Re: [R-SIG-Mac] R CMD …

[Dr Eberhard W Lisse]

That depends.

I would look for

/usr/local/bin/r

or

/usr/local/bin/R

one of them should have been symlinked by the PKG Installer. But then I
use homebrew without the graphic app (I like Rstudio, and TextMate is
also very, very good).


el



On 2021-02-20 17:04 , Peter West wrote:
> I see a lot of references to R CMD on the command line. Can I > assume
> that the R in question is the R executable in Contents > MacOS within
> R.app?
>
> Peter
[...]
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Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC

[Dr Eberhard W Lisse]

Remove the directory where xcrun says it is supposed to live and re-install the 
command line tools?

el

—
Sent from Dr Lisse’s iPhone
On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote:
> I reported on installing xcode tools in my email
> Sat 2/13/2021 3:59 PM
> It didn't help.
>
> I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1.
>
> ____
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 4:44 PM
> To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] 
> Please test R 4.0.4 RC
>
> the Xcode Command line tools are missing. Install them and see what happens.
>
> Did you recently upgrade MacOS?
>
> el
>
> —
> Sent from Dr Lisse’s iPhone
> On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
> That is next. Again a fresh session.
>
>
> setwd('/Users/rmh/Rwd/')
> Sys.setenv(DISPLAY=":0.0")
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
> unable to start device X11
> In addition: Warning messages:
> 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
> running command ''otool' -L 
> '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
> 2: In X11() : unable to open connection to X11 display ''
>
>
>
> and the R session is still alive.
>
>
> This rasies for me a different question. Why should I want X11()?
>
> When X11 was working it was very slow, and didn't allow paging back through
> previous images.
>
> In favor of X11, I think it uses the display space better. X11() has better 
> size and spacing for xlab, ylab, and main than quartz(). But that isn't a 
> strong enough
> reason to use it while develkoping a graph. When I want it to look good,
> I go directly to pdf() and get the spacing that I think looks better.
>
> 
> From: Duncan Murdoch 
> Sent: Saturday, February 13, 2021 4:05 PM
> To: Richard M. Heiberger; R-SIG-Mac
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
> 4.0.4 RC
>
> Have you tried the change to DISPLAY, i.e.
>
> Sys.setenv(DISPLAY=":0.0")
>
> before running X11()?
>
> Duncan Murdoch
>
> On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
> I tried this. It made no difference. Both before and after running
> sudo xcode-select —install
> I ran (in both cases, in a brand new *R* sessio n)
>
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
>
>
> My prior was that the xcode call was irrelevant is that X11() using XQuart 
> 8.0.3beta
> worked with intel R_4.0.3 on the Mac M1.
>
> 
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 3:33 AM
> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>
> that has nothing to do with Xquartz but means you need to install the Command 
> line tools
>
> sudo xcode-select —install
>
> —
> Sent from Dr Lisse’s iPhone
> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> Using the intel R_4.0.4RC on the Mac M1.
>
> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> 8.0.3beta.
> X11() now does not work at all.
>
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> C-c C-c C-c C-c
>
> Force-Killing XQuartz from the Activity Monitor doesn't help.
> I have to Force-kill the R process.
>
> 
> From: R-SIG-Mac  on behalf of Simon Urbanek 
> 
> Sent: Friday, February 12, 2021 6:50 PM
> To: R-SIG-Mac
> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>
> Dear macOS useRs,
>
> please test the latest R 4.0.4 RC builds from
>
> https://mac.r-project.org/
>
> especially if you are running macOS Big Sur. The known issues introduced by 
> Big Sur have been fixed, but I cannot replicate nor test the spurious 
> touchbar warning.
>
> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> they are betas for a reason (=unstable) and break things.
>
> Cheers,
> Simon
>

Re: [R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory"

[Dr Eberhard W Lisse]

space in a directory name?

put the file in ~/Desktop and see what happens then.

If it is a CSV make it moabsitechem.csv and see what that doesn.

el

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 22:29 +0200, Parkhurst, David F. , wrote:
> I’m still having trouble with read.table, as follows (and there IS a plain 
> text document called moabsitechem in this directory:
> > getwd()
> [1] "/Users/DFP/Documents/Documents - David’s iMac/ae/FriendsMonroe"
> > read.table("moabsitechem")
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>   cannot open file 'moabsitechem': No such file or directory
>
> How can I fix this problem?
>
> ___
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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] [External] Re: [External] Re: [External] Please test R 4.0.4 RC

[Dr Eberhard W Lisse]

the Xcode Command line tools are missing. Install them and see what happens.

