz:~$ gcc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5664)

but the version usually doesn't matter - especially not on on 10.6 ;)



Any ideas what I've got set up wrong? Let me know what other system or app 
diagnostics I can supply.



Well, the only useful diagnostics is the config.log - it will tell you exactly 
what the error is ...

Cheers,
Simon




thanks
Carl

(I did finagle an ugly workaround, by bringing home a copy of the installed 
R-gmp package.  I had to go to the Library/Frameworks/... /libs/i386 directory 
and swap in the original gmp.so  file (from the CRAN package) to get things 
mostly working))

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Re: [R-SIG-Mac] odd problem building gmp from source

[Carl Witthoft]

Simon,
thanks for the suggestion.  I downloaded gmp-4.3.1-darwin9-bin3.tar.gz 
from research.att.com and installed per their instructions.


R (2.12.1)  successfully built the "gmp" package from my modified code.

Two problems.  First,  every time I execute a function from gmp,  I get 
something like:


apply.bigz(mxg,2,max)
[1] "17" "18" "19" "20"
R(95552,0xa01f9720) malloc: *** error for object 0x1abf5674: Non-aligned 
pointer being freed

*** set a breakpoint in malloc_error_break to debug
R(95552,0xa01f9720) malloc: *** error for object 0x1abf5674: Non-aligned 
pointer being freed

*** set a breakpoint in malloc_error_break to debug
R(95552,0xa01f9720) malloc: *** error for object 0x1abf5674: Non-aligned 
pointer being freed

*** set a breakpoint in malloc_error_break to debug
R(95552,0xa01f9720) malloc: *** error for object 0x1abf5674: Non-aligned 
pointer being freed

*** set a breakpoint in malloc_error_break to debug

note that the returned values are correct for the "mxg" bigz matrix in 
question.


The other problem seems to be one of search order, in that, for an 
integer matrix mx,


apply(mx,2,max)   works properly.  But   apply(mxg,2,max) fails to 
"find" the bigz method and returns an error:


Rgames> apply(mxg,2,max)
Error in aperm(X, c(s.call, s.ans)) :
  invalid first argument, must be an array

which is because the character matrix 'mxg' was passed to base::apply.

Any ideas?  and thanks again.

Carl

On 1/11/11 9:01 PM, Simon Urbanek wrote:

On Jan 11, 2011, at 6:06 PM, Carl Witthoft wrote:


Hi,
I chose to make a minor edit to the R-source  matrixz.R in the gmp package (not 
to be confused with the GNU gmp library which it calls).

On my Intel iMac at work, running OSX 10.6.4,  it compiled just fine.

for reference, that Mac has:
%gcc -version
i686-apple-darwin10-gcc-4.2.1: no input files

and I honestly forget which version of gmplib I installed.

So, I took the R-gmp source home, where I have an Intel iMac w/ 10.5.8, and I 
get the following foulup:

TheiMac:~/downloads/gmpmod:cgw-507$ ./configure
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... no
configure: error: GNU MP not found, or not 4.1.4 or up, see http://swox.com.gmp

I've tried installing both GNU gmp 4.3.2 and 5.0.1, same problem.  And the 
libraries are in /usr/local/lib, just as they are on my work iMac.



If you have doubt about your builds of gmp you can always pick the one used on 
CRAN if you wish at
http://r.research.att.com/libs/



I thought it might be the compiler, so I checked:

TheiMac:~/downloads/gmpmod:cgw-508$ gcc -version
i686-apple-darwin9-gcc-4.2.1: no input files



You really meant to use --version I presume:

ginaz:~$ gcc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5664)

but the version usually doesn't matter - especially not on on 10.6 ;)



Any ideas what I've got set up wrong? Let me know what other system or app 
diagnostics I can supply.



Well, the only useful diagnostics is the config.log - it will tell you exactly 
what the error is ...

Cheers,
Simon




thanks
Carl

(I did finagle an ugly workaround, by bringing home a copy of the installed 
R-gmp package.  I had to go to the Library/Frameworks/... /libs/i386 directory 
and swap in the original gmp.so  file (from the CRAN package) to get things 
mostly working))

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[R-SIG-Mac] odd problem building gmp from source

[Carl Witthoft]

Hi,
I chose to make a minor edit to the R-source  matrixz.R in the gmp 
package (not to be confused with the GNU gmp library which it calls).


On my Intel iMac at work, running OSX 10.6.4,  it compiled just fine.

for reference, that Mac has:
%gcc -version
i686-apple-darwin10-gcc-4.2.1: no input files

and I honestly forget which version of gmplib I installed.

So, I took the R-gmp source home, where I have an Intel iMac w/ 10.5.8, 
and I get the following foulup:


TheiMac:~/downloads/gmpmod:cgw-507$ ./configure
creating cache ./config.cache
checking for __gmpz_ui_sub in -lgmp... no
configure: error: GNU MP not found, or not 4.1.4 or up, see 
http://swox.com.gmp


I've tried installing both GNU gmp 4.3.2 and 5.0.1, same problem.  And 
the libraries are in /usr/local/lib, just as they are on my work iMac.


I thought it might be the compiler, so I checked:

TheiMac:~/downloads/gmpmod:cgw-508$ gcc -version
i686-apple-darwin9-gcc-4.2.1: no input files


Any ideas what I've got set up wrong? Let me know what other system or 
app diagnostics I can supply.


thanks
Carl

(I did finagle an ugly workaround, by bringing home a copy of the 
installed R-gmp package.  I had to go to the Library/Frameworks/... 
/libs/i386 directory and swap in the original gmp.so  file (from the 
CRAN package) to get things mostly working))


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Re: [R-SIG-Mac] learning R

[Carl Witthoft]

Rolf -- you da man!

