Re: [R-SIG-Mac] Help on reducing size of shared libraries on MacOS on CRAN

[Ken Beath]

A random sample of packages linking to Rcpp shows that many have NOTEs for 
installed package size.

I would avoid using special compiler flags, as this is something that may cause 
problems in the future.

Ken

> On 19 Mar 2023, at 8:27 am, Gilberto Camara  
> wrote:
> 
> Hi Simon
> 
> Many thanks for your quick response.  
> 
> My concern has to do with the CRAN Repository Policies, which state: 
> "Maintainers will be asked to update packages which show any warnings or 
> significant notes”. Since the concept of what are “significant notes" is not 
> clearly defined, it is natural that maintainers would like their packages to 
> be free of any NOTE.
> 
> That said, your explanation is quite helpful and informative.
> 
> Best regards
> Gilberto
> 
> 
> Prof Dr Gilberto Camara
> Senior Researcher
> National Institute for Space Research (INPE), Brazil
> https://gilbertocamara.org/
> =
> 
> 
> 
> 
>> On 18 Mar 2023, at 18:19, Simon Urbanek  wrote:
>> 
>> Gilberto,
>> 
>> Please note that size checks are not really relevant for binary packages - 
>> it is normal for binaries to be large as they may include static libraries 
>> (e.g., rgdal has 273Mb). Also note that 4.8Mb is rather small for a library 
>> since it also includes debugging symbols (CRAN packages are built with 
>> --dsym to make debugging easier) - so is there a particular reason you are 
>> concerned about the size? You can always remove the debugging symbols 
>> (libs/*.dsym) on your machine if you have issues with size.
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> On 19/03/2023, at 07:02, Gilberto Camara  
>>> wrote:
>>> 
>>> Dear R-SIG-MAC members
>>> 
>>> We are the developers of R package sits and would like to ask for your help 
>>> in solving a problem with library size on R macOS binaries. 
>>> 
>>> Before submission to CRAN, version 1.3.0 of sits 
>>> (https://cran.r-project.org/web/packages/sits/index.html) has been tested 
>>> in various environments, including Ubuntu, Fedora, CRAN winbuilder (all 
>>> flavors). We have tested sits-1.3.0 on r-release-mac-x86_64 and 
>>> r-release-macos-arm64 with the following configurations:
>>> 
>>> - r-release-macos-x86_64: R 4.2.2, MacMini 3.2GHz, 6 cores, 32 MB RAM, 
>>> macOS Ventura 3.2.1, Apple clang version 14.0.3 (clang-1403.0.22.14.1).
>>> 
>>> - r-release-macos-arm64: R 4.2.2, MacBookAir, chip ARM M1, 8 cores, 16 MB 
>>> RAM, macOS Monterrey 12.6,  Apple clang version 14.0.0 
>>> (clang-1400.0.29.201). 
>>> 
>>> In our configuration of r-release-macos-x86_64, the installed size is 3.8 
>>> MB, and the libs directory size is 436 KB. On r-release-macos-arm64, the 
>>> installed size is 5.4 MB and the libs directory size is 1.6 MB. 
>>> 
>>> The current CRAN check on sits version 1.3.0 reports a NOTE on 
>>> r-release-macos-arm64 and r-oldrel-macos-arm64, with an installation size 
>>> of 7.3Mb with the libs directory size reported as 4.8Mb. CRAN is using 
>>> Apple clang version 13.0.0 ((clang-1300.0.29.30) on r-release-macos-arm64 
>>> and Apple clang version 12.0.0 (clang-1200.0.32.29) on 
>>> r-oldrel-macos-arm64. 
>>> 
>>> There is a 3.2 MB difference in size between what CRAN reports and what we 
>>> obtain in our tests for r-release-macos-arm64. We would appreciate your 
>>> guidance on how to address this problem and, if possible, point to a 
>>> reliable way to reduce package size in macOS. 
>>> 
>>> Note that our package links to RCpp and RCppArmadillo.
>>> 
>>> Our current Makevars configuration is given below
>>> ==
>>> # suggestion by Dirk Eddelbuettel
>>> SHLIB_CXXLDFLAGS = -Wlto,-S -shared
>>> SHLIB_CXX11LDFLAGS = -Wlto,-S -shared
>>> SHLIB_CXX14LDFLAGS = -Wlto,-S -shared
>>> SHLIB_FCLDFLAGS = -Wlto,-S -shared
>>> SHLIB_LDFLAGS = -Wlto,-S -shared
>>> 
>>> ## suggestion by Dirk Eddelbuettel
>>> PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
>>> PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
>>> 
>>> strippedLib: $(SHLIB)
>>> if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" 
>>> ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
>>> 
>>> clean:
>>> rm -f $(OBJECTS)
>>> 
>>> .phony: strippedLib clean
>>> ===
>>> 
>>> Any help would be much appreciated. 
>>> 
>>> Best regards
>>> Gilberto
>>> 
>>> Prof Dr Gilberto Camara
>>> Senior Researcher
>>> National Institute for Space Research (INPE), Brazil
>>> https://gilbertocamara.org/
>>> =
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
> 
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Re: [R-SIG-Mac] List of unnecessary messages when I plot something in R from Terminal

[Ken Beath]

What may be important is that you are running R 4.2.1 which was replaced by 
4.2.2 on 31 October 2022, and may know a lot more about Ventura.

Also if you are on Ventura it would probably be best to make sure that you are 
upgraded to 13.2 which hopefully has a lot of the bugs fixed.

Ken

> On 12 Feb 2023, at 8:08 am, Christofer Bogaso  
> wrote:
> 
> Hi,
> 
> I am running Big Sur. Below is my sessionInfo()
> 
>> sessionInfo()
> 
> R version 4.2.1 (2022-06-23)
> 
> Platform: x86_64-apple-darwin17.0 (64-bit)
> 
> Running under: macOS Big Sur ... 10.16
> 
> 
> Matrix products: default
> 
> BLAS:   
> /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
> 
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
> 
> 
> locale:
> 
> [1] C/UTF-8/C/C/C/C
> 
> 
> attached base packages:
> 
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> 
> loaded via a namespace (and not attached):
> 
> [1] compiler_4.2.1
> 
> On Sun, Feb 12, 2023 at 1:55 AM Simon Urbanek
>  wrote:
>> 
>> Christofer,
>> 
>> yes, unfortunately this is a known bug in macOS Ventura affecting a lot of 
>> command-line programs that use GUI. Do not upgrade to Ventura (usually a 
>> good advice given the long list of known bugs in Ventura) or wait for a fix 
>> from Apple.
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> On Feb 11, 2023, at 11:28 PM, Christofer Bogaso 
>>>  wrote:
>>> 
>>> Hi,
>>> 
>>> When I plot something in R, then it open Quartz and in the console I
>>> see below messages
>>> 
 plot(1:4)
>>> 
 1   HIToolbox   0x7ff8229a2726 
 _ZN15MenuBarInstance22EnsureAutoShowObserverEv + 102
>>> 
>>> 2   HIToolbox   0x7ff8229a22b8
>>> _ZN15MenuBarInstance14EnableAutoShowEv + 52
>>> 
>>> 3   HIToolbox   0x7ff822946908
>>> SetMenuBarObscured + 408
>>> 
>>> 4   HIToolbox   0x7ff8229464ca
>>> _ZN13HIApplication15HandleActivatedEP14OpaqueEventRefhP15OpaqueWindowPtrh
>>> + 164
>>> 
>>> 5   HIToolbox   0x7ff822940996
>>> _ZN13HIApplication13EventObserverEjP14OpaqueEventRefPv + 252
>>> 
>>> 6   HIToolbox   0x7ff822908bd2
>>> _NotifyEventLoopObservers + 153
>>> 
>>> 7   HIToolbox   0x7ff8229403e6
>>> AcquireEventFromQueue + 494
>>> 
>>> 8   HIToolbox   0x7ff82292f3ec
>>> ReceiveNextEventCommon + 285
>>> 
>>> 9   HIToolbox   0x7ff82292f2b3
>>> _BlockUntilNextEventMatchingListInModeWithFilter + 70
>>> 
>>> 10  AppKit  0x7ff81c136f33 _DPSNextEvent + 
>>> 909
>>> 
>>> 11  AppKit  0x7ff81c135db4
>>> -[NSApplication(NSEvent)
>>> _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1219
>>> 
>>> 12  grDevices.so0x0001086f7a3b input_handler + 
>>> 155
>>> 
>>> 13  libR.dylib  0x000108b142cf
>>> Rstd_ReadConsole + 2127
>>> 
>>> 14  libR.dylib  0x000108a15b74
>>> Rf_ReplIteration + 100
>>> 
>>> 15  libR.dylib  0x000108a174b1 R_ReplConsole + 
>>> 161
>>> 
>>> 16  libR.dylib  0x000108a17402 run_Rmainloop + 
>>> 82
>>> 
>>> 17  libR.dylib  0x000108a1753e Rf_mainloop + 14
>>> 
>>> 18  R   0x00010847af5b main + 27
>>> 
>>> 19  dyld0x7ff818bde310 start + 2432
>>> 
>>> 1   HIToolbox   0x7ff822aa952b
>>> _ZN15MenuBarInstance21IsAutoShowHideAllowedEv + 259
>>> 
>>> 2   HIToolbox   0x7ff8229a233e
>>> _ZN15MenuBarInstance24UpdateAutoShowVisibilityE5Pointh + 34
>>> 
>>> 3   HIToolbox   0x7ff8229117a4
>>> _ZN15MenuBarInstance16ForEachMenuBarDoEU13block_pointerFvPS_E + 46
>>> 
>>> 4   HIToolbox   0x7ff8229a293d
>>> _ZN15MenuBarInstance20AutoShowHideObserverEjP14OpaqueEventRefPv + 165
>>> 
>>> 5   HIToolbox   0x7ff822908bd2
>>> _NotifyEventLoopObservers + 153
>>> 
>>> 6   HIToolbox   0x7ff82293afb8
>>> PostEventToQueueInternal + 700
>>> 
>>> 7   HIToolbox   0x7ff82293c871
>>> _ZL29CreateAndPostEventWithCGEventP9__CGEventjhP17__CFMachPortBoost +
>>> 404
>>> 
>>> 8   HIToolbox   0x7ff822948ee9
>>> _ZL15Convert1CGEventh + 246
>>> 
>>> 9   HIToolbox   0x7ff822948d91
>>> _ZL16MainLoopObserverjP14OpaqueEventRefPv + 41
>>> 
>>> 10  HIToolbox   0x7ff822908bd2
>>> _NotifyEventLoopObservers + 153
>>> 
>>> 11  HIToolbox   0x7ff82292f726
>>> RunCurrentEventLoopInMode + 228
>>> 
>>> 12  HIToolbox   0x7ff82292f396
>>> 

Re: [R-SIG-Mac] Cannot open PDF Vignettes on Ventura

[Ken Beath]

The problem seems to be with the Electron framework they switched to in the 
current version. 

>From https://dailies.rstudio.com/version/2022.07.1+554.pro3/ the previous 
>version works, but not the Electron version. For those that are interested 
>Electron is a newer framework that has the advantage of being completely free, 
>and is what is now used by RStudio rather than Qt.

Ken

> On 7 Feb 2023, at 2:49 pm, Kevin Thorpe  wrote:
> 
> Thanks Simon and Duncan.
> 
> I found the same plugins and removed them. It works correctly in the R.app.
> 
> RStudio still directs me to a browser window at the localhost address 
> 127.0.0.1 and nothing loads. I know RStudio is not R and this list is for R 
> so will probably have to search elsewhere for that solution unless anyone 
> here happens to have an idea.
> 
> Kevin
> 
> -- 
> Kevin E. Thorpe
> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael’s Hospital
> Assistant Professor, Dalla Lana School of Public Health
> University of Toronto
> email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
> 
>> On Feb 6, 2023, at 7:53 PM, Duncan Murdoch  wrote:
>> 
>> That worked for me.  I deleted two plugins from the global 
>> /Library/Internet\ Plug-Ins folder named
>> 
>> AdobePDFViewer.plugin
>> AdobePDFViewerNPAPI.plugin
>> 
>> and dated from 2020.  Now things are fine.
>> 
>> Duncan Murdoch
>> 
>> On 06/02/2023 7:36 p.m., Simon Urbanek wrote:
>>> Kevin,
>>> oh, that's something entirely different - what I was talking about was if 
>>> you use
>>> vignette("survival")
>>> in R it opens a Preview with the vignette.
>>> What you describe seems like a browser plugin issue, because the help 
>>> system is just an html page (assuming you are talking about the html help 
>>> system). So it seems that you may have installed some Adobe browser plugin 
>>> that doesn't work anymore. The plugins live in ~/Library/Internet\ 
>>> Plug-Ins/ (user) and /Library/Internet\ Plug-Ins/ (global), so you should 
>>> remove it from there.
>>> Cheers,
>>> Simon
 On 7/02/2023, at 12:01 PM, Kevin Thorpe  wrote:
 
 When I try to open a PDF vignette (say a vignette from the survival 
 package)from the help system in R it does not open Preview. I cannot 
 actually open any PDF vignettes. All I get is a finder window with the 
 error I previously described. It asks me to select an appropriate viewer. 
 Selecting Preview opens nothing and more errors are thrown to the Console. 
 I could send you and Duncan screenshots off-list, since I know that theses 
 lists are picky about attachments.
 
 The steps I take are:
 
 1. Open the R app.
 2. Start the Help system.
 3. Navigate to the survival package vignettes.
 4. Click the PDF link for the The survival package
 
 Then the errors happen.
 
 I will send a screenshot of the result off list.
 
 Kevin
 
 -- 
 Kevin E. Thorpe
 Head of Biostatistics,  Applied Health Research Centre (AHRC)
 Li Ka Shing Knowledge Institute of St. Michael’s Hospital
 Assistant Professor, Dalla Lana School of Public Health
 University of Toronto
 email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
 
> On Feb 6, 2023, at 4:58 PM, Simon Urbanek  
> wrote:
> 
> Kevin,
> 
> can you then describe in more detail what you are taking about? If you 
> open a PDF vignette in R, it simply calls "open" so it will open in 
> Preview (as that is your system viewer). And you have confirmed that it 
> is what happens, so are you taking about something else? If so, please 
> describe every step you make to reproduce whatever issue you are having.
> 
> Thanks,
> Simon
> 
> 
> On Feb 7, 2023, at 9:58 AM, Kevin Thorpe  wrote:
>> 
>> Yes, it does.
>> 
>> Kevin
>> 
>> -- 
>> Kevin E. Thorpe
>> Head of Biostatistics,  Applied Health Research Centre (AHRC)
>> Li Ka Shing Knowledge Institute of St. Michael’s Hospital
>> Assistant Professor, Dalla Lana School of Public Health
>> University of Toronto
>> email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>> 
>>> On Feb 6, 2023, at 3:56 PM, Duncan Murdoch  
>>> wrote:
>>> 
>>> On 06/02/2023 3:47 p.m., Kevin Thorpe wrote:
 Simon,
 Preview is my default viewer. In the finder window that came up I 
 tried selecting Preview as the viewer to use and it still failed. The 
 following errors went to the Console.
 2023-02-06 15:43:55.448 R[62964:5174302] +[CATransaction synchronize] 
 called within transaction
 2023-02-06 15:43:55.568 R[62964:5174302] +[CATransaction synchronize] 
 called within transaction
 2023-02-06 15:44:03.253 R[62964:5174302] +[CATransaction synchronize] 
 called within transaction
 

Re: [R-SIG-Mac] Unable to library package "affy"

[Ken Beath]

The question is why do you need to install from sources. Using a standard R 
install and then following the instructions at 
https://www.bioconductor.org/install/  and then use 
BiocManager::install(“affy”) It works for me. If it doesn’t for you, then you 
have done something to your installation. Life will be easier if you just use a 
standard installation.