Did you recently upgrade MacOS?

el

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
> That is next. Again a fresh session.
>
>
> > setwd('/Users/rmh/Rwd/')
> > Sys.setenv(DISPLAY=":0.0")
> > X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
> unable to start device X11
> In addition: Warning messages:
> 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
> running command ''otool' -L 
> '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
> 2: In X11() : unable to open connection to X11 display ''
> >
>
>
> and the R session is still alive.
>
>
> This rasies for me a different question. Why should I want X11()?
>
> When X11 was working it was very slow, and didn't allow paging back through
> previous images.
>
> In favor of X11, I think it uses the display space better. X11() has better 
> size and spacing for xlab, ylab, and main than quartz(). But that isn't a 
> strong enough
> reason to use it while develkoping a graph. When I want it to look good,
> I go directly to pdf() and get the spacing that I think looks better.
>
> 
> From: Duncan Murdoch 
> Sent: Saturday, February 13, 2021 4:05 PM
> To: Richard M. Heiberger; R-SIG-Mac
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
> 4.0.4 RC
>
> Have you tried the change to DISPLAY, i.e.
>
> Sys.setenv(DISPLAY=":0.0")
>
> before running X11()?
>
> Duncan Murdoch
>
> On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
> > I tried this. It made no difference. Both before and after running
> > sudo xcode-select —install
> > I ran (in both cases, in a brand new *R* sessio n)
> >
> > > X11()
> > xcrun: error: invalid active developer path 
> > (/Library/Developer/CommandLineTools), missing xcrun at: 
> > /Library/Developer/CommandLineTools/usr/bin/xcrun
> >
> >
> > My prior was that the xcode call was irrelevant is that X11() using XQuart 
> > 8.0.3beta
> > worked with intel R_4.0.3 on the Mac M1.
> >
> > 
> > From: Dr Eberhard W Lisse 
> > Sent: Saturday, February 13, 2021 3:33 AM
> > To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> > Cc: e...@lisse.na
> > Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
> >
> > that has nothing to do with Xquartz but means you need to install the 
> > Command line tools
> >
> > sudo xcode-select —install
> >
> > —
> > Sent from Dr Lisse’s iPhone
> > On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> > Using the intel R_4.0.4RC on the Mac M1.
> >
> > Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> > 8.0.3beta.
> > X11() now does not work at all.
> >
> > X11()
> > xcrun: error: invalid active developer path 
> > (/Library/Developer/CommandLineTools), missing xcrun at: 
> > /Library/Developer/CommandLineTools/usr/bin/xcrun
> > C-c C-c C-c C-c
> >
> > Force-Killing XQuartz from the Activity Monitor doesn't help.
> > I have to Force-kill the R process.
> >
> > 
> > From: R-SIG-Mac  on behalf of Simon 
> > Urbanek 
> > Sent: Friday, February 12, 2021 6:50 PM
> > To: R-SIG-Mac
> > Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
> >
> > Dear macOS useRs,
> >
> > please test the latest R 4.0.4 RC builds from
> >
> > https://mac.r-project.org/
> >
> > especially if you are running macOS Big Sur. The known issues introduced by 
> > Big Sur have been fixed, but I cannot replicate nor test the spurious 
> > touchbar warning.
> >
> > Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> > they are betas for a reason (=unstable) and break things.
> >
> > Cheers,
> > Simon
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

[Dr Eberhard W Lisse]

that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> Using the intel R_4.0.4RC on the Mac M1.
>
> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> 8.0.3beta.
> X11() now does not work at all.
>
> > X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> C-c C-c C-c C-c
>
> Force-Killing XQuartz from the Activity Monitor doesn't help.
> I have to Force-kill the R process.
>
> 
> From: R-SIG-Mac  on behalf of Simon Urbanek 
> 
> Sent: Friday, February 12, 2021 6:50 PM
> To: R-SIG-Mac
> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>
> Dear macOS useRs,
>
> please test the latest R 4.0.4 RC builds from
>
> https://mac.r-project.org/
>
> especially if you are running macOS Big Sur. The known issues introduced by 
> Big Sur have been fixed, but I cannot replicate nor test the spurious 
> touchbar warning.
>
> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> they are betas for a reason (=unstable) and break things.
>
> Cheers,
> Simon
>
> ___
> 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 for macOS Big Sur

[Dr Eberhard W Lisse]

I use the homebrew R for the Intel and then install.packages(), 
update.package() from scripts and  Rstudio’s Tools->.

I don’t have an M1 (yet) but would be interested in seeing how that works on 
the M1. Probably this will pull the sources and hence I would be grateful to 
read about that.


greetings, el

—
Sent from Dr Lisse’s iPhone
On 11 Jan 2021, 10:05 +0200, Patrick Schratz , wrote:
> There is a [native arm64 big sur
> binary](https://github.com/Homebrew/homebrew-core/blob/8a6807be6abb44634e7d6d153348b6bba2a5ddc6/Formula/r.rb#L16)
> in homebrew since some days.
>
> On 10 Jan 2021, at 22:39, Gregory Coats via R-SIG-Mac wrote:
>
> > I purchased a new 13 inch Apple MacBook Pro with the M1 System on a
> > Chip. I understand that R is not yet available compiled for the M1 SoC
> > hardware, and so I am using Apple’s Rosetta 2.
> > However, this MacBook Pro requires Apple macOS Big Sur. From what I
> > see at https://mac.r-project.org/ R has not been compiled for macOS
> > Big Sur. Is there an executable of R for macOS Big Sur available to
> > download?
> > Greg Coats
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> [[alternative HTML version deleted]]
>
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Re: [R-SIG-Mac] Problem R with Big Sur

[Dr Eberhard W Lisse]

Aurélie

This has been discussed here on the list recently and I think the
short term fix is to use Rstudio or R from the command line.