Based on the literary quality of your epistle below, I will be sure to 
call upon your services should I ever need some some organization to be 
sokaled.



Carl


On 12/13/10 1:49 PM, Rolf Turner wrote:


On 13/12/2010, at 10:05 PM, Jari Oksanen wrote:



I just wonder why the other supposed "misuse" was completely ignored in this
thread: there are many things in R that are "begging the question" but
nobody dares to ask.



The phrase ``to beg the question'' means to indulge in circular reasoning;
to assume what is to be proven.  Unfortunately that meaning is becoming lost
in the wilderness of ignorance that surrounds us, and the phrase is almost
universally used to mean ``to raise the question'' or ``to evince the necessity
of an answer to the question''.  The language thus loses subtlety and nuance,
and Newspeak takes over and limits our ability to express our thoughts.  And
that is doubleplus ungood! :-)

cheers,

Rolf Turner


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Re: [R-SIG-Mac] learning R

[Carl Witthoft]

Next to "begging the question,"  the phrase "steep learning curve" is
probably the most misused cliche out there.

A 'learning curve' represents knowledge (or understanding) as a function 
of time.  THerefore,  the steeper the better.
Please help save the English language from descent into Humpty-Dumpty 
land, and train your colleagues in the correct usage of both these terms.


Carl


Message: 2 Date: Thu, 9 Dec 2010 09:51:27 -0800 From: Payam
Minoofar To:
"r-sig-mac@r-project.org" Cc:
"deniz.kellecio...@gmail.com" Subject:
[R-SIG-Mac] R for Mac, good enough?
Message-ID:<53df393b-2037-4b0d-890f-8dbaa1ba1...@meissner.com>
Content-Type: text/plain; charset="us-ascii"

The power of R is virtually unmatched, and R for Mac works extremely
well.

The learning curve is steep, however, and documentation is difficult
to grasp, even though it is abundantly available. I am more partial
to a commercial data analysis package with which I grew up, but I
have done enough work with R on the mac platform to recommend it
highly.



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Re: [R-SIG-Mac] html help and browser vs. Rgui

[Carl Witthoft]

Thanks, Simon.
I'll check out the current settings in my work machine's
org.R-project.R.plist file next week (we have Friday off. Yay!).

Carl
PS I use Firefox both at home and at work as my default, so I *hope* 
that's not the issue.


On 12/9/10 6:17 PM, Simon Urbanek wrote:

Carl,

On Dec 9, 2010, at 5:53 PM, Carl Witthoft wrote:


I have two separate questions about help windows.

First:  I'm running R2.12 at home under 10.5.8, and at work under
10.6.4 (Intel iMacs in both cases).

At home, when I invoke help, e.g.,

?sin ,

I get the help page in the Rgui help window (and my web browser is
not called).

But at work, the Rgui help window opens, remains blank, and the sin
help page shows up in my default web browser.

Is there a way I can either force my work machine to use the Rgui
window, or at the least stop the useless help window from opening
up?



The default is what you see at home - and that is the intended
behavior.

There is a preference "use.external.help" that allows you to use an
external browser (at the request of some users) - you can enable it
using (in Terminal): defaults write org.R-project.R use.external.help
YES

and disable it using defaults delete org.R-project.R
use.external.help

So chances are that you enabled it at some point in the past (maybe?)
- it's definitely NOT the default.

Alternatively (if that's not the issue?) it may be some strange
setting of your browser - but you'd have to provide more detains on
that (e.g. do you use a custom browser instead of Safari which may be
forcing that behavior?).

Cheers, Simon




Am I able to use the Rgui help window at home just thru some luck
of pre-existing conditions (from the  R 2.8 or 2.9 days)?

I checked, and the Library/Frameworks/.../base/R/Rprofile files are
the same on both machines, as are my personal   .Rprofile and
.Renvir files in my home directory.


Second: I noticed that on both machines, when I use the Search bar
in the document editor window (Rgui editor window),  the little
pop-up results panel displays the help page, with properly
functioning links to referenced help pages.  This suggests the help
system is working "behind the scenes" somehow on my work machine,
even though it fails to access the Rgui Help window.Anything I
can do to adjust this?



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[R-SIG-Mac] html help and browser vs. Rgui

[Carl Witthoft]

I have two separate questions about help windows.

First:  I'm running R2.12 at home under 10.5.8, and at work under 10.6.4 
(Intel iMacs in both cases).


At home, when I invoke help, e.g.,
 >  ?sin ,
I get the help page in the Rgui help window (and my web browser is not 
called).


But at work, the Rgui help window opens, remains blank, and the sin help 
page shows up in my default web browser.


Is there a way I can either force my work machine to use the Rgui 
window, or at the least stop the useless help window from opening up?


Am I able to use the Rgui help window at home just thru some luck of 
pre-existing conditions (from the  R 2.8 or 2.9 days)?


I checked, and the Library/Frameworks/.../base/R/Rprofile files are the 
same on both machines, as are my personal   .Rprofile and .Renvir files 
in my home directory.



Second: I noticed that on both machines, when I use the Search bar in 
the document editor window (Rgui editor window),  the little pop-up 
results panel displays the help page, with properly functioning links to 
referenced help pages.  This suggests the help system is working "behind 
the scenes" somehow on my work machine, even though it fails to access 
the Rgui Help window.Anything I can do to adjust this?



Many thanks for your help.


Carl

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