Ken


> On 13 Dec 2022, at 4:18 pm, Bowen Lai  wrote:
> 
> R version: 4.2.2
> Arm64 with M1 SoC
> 
> 
> my problem is totally same as this guy 
> https://support.bioconductor.org/p/9148182/
> so i search in Google and downlaod gfortan is neccessary.
> Therefore, I have download ARM64 Macs: 
> gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz from 
> https://github.com/R-macos/gcc-darwin-arm64/releases/tag/R-4.2.0-release , 
> but i can't understand how to use gfortran in R to library package so the 
> problem is still unsolved.
> 
> 
> 
> 
> In detail, i can't understand the following steps because i am a medical 
> student and know a little about professional CS.
> 
> 
> 
> 
> "This binary installs into /opt/R/arm64/gfortran with an additional symlink 
> in /opt/R/arm64/bin/gfortran. To unpack use
> 
> tar fxz gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
> 
> 
> (prefix with sudo if you need admin permissions to write to /opt/R/arm64). To 
> use set
> 
> export PATH=$PATH:/opt/R/arm64/gfortran/bin
> 
> 
> In addition, /opt/R/arm64/gfortran/SDK has to point to your macOS SDK. The 
> binary above points to MacOSX11.sdk of Xcode Command Line Tools, but you may 
> need to change it to match your installation. We include a script 
> gfortran-update-sdk in the above tar ball that you can simply run (prefix 
> with sudo if you require admin permissions).
> 
> This build has been configured with:
> 
> ../gcc-darwin-arm64/configure --prefix=/opt/R/arm64/gfortran 
> --enable-languages=c,fortran \
>   --with-gmp=/opt/R/arm64 --with-mpc=/opt/R/arm64 --with-mpfr=/opt/R/arm64 \
>   --with-sysroot=/opt/R/arm64/gfortran/SDK"
> Sincerely Yours
> Bowen Lai
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] [External] Xquartz started crashing today

[Ken Beath]

Less than 30 seconds on my iMac, so something is very wrong with your fonts or 
file system.

Ken

> On 6 Jun 2022, at 2:34 pm, Richard M. Heiberger  wrote:
> 
> I am in the middle of validating fonts. The machine has been running for 
> about 12 hours, the Activity Monitor CPU
> time for the Font Book app is currently at 2:35.15. It keeps going up but 
> very slowly.
> The progress bar at the bottom of the Font Validation window has been stuck 
> at about 1% from when it started and hasn't moved.
> How long is this task supposed to take?
> 
>> On Jun 04, 2022, at 00:49, Richard M. Heiberger > > wrote:
>> 
>> Simon,
>> 
>> Thank you for reading this.
>> 
>> I sent what Apple gave me. I had not previously tried reading one of these.
>> So should I be so lucky in the future, then all you need is everything 
>> between
>> Process: R [
>> and the next occurence of
>> Process: 
>> ?
>> 
>> and maybe also the up front stuff before the Process: information.
>> 
>> I already rebooted, installed a new R, and a new Xquartz. Those didn't help.
>> Reinstalling R is probably irrelevant because the problem occurred first in 
>> 4.1-arm64,
>> which is why I upgraded to 4.2-arm64. And it was still there.
>> 
>> This suggests that the problem is with the Fonts. I have never touched them 
>> (on purpose).
>> I will learn a little in the next frew days and see what can be done with 
>> validation.
>> I will let you know. But what made the fonts (if that is indeed the problem) 
>> go invalid.
>> I can't think of anything I did that could be relevant.
>> 
>> Rich
>> 
>> 
>>> On Jun 03, 2022, at 23:32, Simon Urbanek  
>>> wrote:
>>> 
>>> Rich,
>>> 
>>> thanks. You sent a log of all processes on your machine, just the R report 
>>> would have been fine (which is only 18k).
>>> 
>>> The hang occurs in ATSFontFindFromName() where the system is looking for 
>>> fonts, so you could try: a) reboot he machine, b) run Font Book (in 
>>> Applications), c) select all fonts () d) in the menu select File -> 
>>> Validate Fonts e) select any invalid fonts and remove them f) reboot
>>> 
>>> If the problem persists try re-installing the R 4.2.0 release if it makes 
>>> any difference.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
 On Jun 4, 2022, at 3:10 AM, Richard M. Heiberger  wrote:
 
 cover letter for crash report, that also got stopped for being part of a 
 too large email,
 
 
 I am doing nothing different that I know of.
 I start R within emacs using ESS with M-x R
 
 
 R version 4.2.0 Patched (2022-06-02 r82444) -- "Vigorous Calisthenics"
 Copyright (C) 2022 The R Foundation for Statistical Computing
 Platform: aarch64-apple-darwin20 (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.
 
 Natural language support but running in an English locale
 
 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.
 
 Type 'demo()' for some demos, 'help()' for on-line help, or
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.
 
> setwd('/Users/rmh/Rwd2/')
> plot(1:10)
> C-c C-c
 
 
 
 ## it just sits there, completely frozen and ignores C-c C-c
 ## then I Force Quit it from the Activity Monitor
 Process R terminated: 15 at Thu Jun 2 22:39:39 2022
 
 
 Do you want the crash report that the Mac offers to send to Apple?
 
 ---
 I just finished updating all my packages.
 So now the crash generation and report.
 I entered
 
 plot(1:10)
 
 The rotating beachball appeared. No graph, C-c C-c has no effect..
 
 Force Quit from Activity Monitor and CrashReport attached:
 
 
 Just for fun, I started R.app and entered plot(1:10)
 Same freeze and I Force Quit it again.
 I am not bothering with the Crash Report unless you tell me you need it 
 too.
 
 Rich
 
> On Jun 02, 2022, at 23:02, Simon Urbanek  
> wrote:
> 
> Regular R does not use X11 by default, so what exactly are you doing? 
> You'll have to provide more details, the exact way you run R, code to 
> reproduce and where it hangs, ideally with a crash report (which macOS 
> creates on hangs as well).
> 
> Cheers,
> Simon
> 
> 
>> On 3/06/2022, at 2:51 PM, Richard M. Heiberger  wrote:
>> 
>> it makes R unresponsive according to the activity monitor.
>> The only repair I have found is to ForceQuit R from the Activity 
>> Monitor, and start fresh R session.
>> I downloaded a fresh copy of XQuartz-2.8.1.dmg and have the same 
>> negative results.
>> I downloaded a fresh R from 
>> 

Re: [R-SIG-Mac] R-SIG unsubscribe

[Ken Beath]

Apparently "Once a month, your password will be emailed to you as a reminder."

I receive mine on the 1st of each month from mailman-ow...@r-project.org 


Ken

> On 23 Nov 2021, at 9:19 pm, Tony Perry  wrote:
> 
> It's not efficient if I need to enter in a password I can't remember and no
> reminder email comes when this is clicked.  Most sites have a simple
> unsubscribe button.
> 
> 
> 
> On Tue, 23 Nov 2021, 08:31 peter dalgaard,  > wrote:
> 
>> The efficient procedure is to follow the link at the bottom of every mail
>> 
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> (Use the "Unsubscribe or edit options" button near the end of the page.)
>> 
>> -pd
>> 
>> 
>>> On 23 Nov 2021, at 09:14 , Tony Perry  wrote:
>>> 
>>> Dear R-Sig group,
>>> 
>>> I would like tor request to be removed from the R-SIG group.
>>> 
>>> Thank you!
>>> 
>>> Tony
>>> 
>>>  [[alternative HTML version deleted]]
>>> 
>>> ___
>>> 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
>> 
>> 
> 
>   [[alternative HTML version deleted]]
> 
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> 

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Re: [R-SIG-Mac] NaN bug with arima() on Mac

[Ken Beath]

Looking at the returned object there are problems with some of the standard 
errors which are NaN for both aima and arima0. This usually indicates that the 
Hessian doesn’t have the required form. This can be very dependent on the 
system. It also probably means that the model you are fitting is over 
parameterised.

Ken

> On 23 Nov 2021, at 9:21 am, Simon Urbanek  wrote:
> 
> 
> Nikolas,
> 
> what makes you think it is a bug? It is an optimization process, so the 
> objective function is free to produce NaN for unsuitable parameters so it can 
> steer the optimization away from such areas.
> 
> Cheers,
> Simon
> 
> 
>> On Nov 23, 2021, at 2:29 AM, Kuschnig, Nikolas  
>> wrote:
>> 
>> Dear all,
>> 
>> There seems to be a small bug with `arima()` on Mac. For some very specific 
>> data
>> I get the following warning:
>>  Warning message:
>>  In log(s2) : NaNs produced
>> This seems to stem from `.Call(C_ARIMA_Like, x, Z, 0L, FALSE)` in the 
>> `armafn()`
>> objective function. This warning does not occur on Linux or Windows systems 
>> or
>> when using the `arima0()` function.
>> Below is an example that I hope reproduces (please excuse the dependency, I 
>> only
>> encountered it with this data, partly due to my lack of a Mac). Note that the
>> warning in question occurs during estimation, printing always induces a 
>> warning.
>> 
>> 
>> # install.packages("BVAR")
>> library("BVAR")
>> 
>> x <- fred_qd[1:243, 
>> c("GDPC1", "PCECC96", "GPDIC1", "HOANBS", "GDPCTPI", "FEDFUNDS")]
>> x <- fred_transform(x, codes = c(4, 4, 4, 4, 4, 1))
>> Y <- as.matrix(x)[6:nrow(x), ]
>> 
>> ar <- apply(Y, 2, arima, order = c(5, 0, 0)) # Warning only on Mac
>> ar0 <- apply(Y, 2, arima0, order = c(5, 0, 0)) # No warning
>> 
>> 
>> Does anyone have any more information on this? Thanks for the help!
>> 
>> Best,
>> -- 
>> Nikolas Kuschnig
>> 
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Re: [R-SIG-Mac] https://mac.r-project.org/benchmarks/

[Ken Beath]

I ran some tests using my packages and a bootstrapped linear model, and the 
results were that my M1 MacBook Air was faster than my iMac 8-core 2020, and 
that included using 4 parallel cores on the M1 versus 8 on the iMac. 

Ken

> On 1 Nov 2021, at 8:11 am, Simon Urbanek  wrote:
> 
> 
> Tim,
> 
> that is a great idea, those test are really old. Just for the fun of it I 
> have run the tests on my old iMac, but with R 4.1.2 and they still work.
> It's nice to see the huge speed improvements in loops and similar (see below 
> - recall the original tests were scaled to be around 1).
> 
> I have added the page to the repo
> https://github.com/R-macos/R-mac-dev
> so I'd be happy to review PRs, but I'll probably want to re-do it first so it 
> is better organized for comparisons as we have to also accommodate M1 etc.
> 
> Cheers,
> Simon
> 
> ---
> iMac14,2 3.2Ghz i5, macOS 10.4.6, R 4.1.2 vecib/Accelerate BLAS
> 
> 
>   R Benchmark 2.5
>   ===
> Number of times each test is run__:  3
> 
>   I. Matrix calculation
>   -
> Creation, transp., deformation of a 2500x2500 matrix (sec):  
> 0.8296667 
> 2400x2400 normal distributed random matrix ^1000 (sec):  
> 0.1553334 
> Sorting of 7,000,000 random values__ (sec):  
> 0.6383334 
> 2800x2800 cross-product matrix (b = a' * a)_ (sec):  
> 0.2420001 
> Linear regr. over a 3000x3000 matrix (c = a \ b')___ (sec):  
> 0.170 
>  
> Trimmed geom. mean (2 extremes eliminated):  0.29781941072597 
> 
>   II. Matrix functions
>   
> FFT over 2,400,000 random values (sec):  
> 0.331 
> Eigenvalues of a 640x640 random matrix__ (sec):  
> 0.3470001 
> Determinant of a 2500x2500 random matrix (sec):  
> 0.2070001 
> Cholesky decomposition of a 3000x3000 matrix (sec):  
> 0.2543334 
> Inverse of a 1600x1600 random matrix (sec):  
> 0.3456663 
>  
>Trimmed geom. mean (2 extremes eliminated):  0.307686639256803 
> 
>   III. Programmation
>   --
> 3,500,000 Fibonacci numbers calculation (vector calc)(sec):  0.245 
> Creation of a 3000x3000 Hilbert matrix (matrix calc) (sec):  
> 0.2896669 
> Grand common divisors of 400,000 pairs (recursion)__ (sec):  
> 0.2593331 
> Creation of a 500x500 Toeplitz matrix (loops)___ (sec):  
> 0.0415 
> Escoufier's method on a 45x45 matrix (mixed) (sec):  
> 0.2630005 
>  
>Trimmed geom. mean (2 extremes eliminated):  0.255658395143118 
> 
> 
> Total time for all 15 tests_ (sec):  4.618667 
> Overall mean (sum of I, II and III trimmed means/3)_ (sec):  
> 0.286136920519432 
>  --- End of test ---
> 
> 
> 
>> On Nov 1, 2021, at 2:48 AM, Tim Bates  wrote:
>> 
>> I wonder if this (2008/R 2.7) page could be updated with some current 
>> benchmark runs?
>> 
>> Especially current Intel server chips, i9, and M1/+ 
>> 
>> I'm guessing if Simon could help upload the resulting updated page, people 
>> here could contribute bench mark runs on different hardware.
>> 
>> 
>> Also be interesting to see different blas results.
>> 
>> I wonder if either intel or arm chip "neural" cores (dot product engines?) 
>> or multi-core and GPU are being used in current R builds?
>> 
>> tim
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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> 
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Re: [R-SIG-Mac] r-sig-mac@r-project.org - "You can’t open the application “R” because this application is not supported on this Mac"

[Ken Beath]

You could try the Intel version until the problem with ARM is sorted. It should 
run fine but will require Rosetta 2.