I am sure this will sort itself out over time. 

el


On 2021-01-05 11:01 , Univ-Rouen wrote:
> Dear all,
> I have change my MacBook Pro since a few months and now, I have a
> MacBook Pro 16 with a Touch Bar.  Yesterday, I have updated my
> computer with Big Sur and now, when I open R (4.0.3), I have this
> message when R opens or every time a window opens:
> 
> 2021-01-05 09:55:30.150 R[1275:42594] Warning: Expected min height of
> view: () to be less than
> or equal to 30 but got a height of 32.00.  This error will be
> logged once per view in violation.
> 
> Before updating to Big Sur, I had not this problem with Catalina.
> Has anyone had the same problem? How can I fix it?
> Many thanks,
> Aurélie

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Re: [R-SIG-Mac] INSTALL R 4.0.2

[Dr Eberhard W Lisse]

You are most welcome.

The answer to your question lies probably also in Google.

el

On 03/12/2020 14:52, Giuseppe Sant wrote:
> That’s the right way to motivate me.  Will let you know about the
> results.  Last thing, because of the unkind comment can you help me
> solving one thing but radiant?
> I downloaded the packages thank opened it but in Basics->Prob
> calculator the layout is incomplete.  I can only see the graphic, not
> the data over it.  You know why?
> 
>> Il giorno 3 dic 2020, alle ore 13:41, Dr Eberhard W Lisse
 ha scritto:
>>
>> Guiseppe,
>>
>> if you can't google, I do not see a bright future for your exam.
>>
>>
>> el
>>
>>
>>
>> On 03/12/2020 14:37, Giuseppe Sant wrote:
>>> Hi, 
>>> I’m a student and I really need to install version of R 4.0.2 as soon
>>> as possible because I have an important exam that could change my
>>> career.  I’m texting just to have the link to download that version.
>>> Really thankful, 
>>> Giuseppe Santangelo.
[...]

-- 
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e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
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Re: [R-SIG-Mac] INSTALL R 4.0.2

[Dr Eberhard W Lisse]

Guiseppe,

if you can't google, I do not see a bright future for your exam.


el



On 03/12/2020 14:37, Giuseppe Sant wrote:
> Hi, 
> I’m a student and I really need to install version of R 4.0.2 as soon
> as possible because I have an important exam that could change my
> career.  I’m texting just to have the link to download that version.
> Really thankful, 
> Giuseppe Santangelo.
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

-- 
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e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
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Re: [R-SIG-Mac] Problems with R and Big Sur

[Dr Eberhard W Lisse]

sudo xcode-select --install

el

On 2020-12-02 18:52 , Spencer Graves wrote:
> $ clang --version
> Apple clang version 11.0.3 (clang-1103.0.32.59)
> Target: x86_64-apple-darwin20.1.0
> Thread model: posix
> InstalledDir:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
> 
> 
> 
>   ** "sudo rm -rf /Library/Developer/CommandLineTools" deleted
> "CommandLineTools".  Then "sudo xcode-select —install" gave me "invalid
> argument '—install'".  "sudo xcode-select —install" gave me the same.
> 
> 
>   ** Fortunately, I was able to update Xcode from App Store.  Now I
> get:
> 
> 
> $ clang --version
> Apple clang version 12.0.0 (clang-1200.0.32.27)
> Target: x86_64-apple-darwin20.1.0
> Thread model: posix
> InstalledDir:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
> 
> 
> 
>   If you also have a problem with "sudo xcode-select —install", you
> might try the App Store.
> 
> 
>   Thanks, Spencer
> 
> 
> On 2020-12-02 08:18, Gilberto Camara wrote:
>> For me, it worked as follows
>>
>> sudo rm -rf /Library/Developer/CommandLineTools
>> sudo xcode-select —install
>>
>> Best
>> Gilberto
>>
>>
>>> On 2 Dec 2020, at 15:15, Spencer Graves 
>>> wrote:
>>>
>>>   What should I do to "make sure to have installed the latest
>>> version of Apple's development environment, including version 12.0 of
>>> the compiler"?
>>>
>>>
>>>   Thanks,
>>>   Spencer Graves
>>>
>>>
>>> On 2020-12-02 07:36, GilbertoCamara wrote:
>>>> Dear all,
>>>> I am running R 4.0.3 on BigSur without major performance issues. I
>>>> am using RStudio instead of the R GUI.
>>>> I had to build all spatial packages (rgdal, sf, terra and raster)
>>>> from source using the Apple clang version 12.0.0 compiler. I also
>>>> had to build GDAL from scratch, since neither the “homebrew” version
>>>> nor the “kyngchaos” version work well with BigSur.
>>>> If anyone is building packages from source, please make sure to have
>>>> installed the latest version of Apple’s development environment,
>>>> including version 12.0 of the compiler as earlier versions do not
>>>> work well in BigSur.
>>>> Best
>>>> Gilberto
>>>> ===
>>>> Prof Dr Gilberto Camara
>>>> Secretariat Director
>>>> GEO - Group on Earth Observations
>>>>> On 2 Dec 2020, at 14:15, Bob Rudis  wrote:
>>>>>
>>>>> After a bit of git and google poking it seems this is happening to
>>>>> users
>>>>> of MacVim (https://github.com/macvim-dev/macvim/issues/1114) and a few
>>>>> other FOSS projects.
>>>>>
>>>>> In various GH issues (like that one) the issue claims to be
>>>>> resolved by
>>>>> using the latest Xcode & SDK but that’s not likely to be a solution
>>>>> for R
>>>>> GUI (which I’m assuming you're using and where this error is coming
>>>>> up).
>>>>>
>>>>> Some of the threads I saw made it seem like it was happening
>>>>> especially on
>>>>> Touch Bar-equipped MacBook Pros (but that’s not confirmed).
>>>>>
>>>>> When I try R GUI on Big Sur (on the new M1 Mini) — either just plain R
>>>>> scripts or plotting — I do not see this, nor do I see this on my Intel
>>>>> MacBook Pro (both are on the latest Big Sur beta and R 4.0.3).
>>>>>
>>>>> On Dec 2, 2020 at 7:53:26 AM, Spencer Graves
>>>>> 
>>>>> wrote:
>>>>>
>>>>>> I didn't get this with R 4.0.3 under macOS Big Sur 11.0.1 with "time
>>>>>> R CMD build" / check.  I have not tried it under RStudio.
>>>>>>
>>>>>>
>>>>>> sg
>>>>>>
>>>>>>
>>>>>> On 2020-12-02 05:01, Dr Eberhard W Lisse wrote:
>>>>>>
>>>>>> I don't get this in 4.0.3 (using the command line version of R) and I
>>>>>>
>>>>>> don't get this in RStudio 1.3.1093 either.  I use the homebrew
>>>>>> versions
>>>>>>
>>>>>> without the R GUI even installed.
>>&g

