Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 245, Issue 2
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: Send R-SIG-Mac mailing list submissions to r-sig-mac@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/r-sig-mac or, via email, send a message with subject or body 'help' to r-sig-mac-requ...@r-project.org You can reach the person managing the list at r-sig-mac-ow...@r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-SIG-Mac digest..." 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Subject: Digest Footer ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- End of R-SIG-Mac Digest, Vol 245, Issue 2 ***** -- Carl Witthoft personal: c...@witthoft.com The Witthoft Group, Consulting https://witthoftgroup.weebly.com/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] 4.3.1 fails to load
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
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
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@r-project.org
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[R-SIG-Mac] problem with editor in R.app GUI
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
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 -- Carl Witthoft personal: c...@witthoft.com The Witthoft Group, Consulting https://witthoftgroup.weebly.com/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] making rattle run
ce 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 ' -- Carl Witthoft personal: c...@witthoft.com The Witthoft Group, Consulting https://witthoftgroup.weebly.com/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] spontaneous window switches?
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 -- Carl Witthoft personal: c...@witthoft.com The Witthoft Group, Consulting https://witthoftgroup.weebly.com/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] another R crash issue
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
Re: [R-SIG-Mac] [External] Re: problem with Rprof
he 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 -- Carl Witthoft personal: c...@witthoft.com The Witthoft Group, Consulting https://witthoftgroup.weebly.com/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] problem with Rprof
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
[R-SIG-Mac] strange error message
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 -- Carl Witthoft personal: c...@witthoft.com The Witthoft Group, Consulting https://witthoftgroup.weebly.com/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] noob asked for help
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] -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] svn location
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, ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] svn tarball
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, ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Editor beginning-of-line-chomp?
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. -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
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]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
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
Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
ut 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 ___CFXNotificationPost_block_invoke + 80 (CoreFoundation + >>>
[R-SIG-Mac] Strange "NOTE" when running R CMD CHECK
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. -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
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 (AppKit
Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
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, 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) [0x7fff2dd16977] 51 -[_NSBackingLay
Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
/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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Can't open files in 4.0 or 4.01
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problem with CHECK --as-cran on Catalina
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problem with CHECK --as-cran on Catalina
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problem with CHECK --as-cran on Catalina
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Problem with CHECK --as-cran on Catalina
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Transitioning from Mac to LInux?
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? -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] R vs. Microsoft R-Open updates?
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? -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/WitthoftResume ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Help page key bindings
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. -- Carl Witthoft c...@witthoft.com http://witthoft.com/resume ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] hangs under Yosemite redux
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 -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Still have hangs on Open Dialog Box
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 -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] hangs on Open Dialog
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 c...@witthoft.com To: r-sig-mac@r-project.org 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 -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] corrupted plist file again
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 -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] corrupted plist file again
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 c...@witthoft.com 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 -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] OpenFile Dialog hangs
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 ??? (FB7F246D-65AE-35E3-87A5-12D703F71C54 + 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
Re: [R-SIG-Mac] OpenFile hang; fixed not solved
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 -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] feature request: editor match brackets
Yes, I know about SHIFT-CTRL-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 -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] arguments to dev.new()
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 -- Sent from a parallel universe almost, but not entirely, nothing at all like this one. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] OT Re:haxies and injection
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. -- Sent from my Cray XK6 Quidvis recte factum, quamvis humile, praeclarum. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Block commenting - I found it
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
--
Sent from my Cray XK6
Pendeo-navem mei anguillae plena est.
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Re: [R-SIG-Mac] quartz.save tilde
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] Error:
CGImageDestinationCreate destination parameter is nil
--
Message: 2 Date: Wed, 2 Nov 2011 22:21:42 -0400 From: Denis
Chabotchabot.de...@gmail.com 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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Pendeo-navem mei anguillae plena est.
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[R-SIG-Mac] incomplete final line?
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 -- Sent from my Cray XK6 Pendeo-navem mei anguillae plena est. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] packages failed to load
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 quote Message: 4 Date: Tue, 24 May 2011 16:32:41 +1000 From: Ian Reeve ire...@une.edu.au To: r-sig-mac@r-project.org 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] followup: my problems with gmp and gnu MP
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] odd problem building gmp from source
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)) ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