Ken

> On 17 Jul 2021, at 5:39 pm, Lindsay Foreman <19038...@brookes.ac.uk> wrote:
> 
> To whom it may concern, 
> 
> I am so sorry for being such a dunce.  I have been trying and trying to get 
> the R App to work on my MacBook Air running Big Sur V11.4, and am just not 
> making any progress.  It says that the package I have downloaded below should 
> have all the elements I need including the R app GUI.  I get this error 
> message "You can’t open the application “R” because this application is not 
> supported on this Mac"., are you able to help please?
> 
> Your support is much appreciated.
> Lindsay Foreman
> 
> R-4.1.0-arm64.pkg 
>  
> (notarized and signed)
> SHA1-hash: 7354c1b249cab9bafea6ae67c73563303a05fa17
> (ca. 88MB)R 4.1.0 binary for macOS 11 (Big Sur) and higher, Apple silicon 
> arm64 build, signed and notarized package.
> Contains R 4.1.0 framework, R.app GUI 1.76 for Apple silicon Macs (M1 and 
> higher), Tcl/Tk 8.6.11 X11 libraries and Texinfo 6.7.
> Important: this version does NOT work on older Intel-based Macs.
> The above installer package will be misidentified by Apple Installer as Intel 
> architecture although it contains no Intel code. This means you may be asked 
> to install Rosetta 2 even though it is not required. This issue has been 
> fixed in the packaging for future R versions, so if you don't want to install 
> Rosetta 2 please use R-4.1-branch big-sur arm64 installer from 
> mac.R-project.org .
> Note: the use of X11 (including tcltk) requires XQuartz 
> . Always re-install XQuartz when upgrading 
> your macOS to a new major version.
> 
> This release uses Xcode 12.4 and experimental GNU Fortran 11 arm64 fork. If 
> you wish to compile R packages from sources, you may need to download GNU 
> Fortran for arm64 from https://mac.R-project.org/libs-arm64 
> . Any external libraries and tools are 
> expected to live in /opt/R/arm64 to not conflict with Intel-based software 
> and this build will not use /usr/local to avoid such conflicts.
> 
> 
> 
> 
> 
>> On 13 Jul 2021, at 16:32, Dr. Alessio Pruneddu  wrote:
>> 
>> Hi Lindsay,
>> 
>> Thanks a lot for your kind words. I am sorry to hear R is giving you 
>> troubles with Mac. I know for a fact that this might be the case with very 
>> new version of any mac. If you cannot access any standard Windows PC or 
>> laptop, try to download R studio, and in any case, check the compatibility 
>> requirements of the software (R and/or R studio) before you download it, so 
>> that you will not have any surprises.
>> 
>> I hope it helps!!
>> 
>> Alessio.
>> 
>> Il giorno mar 13 lug 2021 alle ore 07:54 Lindsay Foreman 
>> <19038...@brookes.ac.uk > ha scritto:
>> Thank you again for your time and dedication Alessio, I cannot thank you 
>> enough.  The thought of doing this in isolation, without you or the Q gang 
>> for support is a terrifying one!
>> 
>> I have to confess how out of my comfort zone I feel, with the data, the 
>> statistics and the code.  I have tried several time to install the R 
>> software from https://cran.r-project.org/ , but 
>> no matter which one I select and download, when I try and open it I just an 
>> error message "You can’t open the application “R” because this application 
>> is not supported on this Mac.” I have read the FAQ’s but no joy and I cannot 
>> seem to find where I ask for help.  I know you said this is out of your 
>> remit, but any pointers you are able to give to help resolve this would be 
>> much appreciated.  As you say, we will get there, I am just in the midst of 
>> a painful part of the process where I feel completely out of my depth!
>> 
>> Hopefully I can be a trailblazer for Leo and Elizabeth so that when they are 
>> at this stage I can offer some support and guidance.
>> Onwards and upwards,
>> Lindsay
>> 
>> 
>>> On 10 Jul 2021, at 12:02, Dr. Alessio Pruneddu >> > wrote:
>>> 
>>> Dear members of the Q squad,
>>> 
>>> I cannot stress enough how much I am happy to have a chat with you. I just 
>>> thought you would appreciate a few details after yesterday's video chat. 
>>> Please see my comments below;
>>> 
>>> 
>>> Lindsay.
>>> 
>>> Huge apologies for yesterday!. I still hope I was able to give you a 
>>> flavour of what you can expect from the data analysis in R. In your case, I 
>>> would recommend performing the data analysis using the code. Please find 
>>> attached the code specifically related to your study. You will find out a 
>>> slightly more sophisticated line, as you have to instruct the software 
>>> about the free distribution in your sample. However, the sophistication is 
>>> only 

Re: [R-SIG-Mac] Corrupt R installation

[Ken Beath]

With RStudio I just quit, restart and then update the packages.

Ken

> On 11 Jun 2021, at 8:07 am, Simon Urbanek  wrote:
> 
> 
> Those errors come from packages that you didn't re-install - anything that 
> uses /usr/local is not from CRAN. So check 
> /Users/Misha/Library/R/4.0/library/
> Best way is to move the entire tree aside (Eg. rename "library" to "old") to 
> make sure you don't pick up old stuff.
> 
> BTW: you can list packages from a tree even if it's not used by R by using 
> lib.loc, so if you renamed the library as above, you can still list all 
> packages in there by using
> 
> pkg=rownames(installed.packages(lib.loc="/Users/Misha/Library/R/4.0/old"))
> 
> Cheers,
> Simon
> 
> PS: just an aside, avoid using RStudio to perform upgrades as it has issues 
> when packages that it is using get upgraded, using R is safer.
> 
> 
>> On 11/06/2021, at 10:01 AM, moleps islon  wrote:
>> 
>> Allright - I´m way beyond believing I could save my packages and ended up 
>> removing everything (including all versions in R.framework dir.) I 
>> reinstalled from CRAN. But there is still something out of the ordinary. 
>> After installing some of them : Some work, others (meaning most) display 
>> 
>> "Error: package or namespace load failed for ‘tidyr’ in dyn.load(file, 
>> DLLpath = DLLpath, ...):
>> unable to load shared object 
>> '/Users/Misha/Library/R/4.0/library/glue/libs/glue.so':
>>  dlopen(/Users/Misha/Library/R/4.0/library/glue/libs/glue.so, 6): Library 
>> not loaded: /usr/local/opt/r/lib/R/lib/libR.dylib
>>  Referenced from: /Users/Misha/Library/R/4.0/library/glue/libs/glue.so
>>  Reason: image not found"
>> 
>> - but the library is listed both when I run installed.packages() from R and 
>> when I enter the correct directory from the terminal. Moreover - all 
>> privileges are OK within the directory. 
>> 
>> I promise I´ll never try another shortcut in updating R--must have taken me 
>> better part of a week to try and sort this out.
>> 
>> 
>> 
>> 
>> On Thu, Jun 10, 2021 at 8:34 AM peter dalgaard  wrote:
>> Yep. (In the first form, you likely want a stoplist for base and recommended 
>> packages.)
>> 
>> You can also base it on a listing of the library directory. This has the 
>> advantage that you can fairly easily twiddle it to look at older versions 
>> after the upgrade.
>> 
>>> .libPaths()
>> [1] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library"
>>> list.files("/Library/Frameworks/R.framework/Versions")
>> [1] "3.0" "3.1" "3.2" "3.3" "3.4" "3.5" "3.6"
>> [8] "4.0" "Current"
>>> list.files("/Library/Frameworks/R.framework/Versions/3.6/Resources/library")
>>  [1] "assertthat""backports" "base" 
>>  [4] "base64enc" "BH""bitops"   
>>  [7] "boot"  "caTools"   "chron"
>> ...
>>> setdiff(list.files("/Library/Frameworks/R.framework/Versions/3.6/Resources/library"),rownames(installed.packages()))
>> [1] "caTools"  "dplyr""plogr""translations"
>> 
>> (Notice that "translations" is not a package, so  a red herring in this 
>> context)
>> 
>> -pd
>> 
>>> On 10 Jun 2021, at 00:26 , Simon Urbanek  
>>> wrote:
>>> 
>>> 
>>> Um, this is actually a lot easier purely with R - if you want to keep track 
>>> of your favorite packages it is as simple as
>>> 
>>> pkgs = rownames(installed.packages())
>>> writeLines(pkgs, "packages.txt")
>>> 
>>> and oyu have a list of all packages that you can edit if desired. if you 
>>> ever want to re-install then simply
>>> 
>>> pkgs = readLines("packages.txt")
>>> install.packages(pkgs)
>>> 
>>> and if you only want to install missing it's simply
>>> 
>>> missing.pkgs = pkgs[!pkgs %in% rownames(installed.packages())]
>>> install.packages(missing.pkgs)
>>> 
>>> All trivially done in R. It is always beyond me why people come up with 
>>> incredibly convoluted solutions to simple things ..
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>> 
 On 9/06/2021, at 8:55 PM, Dr Eberhard Lisse  wrote:
 
 On 08/06/2021 22:46, moleps islon wrote:
 [...]
> I have no idea why, but my R installation (Mac OS X - Big Sur)
> automatically updates causing havoc with my libraries each time.  My
> Mac is under administration from the university and their software
> center, but they claim it is not their fault - but I still suspect
> them for causing all the trouble.
 [...]
 
 Sounds like Homebrew to me.  If so, or anyway, create a file (before
 updating) which contains something like
 
  #!/usr/bin/env Rscript --vanilla
  #
  # set the Mirror
  #
  local({
 r <- getOption("repos")
  r["CRAN"] <- "https://cloud.r-project.org/;
 options(repos = r)
  })
  install.packages(c(
   "lubridate",
   "tidyverse"
  ), 

Re: [R-SIG-Mac] R 4.1 for my Mac M1 crashing on installing packages

[Ken Beath]

According to RStudio support for ARM R is only available in the RStudio daily 
builds https://dailies.rstudio.com  which are 
very unstable.

Ken

> On 19 May 2021, at 7:33 pm, Renato Morais  
> wrote:
> 
> Hi all,
> 
> I'm new here, so please forgive my clumsy error reporting.
> 
> I have just downloaded *R-4.1-branch.pkg* for my Mac M1, as I wanted to
> finally enjoy a native normal-speed R (for some reason running v 4.0.5 on
> Rosetta was extremely slow on my machine). I also installed the latest
> XQuartz, as indicated (v 2.8.1).
> 
> Sad story is, when I try a simple install.packages command, it first
> appears to ignore me, after returning 'Please select a CRAN mirror for use
> in this session'. if I insist, it crashes. No useful error messages. Trying
> via the Package Installer tab didn't work either. It doesn't find any
> packages, indeed it crashes if I ask it to load the list.
> 
> Trying to open via R.Studio 1.4.1106 was as unsuccessful. In fact, I get a
> nice 'Error starting R' rendered window saying it cannot load my library:
> 
> dyld: could not load inserted library
> '/Library/Frameworks/R.framework/Resources/lib/libR.dylib' because no
> suitable image found. Did find:
> /Library/Frameworks/R.framework/Resources/lib/libR.dylib: mach-o, but wrong
> architecture /Library/Frameworks/R.framework/Resources/lib/libR.dylib:
> stat() failed with errno=1
> 
> In summary, can anybody give me an insight on what might be going on?
> 
> Cheers and thanks in advance,
> Renato
> 
> -- 
> 
> *Renato Morais*
> 
> 
> 
> --
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] more rgl problems

[Ken Beath]

RStudio have a page for reporting bugs at 
https://github.com/rstudio/rstudio/issues/ 
 You may be the first M! bug.

They haven’t progressed my fairly serious bug report about Windows (if you plot 
a graph and the screen hasn’t updated when you start parallel processing then R 
crashes) from 6 weeks ago, so I wouldn’t be anticipating much progress soon.

Ken

> On 18 Feb 2021, at 2:13 pm, Peter West  wrote:
> 
> And speaking of M1 Silicon:
> 
> My XQuartz version is 2.7.11.
> 
> Started R 4.0.4.
> Stopped R 4.0.4
> Started RStudio
> 
>> install.packages("rgl")
> trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz'
> Content type 'application/x-gzip' length 6446159 bytes (6.1 MB)
> ==
> downloaded 6.1 MB
> 
> 
> The downloaded binary packages are in
>   
> /var/folders/jf/mkyz74311796dl4mxx_7tcx8gn/T//RtmpflD1wL/downloaded_packages
>> library(rgl)
> 
> RStudio hangs indefinitely.
> 
> My RStudio is at 1.4.1103.
> 
> Peter
> 
> —
> p...@ehealth.id.au
> “For what does it profit a man if he gains the whole world and loses or 
> forfeits himself?”
> 
>> On 18 Feb 2021, at 10:36 am, Richard M. Heiberger  wrote:
>> 
>> This is repeatable when the lines are all pasted in at once.
>> The example works if I allow some time delay between lines.
>> 
>> This is might be a relative of the one from a few months ago.
>> But this message is about invalid permissions.
>> =
>> 
>> R version 4.0.4 RC (2021-02-12 r79998) -- "Lost Library Book"
>> Copyright (C) 2021 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin17.0 (64-bit)
>> 
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>> 
>> Natural language support but running in an English locale
>> 
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>> 
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>> 
>>> setwd('/Users/rmh/Rwd/')
>>> library(rgl)
>>> x <- matrix(1:3, 1,3)
>>> plot(1:10, col=7)
>>> open3d()
>> error: xp_attach_gl_context returned: 2
>> 
>> *** caught segfault ***
>> address 0x18, cause 'invalid permissions'
>> 
>> Traceback:
>> 1: rgl.open(useNULL)
>> 2: open3d()
>> 
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection: 
>> 
>> 
>> 
>> MacBookAir with the M1 chip using the regular intel version of R from CRAN.
>> Big Sur 11.2.1.
>> The plot(1:10), col=7) ## went by default to the quartz() device.
>> 
>> 
>> I repeated this about 5 times in ESS, and then once in Terminal.
>> 
>> Let me know if you need more information.
>> 
>> 
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> 
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Re: [R-SIG-Mac] Unable to change some members of a vector

[Ken Beath]

This question is not related to Macs, but here is the answer anyway.

First up, anyone who uses R should understand what a factor is. Find an 
introductory text on R and read the section on factors. Even better, read the 
whole book.  It seems that it has been decided that R will not automatically 
add a factor level, which is probably a good idea.

There is an option in the read.table command of stringsAsFactors. You can set 
it to FALSE to obtain character strings. You can also convert the factor to 
character using as.character().

If Excel decides to put strange characters into your data file then that is 
Excel’s problem. I suggest looking at the file with a text editor. The free 
version of BBEdit will work fine. You can read Excel files directly using teh 
readxl package.

Ken

> On 14 Feb 2021, at 9:54 am, Parkhurst, David F.  wrote:
> 
> I have a problem I don’t know how to deal with.  I’ve used read.table to 
> create the data frame called msPdf.  It contains three vectors:  month, site, 
> conc.  Some of the site values look like this:  MLH\xca.  I was able to 
> change that with this command: msPdf$site[13]="MLH”.  That seems to have been 
> allowed because some of the other sites are simply MLH.  But the system won’t 
> let me make the same kind of change in another case:
> msPdf$site[29]="MUH”.  When I ask for that, I get 
> Warning message:
> In `[<-.factor`(`*tmp*`, 29, value = c(5L, 2L, 1L, 11L, 5L, 12L,  :
>   invalid factor level, NA generated
>> #13  May MLH\xca 0.007
> Then if I enter msPdf$site[29], I get this response:
> [1] 
> Levels: CrCr LMO MCE MCH MFSC MLE MLH MLH\xca MUE MUH\xca NFSC SFSC
> 
> In other words, although other sites that were just plain MLH, there were not 
> other sites that were just plain MUH.
> How can I fix this problem?  I have no idea why excel added those \xca bits 
> to a few of the site values.
> 
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Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

[Ken Beath]

It looks like what used to be suggested for stan. Move it elsewhere and then 
see what happens.