Re: [R-SIG-Mac] Problems with R and Big Sur

[Dr Eberhard W Lisse]

clang --version

el

On 02/12/2020 16:15, Spencer Graves wrote:
>   What should I do to "make sure to have installed the latest version of 
> Apple's development environment, including version 12.0 of the compiler"?
> 
> 
>   Thanks,
>   Spencer Graves

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Re: [R-SIG-Mac] Problems with R and Big Sur

[Dr Eberhard W Lisse]

I don't get this in 4.0.3 (using the command line version of R) and I
don't get this in RStudio 1.3.1093 either.  I use the homebrew versions
without the R GUI even installed.

I am sure more detail will be helpful to the developers.

el

On 02/12/2020 11:09, Maria-Angeles Casares-de-Cal via R-SIG-Mac wrote:
> To those in charge of R for Mac OS X: 
> 
> I have installed the new Big Sur operating system and now I always get
> a warning similar to:
> 
> 2020-12-02 09:52:00.647 R[703:11786] Warning: Expected min height of
> view: () to be less than
> or equal to 30 but got a height of 32.00.  This error will be
> logged once per view in violation.
> 
> and the computer becomes very slow.
> 
> Can I do something to fix it, or will we have to wait for an R update?
> 
> Thank you very much for your attention.
> 
> Sincerely,
> 
> María-Ángeles Casares-de-Cal
[...]

-- 
Dr. Eberhard W. Lisse   \ /   Obstetrician & Gynaecologist 
e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
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Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Dr Eberhard W Lisse]

It sounds a little as if the R.app is somehow damaged. 

What do the commands

ls -ls $(which R)
ls -las $(which Rscript)

issued from a terminal show? 

Mine show (abbreviated)

[...] /usr/local/bin/R -> ../Cellar/r/4.0.0_1/bin/R
[...] /usr/local/bin/Rscript -> ../Cellar/r/4.0.0_1/bin/Rscript

I use homebrew and the plain (command line) R, ie not the App 
(installed as cask), with RStudio (installed as cask).

I have the following first line in most of my R scripts

#!/usr/bin/env Rscript

and they all run currently. 

I will wait for 4.0.1 to pitch up on homebrew and see that that does.

The editor scripts have nothing to do with this, they just reference 
the command line R (above). There are equally comfortable ones for 
TextMate2 and AlphaX, and others.

greetings, el

On 08/06/2020 14:13, Carl Witthoft wrote:
> In the meantime, there is a decent alternative.  I found some scripts
> for BBEdit which let you execute code or "source" code directly from
> BBEdit.  See http://bearak.org/code/text/index.html
> 
> On 6/7/20 11:39 PM, John Helly wrote:
>> Fails for me 100%.  If you want to zoom to look at it, I can arrange.
>> Hard to explain how to replicate since it happens right away as soon
>> as I try to do anything.  Running Catalina on a brand-new Mac Pro.
>>
>> J.
>>

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

[Eberhard W Lisse]

Spencer,

you are welcome.

As before, it is really helpful to have a “known state”.

As I may have written before, being disciplined about this (having a 
“handbook”), may be boring, but makes especially uncommon tasks easy.

I have recently gone so far as to replacing all manually uploaded Apps with 
homebrew casks (where available) so now my regular

tlmgr update —self —all
brew upgrade
brew cask upgrade

catches them too :-)-O

el

—
Sent from Dr Lisse’s iPad Mini 5
On 17 May 2020, 19:31 +0200, Spencer Graves , 
wrote:
>       I did more tidying.  "ls -l /usr/local/bin/" contained 854
> objects before I did "rm" on 451 that were alias for objects in
> "/usr/local/texlive/2016".  After I did that, "ls -l /usr/local/bin/"
> contained 403 = 854-451 objects.
>
>
>       Thanks again to Ken Beath, Peter Dalgaard, Eberhard W Lisse,
> Berend Hasselman, marc Schwartz, Adrian Dușa, and everyone else who took
> the time to consider the question.  This had been a problem for me since
> at least early February.  It's good to have it fixed.
>
>
>       Spencer Graves
>
>
> […]

[[alternative HTML version deleted]]

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

[Dr Eberhard W Lisse]

Spencer,

MacTeX 2020 "works" differently from MacTeX 2016.  I had 2016 myself but
don't remember what the difference was and when it changed.

The MacTeX 2020 installation creates

/etc/paths.d/TeX

which contains '/Library/TeX/texbin' which via a convoluted mechanism
survives upgrades to 2021/2022/etc, but is loaded at the end of the
PATH.

If '/Library/TeX/texbin' is in the path before '/usr/local/bin', then
the old/non-functioning symlinks in /usr/local/bin are not reached.

That is why it is helpful to remove /etc/paths.d/TeX and adding
'/Library/TeX/texbin' to the beginning of

/etc/paths

to ensure (after logout/login) that /Library/TeX/texbin comes first.

echo $PATH

will also be informative.


But, even in modern systems with large disk space you might want to
remove old crud collected over the years, which doesn't function any
more, because something might hardwire /usr/local/bin and you have again
a difficult to track down issue.  Never mind that just because a certain
R CMD works now it does not mean it'll survive upgrades.

I like a "known state".

Diligence is boring, I know, but I have started to force myself to
writing everything I (need to) do into a "handbook" and to follow it
religiously (I have 4 machines and support 3, so I even wrote a bash
script to run the MacTeX upgrade).

As an aside, the handbook has grown to 580 pages (25 LyX "child"
documents, one common include.tex, a number of "listing" files and
images, all tied into a Makefile :-)-O so it regenerates if anything
changes and even puts it into the cloud :-)-O

And, you are actually supposed to do something like

rm -fv $(ls -l /usr/local/bin | grep 'texlive' | awk '{print $9}')

which (note the removed year) will remove all links left by previous
MacTeX installations, not just the ones from 2016 :-)-O

By the way, Time Machine is your friend when removing older MacTeX
versions, wich I recently found out myself :-)-O.

el

On 2020-05-15 06:04 , Spencer Graves wrote:
> Hi, Peter et al.:
>
>
>   I'm still overwhelmed.
>
>
>   To limit changes to things I think I understand, my
> '/usr/local/texlive' directory contains subdirectories 2014, 2015, 2016,
> 2020, and texmf-local.  From your comments, I gather that the following
> would be wise:
>
>
> sudo rm -r /usr/local/texlive/2014
>
>
> sudo rm -r /usr/local/texlive/2015
>
>
> sudo rm -r /usr/local/texlive/2016
>
>
>   I did this, and "R CMD check Ecfun_0.2-4.tar.gz" still ran to
> completion without errors.
>
>
>   I don't understand "ls -l /usr/local/bin | grep 'texlive/2016' |
> awk '{print $9}'", but I did "ls -l /usr/local/bin | grep 'texlive/20' >
> texlive_20.txt" and examined texlive_20.txt in R. I found it contained
> 451 lines like the following:
>
>
> lrwxr-xr-x  1 sbgraves  admin48 Jan 13 17:42 a2ping ->
> /usr/local/texlive/2016/bin/x86_64-darwin/a2ping
>
>
>   All had "2016".  I'm inferring from your comments that if anything
> I do calls any of those 451 operations like "a2ping", I will get "not
> found".  If I get that, I gather I'm supposed to "sudo rm
> /usr/local/bin/a2ping" and hope that solves the problem.
>
>
>
>   ???
>   Thanks very much.
>   Spencer Graves
[...]
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e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
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Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?

[Dr Eberhard W Lisse]

Spencer,

If you just google

https://www.google.com/search?q=uninstallpkg

the first link coming up is the right one.  But see below.


Do you have a ~/Downloads directory?  Did you look in there?


So the removing of /usr/local/bin/pdflatex did not remove the old 2019
version.  Which is why I proposed uninstallPKG to get rid of all the old
crud.

To be honest, I reckon you should run TimeMachine and then re-install
Catalina after reformatting your hard disk, restore your home directory
and then carefully (step by step) install the Xcode Command Lime Tools,
homebrew, MacTeX and R, which will give you a known state.

I like to have a consistent, known state, with only one (the latest if
possible) version of everything and if possible via the Software Update
or a package manager (homebrew).


homebrew has what is called Casks, which installs proper MacApps (often
from the original developers’ site).  I check regularly whether there
are (new) casks for apps I have manually installed which I then install
(overwrite) so a

brew upgrade
brew cask upgrade

will sort me out

btw, I just looked and

brew cask install uninstallpkg

will do the deed nicely.