Ken

> On 9 Nov 2020, at 2:57 pm, Goncalo Ferraz  wrote:
> 
> ok, found it! Makevars is where you said it would be and it contains only 
> this line:
> 
> CXX14FLAGS += -O3 -mtune=native -arch x86_64 -ftemplate-depth-256
> 
> Does it seem to mean anything relevant?
> 
>> On Nov 8, 2020, at 11:24 PM, Ken Beath  wrote:
>> 
>> It is actually Makevars. If it is there it will be in the .R directory of 
>> your home folder.
>> 
>> Unless it has been set up for something else, like Rcpp, then it can 
>> probably be deleted. 
>> 
>> Ken
>> 
>>> On 9 Nov 2020, at 12:43 pm, Goncalo Ferraz  wrote:
>>> 
>>> Hi,
>>> 
>>> Yes, at some point there was a problem with schools.stan, it needed an 
>>> extra (empty) line added to the end. But that didn’t solve the problem. I 
>>> tried at least three different tests, with different models, and the same 
>>> thing happens.
>>> 
>>> Tried to get rid of .MakeVars and as I remember it didn’t change anything. 
>>> I wanted to try it again now, but I am not finding a .MakeVars file 
>>> anywhere on my computer. Where should it be?
>>> 
>>> Thanks,
>>> 
>>> Gonçalo
>>> 
>>>> On Nov 8, 2020, at 8:04 PM, Ken Beath  wrote:
>>>> 
>>>> Guessing here. Possibly schools.stan has a problem, that is what teh first 
>>>> error is suggesting. The remaining is a possible problem with .MakeVars 
>>>> which is no longer needed with R. I would also check that files aren’t 
>>>> being saved with a strange encoding.
>>>> 
>>>> Ken
>>>> 
>>>>> On 9 Nov 2020, at 7:25 am, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>>>>  wrote:
>>>>> 
>>>>> Hi:
>>>>> 
>>>>> While it is possible you will get the help you seek here,  I think you 
>>>>> would likely to get more help,  and more knowledgeable help, on this more 
>>>>> specialized issue,  at the Stan Forum.  https://discourse.mc-stan.org.  I 
>>>>> remember seeing in the summaries I get some issues with different 
>>>>> combinations of versions of R,  Stan and compilers.
>>>>> 
>>>>> HTH,
>>>>> 
>>>>> -Roy
>>>>> 
>>>>>> On Nov 8, 2020, at 12:16 PM, Goncalo Ferraz via R-SIG-Mac 
>>>>>>  wrote:
>>>>>> 
>>>>>> Hi, 
>>>>>> 
>>>>>> I’ve been struggling with an rstan problem for weeks. I installed R stan 
>>>>>> following instructions in 
>>>>>> https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan
>>>>>>  
>>>>>> <https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan>
>>>>>>  to the letter, but when I try to compile any model R leaves me hanging 
>>>>>> indefinitely (I’ve waited up to 30 minutes with ridiculously short 
>>>>>> models). When I press esc R says:
>>>>>> 
>>>>>> Warning messages:
>>>>>> 1: In readLines(file, warn = TRUE) :
>>>>>> incomplete final line found on 
>>>>>> '/Users/gferraz/Documents/MAF/R/schools.stan'
>>>>>> 2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = 
>>>>>> TRUE) :
>>>>>> system call failed: Result too large
>>>>>> 3: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = 
>>>>>> TRUE) :
>>>>>> error in running command
>>>>>> 
>>>>>> And then, R won’t quit. I can only close it by force quitting the 
>>>>>> software itself and some R process that is set in motion and appears in 
>>>>>> the Activity Monitor.
>>>>>> 
>>>>>> I have tried everything that was suggested in the stan forum, including 
>>>>>> deleting all the contents of /usr/local, removing xcode, R and 
>>>>>> re-installing everything again.
>>>>>> 
>>>>>> The only thing that I can think of now is to do a clean install of Mac 
>>>>>> OS on my machine and really start from scratch.
>>>>>> 
>>>>>> Anyone has a le

Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

[Ken Beath]

It is actually Makevars. If it is there it will be in the .R directory of your 
home folder.

Unless it has been set up for something else, like Rcpp, then it can probably 
be deleted. 

Ken

> On 9 Nov 2020, at 12:43 pm, Goncalo Ferraz  wrote:
> 
> Hi,
> 
> Yes, at some point there was a problem with schools.stan, it needed an extra 
> (empty) line added to the end. But that didn’t solve the problem. I tried at 
> least three different tests, with different models, and the same thing 
> happens.
> 
> Tried to get rid of .MakeVars and as I remember it didn’t change anything. I 
> wanted to try it again now, but I am not finding a .MakeVars file anywhere on 
> my computer. Where should it be?
> 
> Thanks,
> 
> Gonçalo
> 
>> On Nov 8, 2020, at 8:04 PM, Ken Beath  wrote:
>> 
>> Guessing here. Possibly schools.stan has a problem, that is what teh first 
>> error is suggesting. The remaining is a possible problem with .MakeVars 
>> which is no longer needed with R. I would also check that files aren’t being 
>> saved with a strange encoding.
>> 
>> Ken
>> 
>>> On 9 Nov 2020, at 7:25 am, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>>  wrote:
>>> 
>>> Hi:
>>> 
>>> While it is possible you will get the help you seek here,  I think you 
>>> would likely to get more help,  and more knowledgeable help, on this more 
>>> specialized issue,  at the Stan Forum.  https://discourse.mc-stan.org.  I 
>>> remember seeing in the summaries I get some issues with different 
>>> combinations of versions of R,  Stan and compilers.
>>> 
>>> HTH,
>>> 
>>> -Roy
>>> 
>>>> On Nov 8, 2020, at 12:16 PM, Goncalo Ferraz via R-SIG-Mac 
>>>>  wrote:
>>>> 
>>>> Hi, 
>>>> 
>>>> I’ve been struggling with an rstan problem for weeks. I installed R stan 
>>>> following instructions in 
>>>> https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan
>>>>  
>>>> <https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan>
>>>>  to the letter, but when I try to compile any model R leaves me hanging 
>>>> indefinitely (I’ve waited up to 30 minutes with ridiculously short 
>>>> models). When I press esc R says:
>>>> 
>>>> Warning messages:
>>>> 1: In readLines(file, warn = TRUE) :
>>>> incomplete final line found on 
>>>> '/Users/gferraz/Documents/MAF/R/schools.stan'
>>>> 2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) 
>>>> :
>>>> system call failed: Result too large
>>>> 3: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) 
>>>> :
>>>> error in running command
>>>> 
>>>> And then, R won’t quit. I can only close it by force quitting the software 
>>>> itself and some R process that is set in motion and appears in the 
>>>> Activity Monitor.
>>>> 
>>>> I have tried everything that was suggested in the stan forum, including 
>>>> deleting all the contents of /usr/local, removing xcode, R and 
>>>> re-installing everything again.
>>>> 
>>>> The only thing that I can think of now is to do a clean install of Mac OS 
>>>> on my machine and really start from scratch.
>>>> 
>>>> Anyone has a less radical recommendation?
>>>> 
>>>> Thank you,
>>>> 
>>>> Gonçalo
>>>>[[alternative HTML version deleted]]
>>>> 
>>>> ___
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac@r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> **
>>> "The contents of this message do not reflect any position of the U.S. 
>>> Government or NOAA."
>>> **
>>> Roy Mendelssohn
>>> Supervisory Operations Research Analyst
>>> NOAA/NMFS
>>> Environmental Research Division
>>> Southwest Fisheries Science Center
>>> ***Note new street address***
>>> 110 McAllister Way
>>> Santa Cruz, CA 95060
>>> Phone: (831)-420-3666
>>> Fax: (831) 420-3980
>>> e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/
>>> 
>>> "Old age and treachery will overcome youth and skill."
>>> "From those who have been given much, much will be expected" 
>>> "the arc of the moral universe is long, but it bends toward justice" -MLK 
>>> Jr.
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 

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Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

[Ken Beath]

Guessing here. Possibly schools.stan has a problem, that is what teh first 
error is suggesting. The remaining is a possible problem with .MakeVars which 
is no longer needed with R. I would also check that files aren’t being saved 
with a strange encoding.

Ken

> On 9 Nov 2020, at 7:25 am, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>  wrote:
> 
> Hi:
> 
> While it is possible you will get the help you seek here,  I think you would 
> likely to get more help,  and more knowledgeable help, on this more 
> specialized issue,  at the Stan Forum.  https://discourse.mc-stan.org.  I 
> remember seeing in the summaries I get some issues with different 
> combinations of versions of R,  Stan and compilers.
> 
> HTH,
> 
> -Roy
> 
>> On Nov 8, 2020, at 12:16 PM, Goncalo Ferraz via R-SIG-Mac 
>>  wrote:
>> 
>> Hi, 
>> 
>> I’ve been struggling with an rstan problem for weeks. I installed R stan 
>> following instructions in 
>> https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan
>>  
>> 
>>  to the letter, but when I try to compile any model R leaves me hanging 
>> indefinitely (I’ve waited up to 30 minutes with ridiculously short models). 
>> When I press esc R says:
>> 
>> Warning messages:
>> 1: In readLines(file, warn = TRUE) :
>> incomplete final line found on '/Users/gferraz/Documents/MAF/R/schools.stan'
>> 2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
>> system call failed: Result too large
>> 3: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
>> error in running command
>> 
>> And then, R won’t quit. I can only close it by force quitting the software 
>> itself and some R process that is set in motion and appears in the Activity 
>> Monitor.
>> 
>> I have tried everything that was suggested in the stan forum, including 
>> deleting all the contents of /usr/local, removing xcode, R and re-installing 
>> everything again.
>> 
>> The only thing that I can think of now is to do a clean install of Mac OS on 
>> my machine and really start from scratch.
>> 
>> Anyone has a less radical recommendation?
>> 
>> Thank you,
>> 
>> Gonçalo
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> **
> "The contents of this message do not reflect any position of the U.S. 
> Government or NOAA."
> **
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/
> 
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected" 
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] catalina humbug

[Ken Beath]

clang7 seems to be unnecessary for current R. It isn’t in my system and from 
memory was one of the things I removed to get everything working. This involved 
removing the clang and fortran that had been previously installed. I may have 
needed some other things but my systems will build your package.

Ken

> On 14 Oct 2020, at 10:01 pm, Koenker, Roger W  wrote:
> 
> Simon,
> 
> Thanks,  I still have the same error:
> 
> In file included from mcmb.c:11:
> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file 
> not found
> #include_next 
> 
> I didn’t do anything beyond upgrading R and installing fortran 8.2.0, and the 
> CLT 12.2.
> but I didn’t remove anything, should I have?  I now see:
> 
> yzzy: which clang
> /usr/bin/clang
> yzzy: clang --version
> Apple clang version 12.0.0 (clang-1200.0.32.2)
> Target: x86_64-apple-darwin19.6.0
> Thread model: posix
> InstalledDir: 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
> 
> 
> The last time I faced this sort of thing James suggested this: 
> https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY
> 
> but the names and locations are somewhat different now, so I’m reluctant to 
> experiment.
> 
> Roger
> 
> 
> 
>> On Oct 14, 2020, at 11:48 AM, Simon Urbanek  
>> wrote:
>> 
>> Roger,
>> 
>> the error points to an old local clang - did you remove (or move aside) that 
>> one? Check your /usr/local - you seem to have some old stuff there that is 
>> breaking. That would solve the original issue. You seem to have done a lot 
>> after that error, but didn't tell us what happened then… you can't have the 
>> same error if you removed it ;) 
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>> 
>>> On Oct 14, 2020, at 10:28 PM, Koenker, Roger W  
>>> wrote:
>>> 
>>> I’ve recently “upgraded” to catalina, and compilation of my quantreg 
>>> package failed with:
>>> 
>>> In file included from mcmb.c:11:
>>> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' 
>>> file not found
>>> #include_next 
>>> 
>>> So I’ve tried the following:
>>> 
>>> 1.  Upgraded R to 4.0.3
>>> 2.  Upgraded the fortran compiler to 8.2.0 as suggested.
>>> 3.  Attempted to reinstall command line tools with Xcode-select 
>>> —install.  This fails with
>>> a popup that says:
>>> 
>>> Can’t install the software because it is not currently 
>>> available from the Software Update server.
>>> 4.  Tried again to reinstall Command line tools 12.2 beta 3 from 
>>> https://developer.apple.com/download/more/
>>> which successfully installed, but my stdio.h error persisted.
>>> 5.  Following thread: 
>>> http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html
>>> I  looked at:
>>> 
>>> yzzy: which clang /usr/bin/clang 
>>> yzzy: xcode-select -p 
>>> /Applications/Xcode.app/Contents/Developer 
>>> yzzy: xcrun --show-sdk-path 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
>>> 
>>> but that didn’t speak to me so further googling led me to:
>>> 
>>> https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files
>>> so lurking in: 
>>> /Library/Developer/CommandLineTools/usr/include/c++/v1
>>> is stdio.h, but I’m feeling a bit queasy  at this point and 
>>> would appreciate some  expert advice.
>>> 
>>> Roger
>>> 
>>> ___
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>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
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Re: [R-SIG-Mac] Some introductory questions

[Ken Beath]

> On 7 Sep 2020, at 9:31 am, Mike Feher  wrote:

> 2. Are these objects, etc. stored on disk somewhere, or are they only
> accessible via the interfaces?  For example, I would be interested to see
> the source code for the demo examples to learn how to do certain things, if
> this is possible.  (It appeared as if the code for each demo that is
> executed as part of the ‘demo()’ command displayed in my R console, but I
> just want to be sure about this.)

How to find the demo files is contained in the demo help. Type ?demo

> 4. I tried to read in a set of dummy space-delimited data saved in an
> absolute path on my computer, but it would not work.  I tried something in
> another path that did not have a subfolder with a space in it (I.e. I plan
> on storing my data in a folder called “R Documents” or something similar)
> and that didn’t work either, so I’m still wondering whether or not (a)
> things have to be in the library location (it seems like you could
> customize that) and (b) whether R recognizes spaces in file paths.
> 

Try using file.choose() to locate files using a dialog and it will return the 
full name. Spaces shouldn’t matter provided that everything is enclosed in 
quotes. Most people don’t use absolute references. They set the working 
directory and then just use the name of the file. See under the Misc menu. 

Ken
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Re: [R-SIG-Mac] Daily builds

[Ken Beath]

Still missing.

Ken

> On 23 Jul 2020, at 11:06 pm, Gábor Csárdi  wrote:
> 
> Hi Simon,
> 
> I wonder if the tarballs and the installers for 4.0 and 4.1 are
> missing from https://mac.r-project.org/ on purpose. The logs seem to
> have recent dates, but the installers or the links to them are not
> there?
> 
> Thanks much,
> Gabor
> 
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Re: [R-SIG-Mac] R 4 dumping tons of console messages in Big Sur

[Ken Beath]

That is what happens at times with beta software, and is more likely to be 
Apple’s problem. 

Assuming that you are properly registered put a bug report into Apple.