el

On 2020-05-13 23:31 , Spencer Graves wrote:
>   Thank you all for your comments on this.  I'm overwhelmed, not
> just with the volume of the discussion, but my own ignorance of the
> standard command line protocols.
>
>
>   After trying some but on all of Eberhard Lisse's and Peter
> Dalgaard's suggestions below, the problem disappeard after I executed
> "sudo rm /usr/local/bin/pdflatex".  I tested "R CMD check
> Ecfun_0.2-4.tar.gz" right before I did that, and the problem was still
> there.  It disappeared right after I did that.
>
>
>   Lisse's "UninstallPKG" might have been more graceful, but I
> couldn't find the key to that padlock, so I used something that seems
> more like boltcutters instead -- and it worked.
>
>
>   Thanks again,
>   Spencer Graves
>
>
> On 2020-05-13 09:57, Dr Eberhard W Lisse wrote:
>> Peter,
>>
>> as far as I understand this the idea is to make the binaries of whatever
>> MacTeX you use available in
>>
>> /Library/TeX/texbin
>
>
>   Finder says this was installed yesterday, presumably when I
> installed MacTex.
>>
>> so that it survives the (annual) upgrade of MacTeX or a switch from the
>> Basic to the Big MacTeX or whatever.
>>
>>
>> I would personally not remove the pdflatex, but find something like
>> UninstallPKG
>
>
>   How do I find something like "UninstallPKG"?
>
>
>> and then locate MacTeX in there and remove that (all
>> versions, so all old crud goes away.
>>
>> If you, like me, use MacTeXBasic you can do something like
>
>
>   I don't think I'm using MacTexBasic, but I'm not a big LaTeX user,
> beyond trying to make RMarkdown work these days (and having used LaTeX
> when writing "Functional Data Analysis with R and Matlab with Ramsay and
> Hooker over a decade ago).
>
>>
>> if [ ! -x /usr/local/bin/gawk ]
>
>
>   I don't seem to have gawk installed, at least not there, and
> "gawk" at a Terminal prompt returned, "-bash: gawk: command not found".
>
>> then
>> brew install gawk
>
>
>   I did that, and it seemed to work.  It started "Updating
> Homebrew..." and ended 'For compilers to find readline you may need to
> set:  export LDFLAGS="-L/usr/local/opt/readline/lib";  export
> CPPFLAGS="-I/usr/local/opt/readline/include"'.
>
>> fi
>> tlmgr list --only-installed \
>>| gawk '{gsub(/:/, ""); print $2}' \
>>> ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt
>
>
>   I tried that.  It executed quickly with no output.
>>
>> before uninstalling the old packages,
>
>
>   I don't know what to uninstall nor how to do it nor how to even
> find what I should uninstall, other than ask here (or maybe at
> tex.stackexchange, as Dirk Eddelbuettel had suggested).
>
>
>> then you install the latest and
>> greatest MacTeXBasic
>
>
>   I installed MacTex yesterday, as I indicated earlier in this
> thread.  That may not be enough, but I will skip that for the moment.
>
>
>> and run something like
>>
>> tlmgr update --self
>
>
>   I did this in /Library/TeX/texbin as follows:
>
>
> texbin sbgraves$ tlmgr update --self
>
> tlmgr: Local TeX Live (2019) is older than remote repository (2020).
> Cross release updates are only supported with
>   update-tlmgr-latest(.sh/.exe) --update
>

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

[Dr Eberhard W Lisse]

Peter,

as far as I understand this the idea is to make the binaries of whatever
MacTeX you use available in 

/Library/TeX/texbin

so that it survives the (annual) upgrade of MacTeX or a switch from the 
Basic to the Big MacTeX or whatever.


I would personally not remove the pdflatex, but find something like
UninstallPKG and then locate MacTeX in there and remove that (all
versions, so all old crud goes away.

If you, like me, use MacTeXBasic you can do something like

if [ ! -x /usr/local/bin/gawk ]
then 
brew install gawk
fi
tlmgr list --only-installed \
   | gawk '{gsub(/:/, ""); print $2}' \
   > ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt 

before uninstalling the old packages, then you install the latest and
greatest MacTeXBasic and run something like

tlmgr update --self
tlmgr install $(cat ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt)

and, perhaps

perl -i -p \
-e 's+\$SELFAUTOPARENT/+/usr/local/texlive/+' \
/usr/local/texlive/2020basic/texmf.cnf
texhash

:-)-O

Nowadays, you can just

sudo rm -rf /usr/local/texlive/2019basic

and if you use homebrew you might have /usr/local owned by yourself so
you don't need the sudo.

Time Machine is your friend (as I just noticed) :-)-O

el


On 13/05/2020 15:34, peter dalgaard wrote:
> Hmm, like Eberhard, I'm not too sure this is right.
> 
> A look at ls -l /usr/local/bin should be informative though.
> 
> I haven't been paying that close attention, but I think the history is
> that TeX programs used to live in /usr/local/bin, but then Apple did
> something(?)  so now they go to Library/TeX/texbin (and are really
> links that via several levels of indirection end up somewhere in
> /usr/local/texlive).  However, old installs may still have binaries or
> links in /usr/local/bin.  I would guess that a simple
> 
> sudo rm /usr/local/bin/pdflatex
> 
> could work (possibly remove some other *tex programs as well).
> 
> -pd
[...]


-- 
Dr. Eberhard W. Lisse   \ /   Obstetrician & Gynaecologist 
e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
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Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?

[Dr Eberhard W Lisse]

Ah, yes,

brew install coreutils

:-)-O

Existing accounts using bash remain under bash when upgrading to 
Catalina. And bash remains available so all bash script will continue 
to run :-)-O

el

On 13/05/2020 15:44, Marc Schwartz wrote:
> Hi,
> 
> I will stand to be corrected, but from what I can tell, 'realpath' is
> not part of a default macOS installation, and would need to be
> installed from a third party repo (e.g. homebrew).
> 
> There appear to be shell script incantations that would accomplish the
> same functionality, but in the end, in the absence of these
> approaches, there is not an easy way, under a standard macOS install,
> to trace through the layers of symlinks to the target file.
> 
> You can also do this manually via the Finder, by right clicking on the
> symlink and using Show Original to navigate as well.
> 
> Also, note that under Catalina, the default shell changed from bash to
> zsh.
> 
> Regards,
> 
> Marc

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

[Dr Eberhard W Lisse]

realpath $(which pdflatex)
pdflatex --version


On 13/05/2020 13:00, Spencer Graves wrote:
> Hi, Peter et al.:
> 
> 
>   It looks like you've properly diagnosed my problem.  How do I fix it?
> 
> 
>   "which pdflatex" and "echo $PATH" are as follows:
> 
> 
> $ which pdflatex
> /usr/local/bin/pdflatex
> 
> 
> $ echo $PATH
> /Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/sbgraves/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/opt/local/bin:/opt/local/sbin:/Users/sbgraves/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin
> 
> 
>       I do find "/Library/TeX/texbin/pdflatex" on my hard drive, but "which 
> pdflatex" doesn't find it.
> 
> 
>       Thanks,
>       Spencer Graves
> [...]

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Re: [R-SIG-Mac] 4.0.0

[Dr Eberhard W Lisse]

For all it is worth,

homebrew upgraded R to 4.0.0 on Catalina and I did notice that homebrew
asked for an XCode Command Line Tools upgrade

I then sourced as usual my package.R which installs the ones I use, and
it did install a number of packages from source (which I assusme is
becasue they haven't yet loaded as binary packages).

No drama whatsoever. In particular a complicated :yX report with knitR 
produces the expected result :-)-O

el

On 29/04/2020 16:05, Eric K wrote:
> Running R 3.6 has been working fine. I just upgraded to R 4.0 and I cannot
> build packages from source. I have tried the following:
> 
> 1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation went
> fine, but when I try to build packages from source I get errors like this:
[...]

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Re: [R-SIG-Mac] Graphic problem Rcmdr

[Dr Eberhard W Lisse]

Use Rstudio.

el

On 29/04/2020 08:18, jean benoit TANIS wrote:
> Hi,
> 
> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I
> used to work on R2.6 on Windows).
> 
> When I load the Rcmdr package, this is what I obtain - see picture
> (the drop down menu does not display).
> 
> I manage to have access to the drop-down menu only once despite 20 or
> so attempts of closing and reopening R.
> 
> I have tried to:
> - turn-off nap-app => same issue 
> - uninstall R and rebook and start again => same issue 
> - uninstall XQuartz and reboot and start again => same issue 
> 
> For more information about my system, please find the pictures below 
> 
> PastedGraphic-1.tiff
> PastedGraphic-2.tiff
> 
> Did you encounter this problem before ?  Is there any way you could
> help me solving it ?
> 
> 
> Thank you very much for your help,
> 
> Best wishes,
> 
> 
> JB 
> 
> 
> 
> ___
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> 

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Re: [R-SIG-Mac] MacTeX 2020 and TeX Live Utility (No Longer Included)

[Dr Eberhard W Lisse]

Rainer

Put

function tlcockpit
{
   case "$(java -version 2>&1 | head -1)" in
 *"1.8"*) jar="tlcockpit-jdk8.jar" ;;
 *) jar="tlcockpit.jar" ;;
   esac
   exec java -jar $(kpsewhich --progname="tlcockpit" --format=texmfscripts 
"$jar") 2>&1 >/dev/null &
}


into ~/.aliases or whatever is sourced on login :-)-O. 

You can also use something like Platypus to make a clickable App out of
the shell script which resides in

realpath $(which tlcockpit)

and even use TeX Live Utility's icns file :-)-O

el

On 28/04/2020 10:52, Rainer M Krug wrote:
> You know why I hate java? Here it comes:
> 
> 
[...]
> java.lang.RuntimeException: java.lang.RuntimeException: Error
>   initializing QuantumRenderer: no suitable pipeline found
[...]
> 
> Cheers,
> 
> Rainer

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Re: [R-SIG-Mac] Using XQuartz - any known issues?

[Eberhard W Lisse]

Take Rstudio.

el

—
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On 20 Apr 2020, 21:42 +0200, ANDERSON Niall , wrote:
> Dear all,
>
> I’m relatively new to MacOS and have only recently started trying to use 
> XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for 
> getting good performance out of it (or should it usually run well with 
> default settings)?
>
> On first installation, I found there was a very long lag in menus being 
> populated (i.e. the menu shape was generated, but no usable options were 
> added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s 
> fault, I don’t think). One of my students suggested reducing Output Colors 
> option from the default “Millions” setting. That seems to deal with the 
> problem, thankfully.
>
> Is that typical of XQuartz, and is there anything else I should be doing to 
> get the best performance from it?
>
> Thanks,
>
> Niall Anderson
>
>
> 
>
> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme 
> Co-director, MPH (on campus)
> Room G113B, Doorway 1
> Usher Institute, University of Edinburgh
> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>
> niall.ander...@ed.ac.uk  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>
> Responses to emails are only expected during your working hours
> 
> www.ed.ac.uk/usher | @EdinUniUsher
>
>
>
> The University of Edinburgh is a charitable body, registered in Scotland, 
> with registration number 
> SC005336.___
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Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 205, Issue 13