Ken

> On 25 Jun 2020, at 12:49 am, Timothy Bates  wrote:
> 
> R in pretty-much unusable in Big Sur (OSX beta) - it's generating many more
> than ever warning messages to the console, such that a simple calculation
> fills the page with warnings... e.g:
> 
> 
> (174-19)/15
> [1] 10.3
> 2020-06-24 15:45:31.472 R[4178:38668] 
> is drawing everything
> 2020-06-24 15:45:31.472 R[4178:38668] Drawing rect: {{9, 60}, {278, 323}}:
> 
> 2020-06-24 15:45:31.472 R[4178:38668] drawRow: 0, clip: {{0, 0}, {278,
> 323}} - 
> 2020-06-24 15:45:31.472 R[4178:38668]columnsToDraw:  0x63dd84b0>[number of indexes: 1 (in 1 ranges), indexes: (0)]
> 2020-06-24 15:45:31.472 R[4178:38668] Really drawing cell at row: 0 col: 0
> 2020-06-24 15:45:31.472 R[4178:38668] drawRow: 1, clip: {{0, 0}, {278,
> 323}} - 
> 2020-06-24 15:45:31.472 R[4178:38668]columnsToDraw:  0x63dd8540>[number of indexes: 1 (in 1 ranges), indexes: (0)]
> 2020-06-24 15:45:31.472 R[4178:38668] Really drawing cell at row: 1 col: 0
> 2020-06-24 15:45:31.472 R[4178:38668] drawRow: 2, clip: {{0, 0}, {278,
> 323}} - 
> 2020-06-24 15:45:31.472 R[4178:38668]columnsToDraw:  0x63dd84b0>[number of indexes: 1 (in 1 ranges), indexes: (0)]
> 2020-06-24 15:45:31.472 R[4178:38668] Really drawing cell at row: 2 col: 0
> 2020-06-24 15:45:31.472 R[4178:38668] drawRow: 3, clip: {{0, 0}, {278,
> 323}} - 
> 2020-06-24 15:45:31.472 R[4178:38668]columnsToDraw:  0x63dd8540>[number of indexes: 1 (in 1 ranges), indexes: (0)]
> 2020-06-24 15:45:31.472 R[4178:38668] Really drawing cell at row: 3 col: 0
> 2020-06-24 15:45:31.472 R[4178:38668] drawRow: 4, clip: {{0, 0}, {278,
> 323}} - 
> 2020-06-24 15:45:31.472 R[4178:38668]columnsToDraw:  0x63dd84b0>[number of indexes: 1 (in 1 ranges), indexes: (0)]
> 2020-06-24 15:45:31.472 R[4178:38668] Really drawing cell at row: 4 col: 0
> 2020-06-24 15:45:31.472 R[4178:38668] drawRow: 5, clip: {{0, 0}, {278,
> 323}} - 
> 2020-06-24 15:45:31.472 R[4178:38668]columnsToDraw:  0x63dd8540>[number of indexes: 1 (in 1 ranges), indexes: (0)]
> 2020-06-24 15:45:31.472 R[4178:38668] Really drawing cell at row: 5 col: 0
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] No labels in plots - none of the solutions that I've come across have worked

[Ken Beath]

Will Restore Standard Fonts in Font Book do the same thing? Although if 
reinstalling the system doesn’t work I’m not certain that anything should work.

Ken

> On 17 Jun 2020, at 9:52 pm, Charlie D  wrote:
> 
> Had the same issue. Check your mac font book utility.  In my case Arial was 
> missing entirely. I was able to copy it from another mac I owned. Look in HDD 
> > library > fonts. Copy and paste it to same location on the machine on which 
> it’s missing.  Hope that helps.  
> 
> Charlie DiMaggio
> 
> Sent from my iPad
> 
>> On Jun 17, 2020, at 2:00 AM, J Greenbaum  wrote:
>> 
>> Hi all,
>> 
>> I'm having what appears to be a relatively common problem in R under macOS
>> in that text is not displaying in my plots.  This used to work just fine
>> for me, and still does on my other machines, except for my laptop (MBP
>> 16).  The issue seemed to coincide with my upgrade to 10.15.5.
>> 
>> When plotting, I get warnings similar to:
>> 
>> no font could be found for family "Arial"
>> 
>> I've tried every solution that I've come across on this issue including
>> finding duplicate fonts in 'Font Book', ensuring they all validate
>> properly, and I've even gone nuclear and completely reinstalled my OS!
>> I've tried installing the official R package as well as the homebrew R
>> package.  I've also validated it's not my user account by reproducing the
>> issue under different accounts. Nothing works.
>> 
>> I would love some help in tracking this issue down.  Any insight would be
>> much appreciated.
>> 
>> Thank you!
>> 
>> -J
>> 
>>   [[alternative HTML version deleted]]
>> 
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> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Strange "NOTE" when running R CMD CHECK

[Ken Beath]

Yes, I think it has happened for at least 10 years. I assume that it doesn’t 
get looked at unless there is some other problem.

Ken

> On 15 Jun 2020, at 9:06 am, Timothy Bates  wrote:
> 
> It won’t hold up submission: I believe it's just a NOTE to let the kind 
> people helping with submissions find who the maintainer is.
> 
> Been around for some years, I believe?
> 
> Best, tim
> 
> 
>> On 14 Jun 2020, at 23:21, Carl Witthoft  wrote:
>> 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] Update to versions GEOS 3.8.0, GDAL 3.0.4 and PROJ 7.0.0 in macOS Catalina

[Ken Beath]

sf requires GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0) so I would assume 
that its full functionality is available with these.

Ken

> On 23 May 2020, at 10:08 am, Manuel Spínola  wrote:
> 
> Thank you very much Simon.
> 
> I don't know much about programming so I will keep the current versions.
> 
> I was asking because some of the main spatial packages, as sf and terra, I
> think require the latest versions of gdal and proj to be completely
> functional. That is my understanding, may be I am wrong.
> 
> Best,
> 
> Manuel
> 
> 
> El vie., 22 may. 2020 a las 16:56, Simon Urbanek (<
> simon.urba...@r-project.org>) escribió:
> 
>> Manuel,
>> 
>> see
>> https://github.com/R-macos/recipes
>> you can update the recipes to use the required versions to build a setup
>> that works for your package. Once you do you can issue a pull request so we
>> can update CRAN accordingly.
>> 
>> Please note that it is generally not a good idea to require latests
>> versions as that excludes a large number of users from using your package.
>> Many user don't have control over dependent libraries and must use
>> supported versions. The mainstream LTS versions right now are geos 3.6.2,
>> gdal 2.2.3 and proj 4.9.3 and latest non-LTS are geos 3.7.1, gdal 2.4.0 and
>> proj 5.2.0 which is pretty much the maximum you can realistically require.
>> 
>> Cheers,
>> Simon
>> 
>> 
>> On May 23, 2020, at 7:41 AM, Manuel Spínola  wrote:
>> 
>> Dear list members,
>> 
>> Sorry for crossposting.  I sent this message to the r-sig-geo but
>> apparently no many people know how to do this in MacOS.  I am working with
>> R 4.0.0 and macOS Catalina 10.15.4
>> 
>> I am working with spatial package that to have full functionality depend on
>> updated versions of:
>> 
>> GEOS 3.8.0, GDAL 3.0.4 and PROJ 7.0.0
>> 
>> Best,
>> 
>> Manuel
>> 
>> --
>> *Manuel Spínola, Ph.D.*
>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>> Universidad Nacional
>> Apartado 1350-3000
>> Heredia
>> COSTA RICA
>> mspin...@una.cr 
>> mspinol...@gmail.com
>> Teléfono: (506) 8706 - 4662
>> Personal website: Lobito de río <
>> https://sites.google.com/site/lobitoderio/>
>> Institutional website: ICOMVIS 
>> 
>> [[alternative HTML version deleted]]
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> 
>> 
> 
> -- 
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> mspin...@una.cr 
> mspinol...@gmail.com
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río 
> Institutional website: ICOMVIS 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Cannot compile Fortran on macOS

[Ken Beath]

Success. I also removed everything from /usr/local then reinstalled MacTex, R 
and gfortran, and now I can build on both 4.0 and 4.1. Presumably something has 
changed in the builds between 4.0 and 4.1 and that has interacted with the 
accumulated nearly 6 years of mess in /usr/local. 

> On 20 May 2020, at 5:34 pm, Adelchi Azzalini  wrote:
> 
> 
> 
>> On 20 May 2020, at 08:44, Adelchi Azzalini  wrote:
>> 
>> Thanks to everyone that provided suggestions.
>> 
>> I was about to follow the recommended step of renaming /usr/local and 
>> reinstall a bunch of programs.
>> However, that renaming is blocked, presumably by Apple System Integrity 
>> Protection. 
>> Is there any alternative to disabling this Apple "feature"?
>> Do you recommend to re-instate it after the re-construction of /usr/local/ ?
>> As you see, I am not familiar with Apple tricks.
>> 
>> Thanks again,
>> 
>> Adelchi
> 
> 
> Please ignore the message above. 
> Right after sending it, I realized that the simple workaround was to move 
> everything in
>  /usr/local/
> to
>  /usr/local/local-2020520/
> 
> After reinstalling R, TeX, etc... compilation now works fine!
> 
> Thanks for your effective help.
> 
> Adelchi
> 
> 
>> 
>> 
>> 
>>> On 20 May 2020, at 05:50, Simon Urbanek  wrote:
>>> 
>>> 
>>> Adelchi,
>>> 
>>> as pointed out you have conflicting libraries in /usr/local - likely from 
>>> some conflicting package manager. I would recommend re-naming /usr/local to 
>>> remove the issue and installing a clean GNU Fortran (see 
>>> http://mac.r-project.org/tools/ or from the official GNU Fortran pages 
>>> which use the same binary), that's all you really need.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>> 
 On 20/05/2020, at 1:45 AM, Adelchi Azzalini  wrote:
 
 Hi. 
 In essence, my problem is that I cannot install a package which requires 
 Fortran-77 compilation on my Mac.
 
 More in detail, this is my own package 'mnormt' which exists on CRAN since 
 2006; it is currently at version 1.5-7. It has been developed in 
 successive versions on a Linux machine, where it compiles with no 
 problems. The macOS and MS-windows versions are created on CRAN, where it 
 passes all pertaining checks.
 
 Now, in the new pandemic world, I need create a new version of the 
 package, but working from home, hence using my Mac laptop instead of the 
 Linux desktop as in the past. Unfortunately, compilation or loading does 
 not work. If I run 
 
 R CMD check mnormt_1.5-7.tar.gz
 
 first I get a bunch of warning messages such as
 
 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) 
   [-Wconversion]
 Warning: ‘lxchng’ may be used uninitialized in this function 
 [-Wmaybe-uninitialized]
 Warning: Label 10 at (1) defined but not used [-Wunused-label]
 
 and finally it crashes with
 
 Error: package or namespace load failed for ‘mnormt’:
 .onLoad failed in loadNamespace() for 'mnormt', details:
 call: dyn.load(file, DLLpath = DLLpath, ...)
 error: unable to load shared object 
 '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so':
 dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so,
  6): Symbol not found: ___addtf3
 Referenced from: /usr/local/lib/libquadmath.0.dylib
 Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
 in /usr/local/lib/libquadmath.0.dylib
 Error: loading failed
 
 Needless to say, I have no idea what this "addtf3" is or it should be. 
 There is no such a symbol in the Fortran code.
 
 I believe to have installed all ingredients indicated at 
 https://mac.r-project.org/tools/
 See the list below with details about my system and other installed tools.
 
 Any suggestions for sorting this out?
 
 Adelchi Azzalini
 
 
 ---
 Installation info:
 
 R> R.version
_   
 platform   x86_64-apple-darwin17.0 
 arch   x86_64  
 os darwin17.0  
 system x86_64, darwin17.0  
 status 
 major  4   
 minor  0.0 
 year   2020
 month  04  
 day24  
 svn rev78286   
 language   R   
 version.string R version 4.0.0 (2020-04-24)
 nickname   Arbor Day   
 
 --- macOS Mojave 10.14.6
 
 --- Xcode version 11.3.1
 
 --- Fortran
 
 [aa@mac-2013:~] gfortran -v
 Using built-in specs.
 COLLECT_GCC=gfortran
 

Re: [R-SIG-Mac] Cannot compile Fortran on macOS

[Ken Beath]

Simon,

I’m going to investigate further, but the problem is that 4.0 works fine but 
4.1 doesn’t. I will check what is going wrong.

Ken

> On 20 May 2020, at 1:47 pm, Simon Urbanek  wrote:
> 
> Ken,
> 
> R can be built with just Xcode and GFortran (see also 
> http://mac.r-project.org/tools/ ). If you have issues, those are very often 
> due to conflicting package managers (Homebrew, macoports, fink ...) so a good 
> exercise is to simply re-name /usr/local/ and setup a clean environment as 
> above which is known to work. If you use CRAN R builds (either release or 
> from http://mac.r-project.org/ ) then most packages will compile with just 
> Xcode alone.
> 
> Cheers,
> Simon
> 
> 
>> On 20/05/2020, at 12:58 PM, Ken Beath  wrote:
>> 
>> Plus one of the duties of package managers is to make sure that they build 
>> and pass CRAN checks. Doing that with a non standard environment seems a bit 
>> risky.
>> 
>> At the moment I can’t get anything to build on R-Devel which is making life 
>> difficult and I may raise a question if it still isn’t working when I’ve 
>> finished with the new experience that is online teaching.
>> 
>>> On 20 May 2020, at 10:49 am, David Winsemius  wrote:
>>> 
>>> 
>>> On 5/19/20 1:46 PM, Yoshihiko Baba via R-SIG-Mac wrote:
>>>> Adelchi,
>>>> 
>>>> Why don’t you try Fink version of R?
>>>> 
>>>> Fink build mnormt on R 4.0 as well (although it is experimental).
>>>> https://github.com/fink/fink-distributions/issues/623
>>> 
>>> 
>>> This should be considered contrary to recommended practice: From the 
>>> page for macOS tools that was cited by the OP we see:
>>> 
>>> 
>>> "Although it is possible to compile R using tools from other package 
>>> managers such as Homebrew, MacPorts or Fink, such binaries are by 
>>> definition incompatible with macOS native libraries and applications. If 
>>> you choose one of those package managers, make sure you 
>>> compile/everything/using those tools including R and all packages and 
>>> libraries you intend to use."
>>> 
>>> 
>>> I think it should have been offered as advice to only be followed by 
>>> persons with great experience in compiling and building packages on Macs.
>>> 
>>> Best;
>>> 
>>> David
>>> 
>>>> 
>>>> Fink allows you to install different versions of R (3.6, 3.5, 3.4, 3.3, 
>>>> 3.2 and 3.1).
>>>> 
>>>> For different versions, CRAN packages are separately installed 
>>>> (/sw/lib/R/3.6/site-library  and so on).
>>>> 
>>>> 
>>>>> 2020/05/19 22:45、Adelchi Azzalini のメール:
>>>>> 
>>>>> Hi.
>>>>> In essence, my problem is that I cannot install a package which requires 
>>>>> Fortran-77 compilation on my Mac.
>>>>> 
>>>>> More in detail, this is my own package 'mnormt' which exists on CRAN 
>>>>> since 2006; it is currently at version 1.5-7. It has been developed in 
>>>>> successive versions on a Linux machine, where it compiles with no 
>>>>> problems. The macOS and MS-windows versions are created on CRAN, where it 
>>>>> passes all pertaining checks.
>>>>> 
>>>>> Now, in the new pandemic world, I need create a new version of the 
>>>>> package, but working from home, hence using my Mac laptop instead of the 
>>>>> Linux desktop as in the past. Unfortunately, compilation or loading does 
>>>>> not work. If I run
>>>>> 
>>>>> R CMD check mnormt_1.5-7.tar.gz
>>>>> 
>>>>> first I get a bunch of warning messages such as
>>>>> 
>>>>> Warning: Possible change of value in conversion from REAL(8) to 
>>>>> INTEGER(4)   [-Wconversion]
>>>>> Warning: ‘lxchng’ may be used uninitialized in this function 
>>>>> [-Wmaybe-uninitialized]
>>>>> Warning: Label 10 at (1) defined but not used [-Wunused-label]
>>>>> 
>>>>> and finally it crashes with
>>>>> 
>>>>> Error: package or namespace load failed for ‘mnormt’:
>>>>> .onLoad failed in loadNamespace() for 'mnormt', details:
>>>>> call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>> error: unable to load shared object 
>>>>> '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00n

Re: [R-SIG-Mac] Cannot compile Fortran on macOS

[Ken Beath]

Plus one of the duties of package managers is to make sure that they build and 
pass CRAN checks. Doing that with a non standard environment seems a bit risky.

At the moment I can’t get anything to build on R-Devel which is making life 
difficult and I may raise a question if it still isn’t working when I’ve 
finished with the new experience that is online teaching.

> On 20 May 2020, at 10:49 am, David Winsemius  wrote:
> 
> 
> On 5/19/20 1:46 PM, Yoshihiko Baba via R-SIG-Mac wrote:
>> Adelchi,
>> 
>> Why don’t you try Fink version of R?
>> 
>> Fink build mnormt on R 4.0 as well (although it is experimental).
>> https://github.com/fink/fink-distributions/issues/623
> 
> 
> This should be considered contrary to recommended practice: From the 
> page for macOS tools that was cited by the OP we see:
> 
> 
> "Although it is possible to compile R using tools from other package 
> managers such as Homebrew, MacPorts or Fink, such binaries are by 
> definition incompatible with macOS native libraries and applications. If 
> you choose one of those package managers, make sure you 
> compile/everything/using those tools including R and all packages and 
> libraries you intend to use."
> 
> 
> I think it should have been offered as advice to only be followed by 
> persons with great experience in compiling and building packages on Macs.
> 
> Best;
> 
> David
> 
>> 
>> Fink allows you to install different versions of R (3.6, 3.5, 3.4, 3.3, 3.2 
>> and 3.1).
>> 
>> For different versions, CRAN packages are separately installed 
>> (/sw/lib/R/3.6/site-library  and so on).
>> 
>> 
>>> 2020/05/19 22:45、Adelchi Azzalini のメール:
>>> 
>>> Hi.
>>> In essence, my problem is that I cannot install a package which requires 
>>> Fortran-77 compilation on my Mac.
>>> 
>>> More in detail, this is my own package 'mnormt' which exists on CRAN since 
>>> 2006; it is currently at version 1.5-7. It has been developed in successive 
>>> versions on a Linux machine, where it compiles with no problems. The macOS 
>>> and MS-windows versions are created on CRAN, where it passes all pertaining 
>>> checks.
>>> 
>>> Now, in the new pandemic world, I need create a new version of the package, 
>>> but working from home, hence using my Mac laptop instead of the Linux 
>>> desktop as in the past. Unfortunately, compilation or loading does not 
>>> work. If I run
>>> 
>>> R CMD check mnormt_1.5-7.tar.gz
>>> 
>>> first I get a bunch of warning messages such as
>>> 
>>> Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) 
>>>   [-Wconversion]
>>> Warning: ‘lxchng’ may be used uninitialized in this function 
>>> [-Wmaybe-uninitialized]
>>> Warning: Label 10 at (1) defined but not used [-Wunused-label]
>>> 
>>> and finally it crashes with
>>> 
>>> Error: package or namespace load failed for ‘mnormt’:
>>> .onLoad failed in loadNamespace() for 'mnormt', details:
>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>  error: unable to load shared object 
>>> '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so':
>>>  
>>> dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so,
>>>  6): Symbol not found: ___addtf3
>>>  Referenced from: /usr/local/lib/libquadmath.0.dylib
>>>  Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
>>> in /usr/local/lib/libquadmath.0.dylib
>>> Error: loading failed
>>> 
>>> Needless to say, I have no idea what this "addtf3" is or it should be. 
>>> There is no such a symbol in the Fortran code.
>>> 
>>> I believe to have installed all ingredients indicated at 
>>> https://mac.r-project.org/tools/
>>> See the list below with details about my system and other installed tools.
>>> 
>>> Any suggestions for sorting this out?
>>> 
>>> Adelchi Azzalini
>>> 
>>> 
>>> ---
>>> Installation info:
>>> 
>>> R> R.version
>>>   _
>>> platform   x86_64-apple-darwin17.0
>>> arch   x86_64
>>> os darwin17.0
>>> system x86_64, darwin17.0
>>> status
>>> major  4
>>> minor  0.0
>>> year   2020
>>> month  04
>>> day24
>>> svn rev78286
>>> language   R
>>> version.string R version 4.0.0 (2020-04-24)
>>> nickname   Arbor Day
>>> 
>>> --- macOS Mojave 10.14.6
>>> 
>>> --- Xcode version 11.3.1
>>> 
>>> --- Fortran
>>> 
>>> [aa@mac-2013:~] gfortran -v
>>> Using built-in specs.
>>> COLLECT_GCC=gfortran
>>> COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper
>>> Target: x86_64-apple-darwin18
>>> Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran 
>>> --with-gmp=/Users/fx/devel/gcc/build_package/deps 
>>> --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 
>>> --disable-multilib --with-native-system-header-dir=/usr/include 
>>> --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>>> Thread model: posix
>>> gcc version 

Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?

[Ken Beath]

Your package passes checks on my machine perfectly. It has R 4.0.0 with RStudio 
and TexLive 2020 with updates to a week or two ago.

Ken

> On 13 May 2020, at 8:17 am, Spencer Graves  
> wrote:
> 
> Hello, All:
> 
> 
>   Might "R CMD check" on Mac use obsolete LaTeX software?
> 
> 
>   I ask, because "R CMD check" on my Mac started reporting LaTeX 
> errors on *.Rd files that previously passed "R CMD check" without 
> problems.  Dirk Eddelbuettel recommended I ask tex.stackexchange about 
> that.  I did that and got the following:
> 
> 
> * "In a current tex system \textasciigrave should work with 
> your families - they don't have the glyph but latex will fall back 
> without error. In older systems it could give an error."
> 
> 
> See:
> 
> 
> https://tex.stackexchange.com/questions/543783/package-textcomp-error-symbol-textasciigrave-not-provided
> 
> 
>   Comments?
>   Thanks,
>   Spencer Graves
> 
> 
> p.s.  An earlier post on this issue to r-pkg-devel is copied below.
> 
> 
>  Forwarded Message 
> Subject:  [R-pkg-devel] Error: Symbol \textasciigrave not provided by 
> (textcomp)
> Date: Sun, 16 Feb 2020 14:21:17 -0600
> From: Spencer Graves 
> To:   r-package-de...@r-project.org
> 
> 
> 
> Hello, All:
> 
> 
>   "R CMD check Ecfun_0.2-4.tar.gz" ends with 8 repetitions of the 
> following:
> 
> 
> ! Package textcomp Error: Symbol \textasciigrave not provided by
> (textcomp)font family zi4 in TS1 encoding.
> (textcomp)Default family used instead.
> 
> See the textcomp package documentation for explanation.
> * checking PDF version of manual without hyperrefs or index ... ERROR
> * DONE
> 
> 
>   This is using R 3.6.2 under macOS 10.15.3 applied to the current 
> development version of "https://github.com/sbgraves237/Ecfun;.  Travis 
> CI reported that the build passed;  see 
> "https://travis-ci.org/sbgraves237/Ecfun/builds/650505913?utm_medium=notification_source=email;.
>  
> 
> 
> 
>   This looks to me like it's complaining about the use of the back 
> tick character ("`", below "~" on the top left key on a standard 
> American English keyboard), which I assume is equivalent to 
> "\textasciigrave" in certain contexts.
> 
> 
>   Six out of those 8 repetitions occur in the examples sections of 
> files "grepNonStandardCharacters.Rd", "subNonStandardCharacters.Rd", and 
> "subNonStandardNames.Rd". Those functions were written to fix parsing 
> errors with names like "Raúl" that had been mangled by different 
> software before I could get it into R.
> 
> 
>   After a day's work failed to produce a work around, I decided to 
> ask this group.
> 
> 
>   What do you suggest?
>   Thanks,
>   Spencer Graves
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] damned Catalina

[Ken Beath]

Try another repository. It works fine with the main CRAN and teh RStudio 
repositories.

Ken

> On 18 Dec 2019, at 10:50 pm, bruno apolloni  wrote:
> 
> Dear All
> 
> among disasters of the new operating system Catalina, this one concerns R.
> 
> Trying to install “regtools"  the answer by Crane R consolle is 
> 
> unable to access index for repository 
> https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 
> 
> 
> The same  for “devtools”. This happens on my Mac with Catalina OS. The same 
> installation on same Crane R but  on a laptop of colleauge of mine endowed 
> with previous OS (el captain) succeeds without any problem.
> 
> Any remedy to suggest?
> 
> Thanks a lot
> 
> Bruno
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] segfault with raster package

[Ken Beath]

This works fine for me using R 3.6.2 on MacOS 10.15.2

The only difference from a standard installation is that I have the setup for 
Rcpp, but that shouldn’t change anything.

Ken



> On 17 Dec 2019, at 8:34 am, Marc Girondot via R-SIG-Mac 
>  wrote:
> 
> When I load the last version of raster package in MacOS, I get a segfault:
> 
> This is similar to the problem described here:
> 
> https://r.789695.n4.nabble.com/Raster-package-crash-with-segmentation-fault-td4759487.html
> 
> or here
> 
> https://github.com/rspatial/raster/issues/63
> 
> The last working version for me is the 2.5-8 installed with:
> 
> require(devtools)
> install_version("raster", version = "2.5-8", repos 
> ="http://cran.us.r-project.org;)
> 
> I would like know if the problem with the raster package is common in macOSX 
> or if there is something special for me.
> 
> Thanks a lot
> 
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Re: [R-SIG-Mac] Error when fitting a brms model, maybe associated with Catalina MacOS

[Ken Beath]

Did you install rstan last?

Ken

> On 15 Dec 2019, at 10:28 am, Manuel Spínola  wrote:
> 
> Dear list members,
> 
> I updated everything, Catalina, Xcode, CLT, R 3.6.2, rstan from source, and 
> installed the r-macos-rtools, but I still have problems.
> 
> library(brms)
> group <- rep(c("treat", "placebo"), each = 30)
> symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = 0, sd = 1))
> dat1 <- data.frame(group, symptom_post)
> 
> fit1 <- brm(bf(symptom_post ~ group, sigma ~ group), 
> data = dat1, family = gaussian())
> 
> Chain 4: Iteration:1 / 2000 [  0%]  (Warmup)
> [1] "Error in sampler$call_sampler(args_list[[i]]) : "
> [2] "  c++ exception (unknown reason)"
> error occurred during calling the sampler; sampling not done
> 
> 
> 
> 
> 
> 
> El jue., 12 dic. 2019 a las 12:51, Balamuta, James Joseph 
> () escribió:
> Greetings and Salutations All,
> 
> Great to see the `r-macos-rtools` installer popping up! As the author of it, 
> please note that it's an unofficial (non-CRAN backed) installer that seeks to 
> automatically establish the CRAN toolchain in a friendly GUI installer. We 
> developed it to help out students in STAT 385 @ UIUC [ http://stat385.com/ ]  
> setup the correct developer environment in a uniform manner as there wasn't 
> really any prior installer packages made available at the time. We're 
> grateful for the financial support that was given by Timothy Bates to sign 
> the installer.
> 
> With this being said, each step the installer takes is documented across a 
> README file, installer splash screen, and by a post.
> 
> README Overview: 
> https://github.com/rmacoslib/r-macos-rtools#what-does-the-installer-do 
> Installer Splash: 
> https://raw.githubusercontent.com/rmacoslib/r-macos-rtools/master/readme_img/lock_icon.png
>  
> Post: 
> https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/
>  
> 
> That said, there is also Appendix C.3 macOS of R Installation and 
> Administration [ 
> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS ] that 
> goes over the details in greater depth.
> 
> For those who are worried about security, please note that we've taken steps 
> to ensure secure downloads by verifying the installer hashes prior to 
> installing per prior remarks by Simon regarding earlier versions of the 
> installer [ see the prior discussion and my response here: 
> https://stat.ethz.ch/pipermail/r-sig-mac/2018-May/012745.html ]. 
> 
> Lastly, and perhaps more critically, please note that just using Xcode CLI is 
> not sufficient as it does not match the prescribed compilation toolchain 
> (clang7 with OpenMP enabled and gfortran). 
> 
> Best,
> 
> JJB
> 
> On 12/11/19, 7:25 PM, "R-SIG-Mac on behalf of Manuel Spínola" 
>  wrote:
> 
> An update.
> 
> Before doing the suggested installation, I updated Catalina to 10.5.2,
> Xtools to 11.3 and the Command Line Tools and it works.
> 
> Manuel
> 
> El mié., 11 dic. 2019 a las 16:05, Ken Beath ()
> escribió:
> 
> > No, it only downloads and installs the right compilers and updates
> > Makevars and REnvirons. These are what Stan and RCpp require so you 
> could
> > do these manually.
> >
> > What it does is described at https://github.com/rmacoslib/r-macos-rtools
> >
> > Ken
> >
> > > On 12 Dec 2019, at 1:14 am, Manuel Spínola  
> wrote:
> > >
> > > Thank you very much to all.
> > >
> > > Does Installing the macos-rtools could affect R in other ways?
> > >
> > > Manuel
> > >
> > > El mié., 11 dic. 2019 a las 6:56, Ken Beath ()
> > escribió:
> > > What worked for me was installing the tools using
> > https://github.com/rmacoslib/r-macos-rtools/releases
> > >
> > > and then installing rstan from source ie
> > install.packages(“rstan”,type=“source) as suggested on one of the stan
> > forums
> > >
> > > Ken
> > >
> > > > On 11 Dec 2019, at 11:09 am, Manuel Spínola 
> > wrote:
> > > >
> > > > Dear list members,
> > > >
> > > > When trying to fit this example from the CRAN repository fro brms, I
> > got
> > > > the following error message after the 4th chain.  I am using R 
> 3.6.1 in
> > > > Catalina MacOS.
> > > >
> > > >
> &g

Re: [R-SIG-Mac] Error when fitting a brms model, maybe associated with Catalina MacOS

[Ken Beath]

No, it only downloads and installs the right compilers and updates Makevars and 
REnvirons. These are what Stan and RCpp require so you could do these manually.

What it does is described at https://github.com/rmacoslib/r-macos-rtools

Ken

> On 12 Dec 2019, at 1:14 am, Manuel Spínola  wrote:
> 
> Thank you very much to all.
> 
> Does Installing the macos-rtools could affect R in other ways?
> 
> Manuel
> 
> El mié., 11 dic. 2019 a las 6:56, Ken Beath () escribió:
> What worked for me was installing the tools using 
> https://github.com/rmacoslib/r-macos-rtools/releases
> 
> and then installing rstan from source ie 
> install.packages(“rstan”,type=“source) as suggested on one of the stan forums
> 
> Ken
> 
> > On 11 Dec 2019, at 11:09 am, Manuel Spínola  wrote:
> > 
> > Dear list members,
> > 
> > When trying to fit this example from the CRAN repository fro brms, I got
> > the following error message after the 4th chain.  I am using R 3.6.1 in
> > Catalina MacOS.
> > 
> > 
> > library(brms)
> > 
> > group <- rep(c("treat", "placebo"), each = 30)
> > symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = 0, sd = 1))
> > dat1 <- data.frame(group, symptom_post)
> > 
> > fit1 <- brm(bf(symptom_post ~ group, sigma ~ group),
> >data = dat1, family = gaussian())
> > 
> > 
> > [1] "Error in sampler$call_sampler(args_list[[i]]) : "
> > [2] "  c++ exception (unknown reason)"
> > error occurred during calling the sampler; sampling not done
> > 
> > I think is a problem with Catalina MacOS, but I don´t know how to solve it.
> > 
> > Manuel
> > 
> > -- 
> > *Manuel Spínola, Ph.D.*
> > Instituto Internacional en Conservación y Manejo de Vida Silvestre
> > Universidad Nacional
> > Apartado 1350-3000
> > Heredia
> > COSTA RICA
> > mspin...@una.cr 
> > mspinol...@gmail.com
> > Teléfono: (506) 8706 - 4662
> > Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
> > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
> > 
> >   [[alternative HTML version deleted]]
> > 
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > 
> 
> 
> 
> -- 
> Manuel Spínola, Ph.D. 
> Instituto Internacional en Conservación y Manejo de Vida Silvestre 
> Universidad Nacional 
> Apartado 1350-3000 
> Heredia 
> COSTA RICA 
> mspin...@una.cr 
> mspinol...@gmail.com 
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río 
> Institutional website: ICOMVIS

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Re: [R-SIG-Mac] Error when fitting a brms model, maybe associated with Catalina MacOS

[Ken Beath]

What worked for me was installing the tools using 
https://github.com/rmacoslib/r-macos-rtools/releases

and then installing rstan from source ie install.packages(“rstan”,type=“source) 
as suggested on one of the stan forums

Ken

> On 11 Dec 2019, at 11:09 am, Manuel Spínola  wrote:
> 
> Dear list members,
> 
> When trying to fit this example from the CRAN repository fro brms, I got
> the following error message after the 4th chain.  I am using R 3.6.1 in
> Catalina MacOS.
> 
> 
> library(brms)
> 
> group <- rep(c("treat", "placebo"), each = 30)
> symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = 0, sd = 1))
> dat1 <- data.frame(group, symptom_post)
> 
> fit1 <- brm(bf(symptom_post ~ group, sigma ~ group),
>data = dat1, family = gaussian())
> 
> 
> [1] "Error in sampler$call_sampler(args_list[[i]]) : "
> [2] "  c++ exception (unknown reason)"
> error occurred during calling the sampler; sampling not done
> 
> I think is a problem with Catalina MacOS, but I don´t know how to solve it.
> 
> Manuel
> 
> -- 
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> mspin...@una.cr 
> mspinol...@gmail.com
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río 
> Institutional website: ICOMVIS 
> 
>   [[alternative HTML version deleted]]
> 
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

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Re: [R-SIG-Mac] Saving a *.R file hangs R GUI under certain sequences of operations

[Ken Beath]

I have Catalina and it works perfectly, as far as this goes.

Ken

> On 24 Oct 2019, at 9:13 am, Bryan Hanson  wrote:
> 
> Duncan…
> 
> I’m creating a new file. The menu item is “New Document”.   I called it *.R 
> to distinguish it from “New Rd Document”, and since when you attempt to save 
> it the suggested name is “untitled.R”.
> 
> I don’t see anything in the console.  When I click an existing folder in the 
> dialog, there is a brief delay and then the pinwheel, then it’s stuck.
> 
> Bryan
> 
>> On Oct 23, 2019, at 5:39 PM, Duncan Murdoch  wrote:
>> 
>> On 23/10/2019 4:32 p.m., Bryan Hanson wrote:
>>> I have found a sequence of actions that causes the R GUI on Mac to hang:
>>> 1. Launch R GUI.
>>> 2. Open an empty *.R file via the button or menu or shortcut.
>> 
>> Could you clarify this:  Are you opening an existing file that is empty, or 
>> creating a new document?  I don't see any way to specify *.R in the former, 
>> and I don't see a problem with the latter.  A bit more below...
>> 
>>> 3. Add something to the file.
>>> 4. Save the file via menu or shortcut (technically a Save as…).  In the 
>>> save dialog box:
>>>  a. If you save in whatever directory is pointing to, everything works fine.
>>>  b. If you attempt to change the directory, for instance by clicking on the 
>>> icon for a folder w/i the current directory, one gets the pinwheel of death 
>>> and R must be forced to quit.
>>> Can anyone else reproduce this?
>>> Bryan
>>> sessionInfo:
>>> R version 3.6.1 (2019-07-05)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS Mojave 10.14.6
>> 
>> I'm using the same R, but macOS High Sierra 10.13.6.
>> 
>> At some point in the exercise I saw this warning in the console:
>> 
>> objc[27995]: Class FIFinderSyncExtensionHost is implemented in both 
>> /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit 
>> (0x7fffadb52cd0) and 
>> /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride
>>  (0x112670cd8). One of the two will be used. Which one is undefined.
>> 
>> It might be that in the newer MacOS this is fatal.
>> 
>> Duncan Murdoch
>> 
>>> Matrix products: default
>>> BLAS:   
>>> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
>>> 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] stats graphics  grDevices utils datasets  methods
>>> [7] base
>>> loaded via a namespace (and not attached):
>>> [1] compiler_3.6.1
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>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
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Re: [R-SIG-Mac] R, ape, and read.nexus()

[Ken Beath]

That looks like a package issue, so I would contact the author. Some authors 
can be very helpful.

Ken

> On 2 Sep 2019, at 12:05 pm, Timothy Dickinson  
> wrote:
> 
> I have repeatedly been encountering a problem reading into R nexus files that 
> I created in PAUP* 4.0a. I use the savetrees command in PAUP in order to get 
> rid of edge lengths in .tre files received from my collaborator. This is 
> useful to me since I thought I could edit things like tree and tip labels in 
> the nexus file. But even without modifying the file exported by PAUP, I 
> encounter this error message when I try to read the file into R (3.6.0 
> running on a Mac under OS 10.12.6). The Translate block has 26 labels, for 
> the 26 taxa.
> 
>> read.nexus("CDS_loci.treefile244.nex")
> 244 phylogenetic trees
> Warning message:
> In matrix(x, ncol = 2, byrow = TRUE) :
>  data length [51] is not a sub-multiple or multiple of the number of rows [26]
>> 
> 
> Any suggestions as to what the problem might be would be most welcome.
> 
> Thank you, ---tad.
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Memory Exhausted

[Ken Beath]

Try this 
https://stackoverflow.com/questions/51295402/r-on-macos-error-vector-memory-exhausted-limit-reached
 and the links.

Ken


> On 7 Jul 2019, at 1:22 pm, Alex  wrote:
> 
> Hello all,
> 
> I am new in R studio. I have a big data to run using RStudio. I keep
> getting "Error: vector memory exhausted (limit reached?)”  I am using MAC
> version"10.13.6 (17G6030)”.
> 
> I am using the Rstudion “
> R version 3.5.1 (2018-07-02)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS High Sierra 10.13.6”
> 
> Any help would be greatly appreciated.
> 
> Best,
> Alex
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Mac OS X Yosemite 10.10.5

[Ken Beath]

3.3 built for Mavericks at http://r.research.att.com should work.

Ken

> On 6 Sep 2018, at 4:27 am, Braden Justice  wrote:
> 
> Hello, I can’t seem to find a version that works for my mac, in the subject 
> line I’ve included my software. Do you know any versions of R that will work 
> for me?? Thank you so much!
> 
> -Braden
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Re: [R-SIG-Mac] Mac-only problem using readOGR(), which uses ogrInfo(), to read a shapefile from a directory on a USB pen drive

[Ken Beath]

My thought is that it might be that USB drives are usually MSDOS formatted. 
Usually not a problem but rgdal works with directories. Formatting  in a Mac 
with Disk Utility might be a work-around, with the limitation that the USB will 
only work in Macs.

I would also try verbose=TRUE which may give more information.

In the absence of other ideas contacting the package author can help.

Ken

> On 4 Mar 2017, at 3:32 am, D G. Rossiter  wrote:
> 
> I ran across a Mac-only problem using readOGR(), which uses ogrInfo(), to 
> read a shapefile from a directory on a USB pen drive. I tested the behaviour 
> on a Windows 10 machine and did not get the problem. 
> 
> Trying to read from the USB drive, with relative and full paths:
> 
>> setwd("/Volumes/ISPRS/“) # this is my connected USB drive
>> list.files() 
> [1] "map7100.dbf"  "map7100.prj" 
> [3] "map7100.sbn"  "map7100.sbx" 
> [5] "map7100.shp"  "map7100.shp.xml" 
> [7] "map7100.shx"  
>> file.exists("map7100.shp")
> [1] TRUE
>> usa <- readOGR(dsn=".", layer="map7100")
> Error in ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = 
> use_iconv,  : 
>  Cannot open data source
>> usa <- readOGR(dsn="/Volumes/ISPRS", layer="map7100")
> Error in ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = 
> use_iconv,  : 
>  Cannot open data source
> 
> But, readOGR reads the shapefile correctly if it’s located on the Mac’s 
> internal drive:
> 
>> setwd("/Users/rossiter/data/edu/dgeostats/ex")
>> file.exists("./ds/NEweather/map7100.shp")
> [1] TRUE
>> usa <- readOGR(dsn="./ds/NEweather", layer="map7100")
> OGR data source with driver: ESRI Shapefile 
> Source: "./ds/NEweather", layer: "map7100"
> with 7926 features
> It has 19 fields
> 
> All packages are up to date. Here is the sessionInfo():
> 
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
> 
> 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] stats graphics  grDevices utils datasets  methods   base 
> 
> other attached packages:
> [1] ggplot2_2.2.1  sf_0.3-4   maptools_0.9-1 rgdal_1.2-5   
> [5] sp_1.2-4   gstat_1.1-4   
> 
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.9  plyr_1.8.4   xts_0.9-7tools_3.3.2 
> [5] digest_0.6.12evaluate_0.10tibble_1.2   gtable_0.2.0
> [9] lattice_0.20-34  DBI_0.5-1yaml_2.1.14  stringr_1.2.0   
> [13] knitr_1.15.1 rprojroot_1.2grid_3.3.2   spacetime_1.2-0 
> [17] foreign_0.8-67   rmarkdown_1.3udunits2_0.13magrittr_1.5
> [21] backports_1.0.5  scales_0.4.1 intervals_0.15.1 htmltools_0.3.5 
> [25] units_0.4-2  rsconnect_0.7assertthat_0.1   colorspace_1.3-2
> [29] labeling_0.3 stringi_1.1.2lazyeval_0.2.0   munsell_0.4.3   
> [33] FNN_1.1  zoo_1.7-14  
> 
> This is a problem because several of my students have OS/X machines and like 
> to work from USB-connected external drives.
> 
> D G (David) Rossiter
> Section of Soil & Crop Sciences
> Cornell University
> http://www.css.cornell.edu/faculty/dgr2/
> 
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Re: [R-SIG-Mac] Mac-only problem using readOGR(), which uses ogrInfo(), to read a shapefile from a directory on a USB pen drive

[Ken Beath]

My thought is that it might be that USB drives are usually MSDOS formatted. 
Generally not a problem but maybe a problem because rgdal works with 
directories. Formatting  in a Mac with Disk Utility might be a work-around, 
with the limitation that the USB will only work in Macs.

I would also try verbose=TRUE which may give more information.

In the absence of other ideas contacting the package maintainer may help.

Ken

> On 4 Mar 2017, at 3:32 am, D G. Rossiter  wrote:
> 
> I ran across a Mac-only problem using readOGR(), which uses ogrInfo(), to 
> read a shapefile from a directory on a USB pen drive. I tested the behaviour 
> on a Windows 10 machine and did not get the problem. 
> 
> Trying to read from the USB drive, with relative and full paths:
> 
>> setwd("/Volumes/ISPRS/“) # this is my connected USB drive
>> list.files() 
> [1] "map7100.dbf"  "map7100.prj" 
> [3] "map7100.sbn"  "map7100.sbx" 
> [5] "map7100.shp"  "map7100.shp.xml" 
> [7] "map7100.shx"  
>> file.exists("map7100.shp")
> [1] TRUE
>> usa <- readOGR(dsn=".", layer="map7100")
> Error in ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = 
> use_iconv,  : 
>  Cannot open data source
>> usa <- readOGR(dsn="/Volumes/ISPRS", layer="map7100")
> Error in ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = 
> use_iconv,  : 
>  Cannot open data source
> 
> But, readOGR reads the shapefile correctly if it’s located on the Mac’s 
> internal drive:
> 
>> setwd("/Users/rossiter/data/edu/dgeostats/ex")
>> file.exists("./ds/NEweather/map7100.shp")
> [1] TRUE
>> usa <- readOGR(dsn="./ds/NEweather", layer="map7100")
> OGR data source with driver: ESRI Shapefile 
> Source: "./ds/NEweather", layer: "map7100"
> with 7926 features
> It has 19 fields
> 
> All packages are up to date. Here is the sessionInfo():
> 
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
> 
> 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] stats graphics  grDevices utils datasets  methods   base 
> 
> other attached packages:
> [1] ggplot2_2.2.1  sf_0.3-4   maptools_0.9-1 rgdal_1.2-5   
> [5] sp_1.2-4   gstat_1.1-4   
> 
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.9  plyr_1.8.4   xts_0.9-7tools_3.3.2 
> [5] digest_0.6.12evaluate_0.10tibble_1.2   gtable_0.2.0
> [9] lattice_0.20-34  DBI_0.5-1yaml_2.1.14  stringr_1.2.0   
> [13] knitr_1.15.1 rprojroot_1.2grid_3.3.2   spacetime_1.2-0 
> [17] foreign_0.8-67   rmarkdown_1.3udunits2_0.13magrittr_1.5
> [21] backports_1.0.5  scales_0.4.1 intervals_0.15.1 htmltools_0.3.5 
> [25] units_0.4-2  rsconnect_0.7assertthat_0.1   colorspace_1.3-2
> [29] labeling_0.3 stringi_1.1.2lazyeval_0.2.0   munsell_0.4.3   
> [33] FNN_1.1  zoo_1.7-14  
> 
> This is a problem because several of my students have OS/X machines and like 
> to work from USB-connected external drives.
> 
> D G (David) Rossiter
> Section of Soil & Crop Sciences
> Cornell University
> http://www.css.cornell.edu/faculty/dgr2/
> 
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Re: [R-SIG-Mac] R.app crashes at startup on MacOS Sierra

[Ken Beath]

I’ve had no trouble with using RStudio so it is definitely a GUI problem. I’ve 
also had no trouble with TeXShop so I assume that whatever LaTex editor you are 
using is the problem. 

Ken

> On 1 Mar 2017, at 4:42 pm, David Diez  wrote:
> 
> Anyone have any luck with figuring this out? I have the same problem on both 
> my personal and work computers immediately after installing Sierra.
> 
> I'm not sure if it's related, but LaTeX has also been giving me issues ever 
> since I installed Sierra on my personal machine.
> 
> I'm close to completely wiping my personal machine to try to fix the R and 
> LaTeX issues. If I do, I'll report back on if it fixes the issue.
> 
> Thanks,
> David
> 
> 
> On Sunday, February 5, 2017 at 1:37:10 AM UTC-8, Patricia Gouzien wrote:
> Hello,
> 
> I am experiencing the following issues:
> R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>   Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> [R.app GUI 1.68 (7288) x86_64-apple-darwin13.4.0]
> 
> 
>  
> 
> 
> 
> 
> Selection: 
> 
> R crashes. Any help on this is greatly appreciated.
> Sierra 10.12.2
> 
> Thanks so much!
> Pat
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Re: [R-SIG-Mac] Recurring problem to run R with SPSS 24

[Ken Beath]

I would be surprised if anyone on this mailing list runs R analyses through 
SPSS. What SPSS and SAS have done is to say, well people want to do analyses 
that are available in R that we can’t be bothered implementing, so we will give 
them an interface, and it seems not a very good one.

It should not take long to learn how to read in the data in R, produce the 
analysis and output the results. Try this 
http://www.ats.ucla.edu/stat/r/dae/tobit.htm

Ken


> On 22 Dec. 2016, at 10:08 am, Andreas Schröder 
>  wrote:
> 
> Dear all, 
> 
> my last post about the non-compatibility of R essentials with SPSS 24 could 
> not be resolved and an employee of IBM suggested to install spss 22 which 
> runs with R 2.15.  I purchased this “older licence” today. 
> 
> So far so good, but already the installation of the required R 2.15.(2) does 
> not work because apparently the installer does not recognise Sierra 10.12.2 
> as a newer built than OS X 10.  Any suggestions? Google search yields 
> solutions that involve programming to my understanding which I am not capable 
> of.
> 
> 
> I am very frustrated right now because I feel simply cheated by IBM. Did 
> anyone experience the same issue?
> 
> I did all installations exactly as suggested by the IBM manuals and simply 
> want to run a Tobit-Regression.
> 
> Thank you for every input.
> 
> Best, 
> 
> Andreas 
> 
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Re: [R-SIG-Mac] Fortran on MacOS Sierra

[Ken Beath]

lme4 and fastGHQuad

Ken

> On 30 Sep. 2016, at 10:46 pm, Bob Rudis <b...@rud.is> wrote:
> 
> Glad you're up and running!
> 
> ​If you have some specific examples I can try to reproduce (and report) as I 
> load the betas (I'm on beta 2 now).
> 
> -Bob
> 
> On Fri, Sep 30, 2016 at 8:26 AM, Ken Beath <k...@kjbeath.com.au> wrote:
> Thanks, yes I sorted it out. I’d read the bit on Makevars but it just didn’t 
> seem what I wanted.
> 
> There are some problems with the 10.12.1 beta which affect built libraries 
> but at the moment I will just hope they go away.
> 
> Ken
> 
> > On 30 Sep. 2016, at 9:26 pm, Bob Rudis <b...@rud.is> wrote:
> >
> > Coudert's packages are unsigned which seems like a significant oversight 
> > and a CRAN manual entry recommending installing unsigned binaries does not 
> > sit well with me and may not work in the next macOS release.
> >
> > Ken: to avoid you having to dig you need to download 
> > <http://coudert.name/software/gfortran-6.1-ElCapitan.dmg> and install it, 
> > overriding the security warning (ugh).
> >
> > You then need to add this to your ~/.R/Makevars (or to the site one)
> >
> > F77 = /usr/local/gfortran/bin/gfortran
> > FC = /usr/local/gfortran/bin/gfortran
> > FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
> > -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
> >
> > You'll still get the massive amount of warnings (they aren't harmful) but 
> > the pkg will compile/install from source.
> >
> >
> > On Fri, Sep 30, 2016 at 5:04 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk> 
> > wrote:
> > This seems to be Sierra, which has 'tidied up' system libraries.
> >
> > The recommendation for El Capitan at http://coudert.name/software.html also 
> > works correctly on Sierra. (See the manual, preferably before posting.)
> >
> > There are good reasons why the posting guide asks for 'at a minimum' the 
> > output of sessionInfo() 
> >
> > On 30/09/2016 09:31, Ken Beath wrote:
> > I tried to build frailtypack from source using R 3.3.1 and it failed with 
> > the following message (after a ridiculous amount of warnings)
> >
> > gfortran-4.8 -dynamiclib -Wl,-headerpad_max_install_names -undefined 
> > dynamic_lookup -single_module -multiply_defined suppress 
> > -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 
> > frailtypack.so Adonnees.o AparamMultive.o Aparameters.o aGhermite.o 
> > aaOptim.o aaOptimres.o aaUseFunction.o aaUseFunctionG.o aamarq98o.o 
> > additive.o afuncpasres.o ahrmsym.o aresidusMartingale.o atestWald.o 
> > distance.o epoce.o epoce_log.o epoce_long.o frailtypack.o funcpaG_tps.o 
> > funcpaGcpm.o funcpaGcpm_intcens.o funcpaGcpm_log.o funcpaGsplines.o 
> > funcpaGsplines_intcens.o funcpaGsplines_log.o funcpaGweib.o 
> > funcpaGweib_intcens.o funcpaGweib_log.o funcpaMultivCpm.o 
> > funcpaMultivSplines.o funcpaMultivWeib.o funcpaacpm.o funcpaasplines.o 
> > funcpaaweib.o funcpaj_tps.o funcpajcpm.o funcpajcpm_log.o funcpajgeneral.o 
> > funcpajlongisplines.o funcpajlongiweib.o funcpajsplines.o 
> > funcpajsplines_fam.o funcpajsplines_intcens.o funcpajsplines_log.o 
> > funcpajweib.o funcpajweib_fam.o funcpajweib_intcens.o funcpajweib_log.o 
> > f... 
> > gfortran-4.8: warning: couldn’t understand kern.osversion ‘16.0.0
> > ld: library not found for -ldylib1.o
> > collect2: error: ld returned 1 exit status
> > make: *** [frailtypack.so] Error 1
> > ERROR: compilation failed for package ‘frailtypack’
> >
> > I was going to attempt the build with gfortran 4.2 but haven’t been able to 
> > revert back from 4.8
> >
> > So does it happen with 4.2 and if not, how can I revert back?
> >
> > If not is this an R problem or the package?
> >
> > --
> > Brian D. Ripley,  rip...@stats.ox.ac.uk
> > Emeritus Professor of Applied Statistics, University of Oxford
> >
> > ___
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> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> 
> 
> 

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Re: [R-SIG-Mac] Fortran on MacOS Sierra

[Ken Beath]

Thanks, yes I sorted it out. I’d read the bit on Makevars but it just didn’t 
seem what I wanted.

There are some problems with the 10.12.1 beta which affect built libraries but 
at the moment I will just hope they go away.

Ken

> On 30 Sep. 2016, at 9:26 pm, Bob Rudis <b...@rud.is> wrote:
> 
> Coudert's packages are unsigned which seems like a significant oversight and 
> a CRAN manual entry recommending installing unsigned binaries does not sit 
> well with me and may not work in the next macOS release.
> 
> Ken: to avoid you having to dig you need to download 
> <http://coudert.name/software/gfortran-6.1-ElCapitan.dmg> and install it, 
> overriding the security warning (ugh).
> 
> You then need to add this to your ~/.R/Makevars (or to the site one)
> 
> F77 = /usr/local/gfortran/bin/gfortran
> FC = /usr/local/gfortran/bin/gfortran
> FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
> -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
> 
> You'll still get the massive amount of warnings (they aren't harmful) but the 
> pkg will compile/install from source.
> 
> 
> On Fri, Sep 30, 2016 at 5:04 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk> 
> wrote:
> This seems to be Sierra, which has 'tidied up' system libraries.
> 
> The recommendation for El Capitan at http://coudert.name/software.html also 
> works correctly on Sierra. (See the manual, preferably before posting.)
> 
> There are good reasons why the posting guide asks for 'at a minimum' the 
> output of sessionInfo() 
> 
> On 30/09/2016 09:31, Ken Beath wrote:
> I tried to build frailtypack from source using R 3.3.1 and it failed with the 
> following message (after a ridiculous amount of warnings)
> 
> gfortran-4.8 -dynamiclib -Wl,-headerpad_max_install_names -undefined 
> dynamic_lookup -single_module -multiply_defined suppress 
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 
> frailtypack.so Adonnees.o AparamMultive.o Aparameters.o aGhermite.o aaOptim.o 
> aaOptimres.o aaUseFunction.o aaUseFunctionG.o aamarq98o.o additive.o 
> afuncpasres.o ahrmsym.o aresidusMartingale.o atestWald.o distance.o epoce.o 
> epoce_log.o epoce_long.o frailtypack.o funcpaG_tps.o funcpaGcpm.o 
> funcpaGcpm_intcens.o funcpaGcpm_log.o funcpaGsplines.o 
> funcpaGsplines_intcens.o funcpaGsplines_log.o funcpaGweib.o 
> funcpaGweib_intcens.o funcpaGweib_log.o funcpaMultivCpm.o 
> funcpaMultivSplines.o funcpaMultivWeib.o funcpaacpm.o funcpaasplines.o 
> funcpaaweib.o funcpaj_tps.o funcpajcpm.o funcpajcpm_log.o funcpajgeneral.o 
> funcpajlongisplines.o funcpajlongiweib.o funcpajsplines.o 
> funcpajsplines_fam.o funcpajsplines_intcens.o funcpajsplines_log.o 
> funcpajweib.o funcpajweib_fam.o funcpajweib_intcens.o funcpajweib_log.o f... 
> 
> gfortran-4.8: warning: couldn’t understand kern.osversion ‘16.0.0
> ld: library not found for -ldylib1.o
> collect2: error: ld returned 1 exit status
> make: *** [frailtypack.so] Error 1
> ERROR: compilation failed for package ‘frailtypack’
> 
> I was going to attempt the build with gfortran 4.2 but haven’t been able to 
> revert back from 4.8
> 
> So does it happen with 4.2 and if not, how can I revert back?
> 
> If not is this an R problem or the package?
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
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[R-SIG-Mac] Fortran on MacOS Sierra

[Ken Beath]

I tried to build frailtypack from source using R 3.3.1 and it failed with the 
following message (after a ridiculous amount of warnings)

gfortran-4.8 -dynamiclib -Wl,-headerpad_max_install_names -undefined 
dynamic_lookup -single_module -multiply_defined suppress 
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 
frailtypack.so Adonnees.o AparamMultive.o Aparameters.o aGhermite.o aaOptim.o 
aaOptimres.o aaUseFunction.o aaUseFunctionG.o aamarq98o.o additive.o 
afuncpasres.o ahrmsym.o aresidusMartingale.o atestWald.o distance.o epoce.o 
epoce_log.o epoce_long.o frailtypack.o funcpaG_tps.o funcpaGcpm.o 
funcpaGcpm_intcens.o funcpaGcpm_log.o funcpaGsplines.o funcpaGsplines_intcens.o 
funcpaGsplines_log.o funcpaGweib.o funcpaGweib_intcens.o funcpaGweib_log.o 
funcpaMultivCpm.o funcpaMultivSplines.o funcpaMultivWeib.o funcpaacpm.o 
funcpaasplines.o funcpaaweib.o funcpaj_tps.o funcpajcpm.o funcpajcpm_log.o 
funcpajgeneral.o funcpajlongisplines.o funcpajlongiweib.o funcpajsplines.o 
funcpajsplines_fam.o funcpajsplines_intcens.o funcpajsplines_log.o 
funcpajweib.o funcpajweib_fam.o funcpajweib_intcens.o funcpajweib_log.o f... 

gfortran-4.8: warning: couldn’t understand kern.osversion ‘16.0.0
ld: library not found for -ldylib1.o
collect2: error: ld returned 1 exit status
make: *** [frailtypack.so] Error 1
ERROR: compilation failed for package ‘frailtypack’

I was going to attempt the build with gfortran 4.2 but haven’t been able to 
revert back from 4.8

So does it happen with 4.2 and if not, how can I revert back?

If not is this an R problem or the package?

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Re: [R-SIG-Mac] Problem using the R.app GUI Package Installer

[Ken Beath]

In the Install Packages dialog there is an Other Repository option and that 
seems to be permanent.

It can also be changed in the Preferences.

> On 29 Sep. 2016, at 8:13 am, Duncan Murdoch  wrote:
> 
> On 28/09/2016 5:26 PM, Joseph Kunkel wrote:
>> I got this error message working under R version 3.3.0  trying to use the 
>> Mac [R.app GUI 1.68 (7238) x86_64-apple-darwin13.4.0]  Packages & Data/ 
>> Package Installer
>> 
>> R error message:
>> Warning: unable to access index for repository 
>> http://cran.at.r-project.org/bin/macosx/mavericks/contrib/3.3:  cannot open 
>> URL 'http://cran.at.r-project.org/bin/macosx/mavericks/contrib/3.3/PACKAGES'
>> 
>> I checked for upgrades and installed R version 3.3.1
>> 
>> I got the same error message once again.
>> 
>> Luckily I remembered that I could install libraries from within R and thus 
>> used:
>> 
>>> install.packages('RCurl', dependencies=TRUE, 
>>> repos='http://cran.rstudio.com/')
>> 
>> But I am wondering if the malfunction of the GUI approach is something I can 
>> fix or is temporary?
>> 
> 
> That was probably a temporary problem, or a local network problem for you:  I 
> can get the URL to open.
> 
> But in general, to change the default mirror in R.app, run chooseCRANmirror() 
> in the console.  I forget whether that changes it for the session or 
> permanently.
> 
> Duncan Murdoch
> 
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Re: [R-SIG-Mac] Problems with R CMD config

[Ken Beath]

> On 1 Sep 2016, at 5:46 PM, Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote:
> 
> On 01/09/2016 00:43, Ken Beath wrote:
>> I’m trying to use STAN which uses R CMD config to check the availability of 
>> the compilers.
>> 
>> This works fine on my MacBook but on my iMac I have the documents on a 
>> separate hard drive. Within R CMD config it uses the location of the home  
>> folder which because of my choice of name of hard drive has a space in it, 
>> and that causes problems with the batch file. In the following the volume 
>> should be Ken Main.
>> 
>> Kens-iMac:~ kjbeath1$ R CMD config CXX
>> make: /Volumes/Ken: No such file or directory
>> make: *** No rule to make target `/Volumes/Ken'.  Stop.
>> 
>> For those who are wondering why I don’t just change the name, this produces 
>> problems with other software.
>> 
>> Any ideas on a solution?
> 
> Edit the script config.
> 
> We have nothing to reproduce here (what is your home directory?), but I am 
> guessing that in
> 
>elif test -f "${HOME}/.R/Makevars-${R_PLATFORM}"; then
>  makefiles="${makefiles} -f ${HOME}/.R/Makevars-${R_PLATFORM}"
>elif test -f "${HOME}/.R/Makevars"; then
>  makefiles="${makefiles} -f ${HOME}/.R/Makevars"
> 
> you need \"${HOME}\" twice.
> 

Yes, works perfectly.

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[R-SIG-Mac] Problems with R CMD config

[Ken Beath]

I’m trying to use STAN which uses R CMD config to check the availability of the 
compilers.

This works fine on my MacBook but on my iMac I have the documents on a separate 
hard drive. Within R CMD config it uses the location of the home  folder which 
because of my choice of name of hard drive has a space in it, and that causes 
problems with the batch file. In the following the volume should be Ken Main.

Kens-iMac:~ kjbeath1$ R CMD config CXX
make: /Volumes/Ken: No such file or directory
make: *** No rule to make target `/Volumes/Ken'.  Stop.

For those who are wondering why I don’t just change the name, this produces 
problems with other software.

Any ideas on a solution?

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