[Eberhard W Lisse]

I think I will play with this over the weekend, especially if the calm before 
the storm prevails.

el

—
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On 2 Apr 2020, 22:21 +0200, Duncan Murdoch , wrote:
> That lists "base" as a package, as well as the other base and
> recommended packages. That's not what Dr. Lisse was looking for: he
> wanted "all user installed (additional) packages, ie not the ones that
> come with R?".
>
> Duncan Murdoch
>
> On 02/04/2020 10:47 a.m., Colin A. Smith wrote:
> > This will do it as well:
> >
> > package_list <- tapply(rownames(installed.packages()), 
> > installed.packages()[,"LibPath"], c)
> >
> > Bonus to find out which library directories are writable by the user:
> >
> > file.access(names(package_list), mode=2) == 0
> >
> > Cheers,
> >
> > Colin
> >
> > > On Apr 2, 2020, at 10:36, Michael Hall  wrote:
> > >
> > > > On Apr 2, 2020, at 6:10 AM, r-sig-mac-requ...@r-project.org wrote:
> > > >
> > > > > Is there a way of (only) listing all user installed (additional)
> > > > > packages, ie not the ones that come with R?
> > >
> > > https://www.r-bloggers.com/list-of-user-installed-r-packages-and-their-versions/
> > >  
> > > 
> > >
> > > Sys.getenv()
> > > …
> > > R_LIBS_USER ~/Library/R/3.6/library
> > > …
> > >
> > > list.files('~/Library/R/3.6/library')
> > > [1] "alphavantager" "BBmisc" "brew" "C50"
> > > [5] "checkmate" "clisymbols" "coda" "commonmark”
> > > ...
> >
> > ___
> > 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] Homebrew

[Dr Eberhard W Lisse]

Rainer,

I am definitively interested.

But, as a disclaimer, I am an elderly Gynecologist only dabbling in R
and a little in Perl :-)-O. 

el

On 02/04/2020 12:43, Rainer M Krug wrote:
> 
> 
>> On 2 Apr 2020, at 12:17, Duncan Murdoch 
>> wrote:
>>
>> On 02/04/2020 5:58 a.m., Dr Eberhard W Lisse wrote:
>>> New thread :-)-O
>>> I am wondering if I should not try to figure out how automate this.
>>> Is there a way of (only) listing all user installed (additional)
>>> packages, ie not the ones that come with R?
> 
> I had something similar in mind - here is my repo which collects ides
> (no code yet) https://github.com/rkrug/install
> 
> If you are interested, we could get this going.
> 
> If I understand correctly, this would be very useful in many cases.
> 
>>
>> Look at the "Priority" column in installed.packages().  "base" is
>> part of R, "recommended" is normally distributed with R.
>> "recommended" packages can be updated after R is installed, "base"
>> packages can't.
> 
> That is a good idea.  We should take this forward.
> 
>>
>> If you just copy all the packages to the new library that aren't
>> already there, and run update.packages(checkBuilt = TRUE) R will
>> re-install everything that was originally installed under an earlier
>> version.
> 
> 
> Cheers,
> 
> Rainer
[...]

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Re: [R-SIG-Mac] Homebrew

[Dr Eberhard W Lisse]

Argument for homebrew:

brew upgrade

which will figure out what needs to be upgraded so I don't have 
manually keep track of it.


BTW, it usually pulls the binary, and these have worked without any 
issues for many years, the last time something went wrong on the 
Download and it pulled the source. I don't care either way.

Packages must be installed from source, but not as source. R will look 
for the package on CRAN like any other and usually takes the binary, 
sometimes asking whether it should take a (newer) source )of the 
package)

The first run of (re-)installing additional packages does indeed take 
some time, but it doesn't happen often.

The point is that there is a channel for issues with homebrew packages 
but few people (especially when desperate) will take the time :-)-O

greetings, el

 02/04/2020 13:09, Rainer M Krug wrote:
> 
> 
>> On 2 Apr 2020, at 12:56, Hervé Pagès  wrote:
>>
>> Just for a minute let's ignore the fact that installing R via
>> Homebrew is not considered a good option by the competent authorities
>> (which sounds like a good enough reason to stay away from it).  I'm
>> still wondering: what's the benefit vs installing the official CRAN
>> binary?  Just curious.
> 
> Arguments against homebrew:
> 
> Not an official response, but in the past, homebrew was compiling
> everything on the local machine.  This is not the case anymore, and
> the default installation in homebrew, installs a binary.
> 
> All packages need to be installed from source.  This takes time, but I
> had no problems with any of the packages I use.
> 
> Just some tidbits from previous discussions.
> 
> But I would like to also hear the official reason (no resources would
> be a good enough justification as well).
> 
> Arguments for homebrew:
> 
> it is more Linux like, in the way that you have more control over the
> tools used.  e.g. when still using the official R installation, I
> regularly used different versions of GDAL in R, GRASS, …, which can
> cause inconsistencies.
> 
> The installation is done without requiring root privileges, which is a
> big advantage (as I see it).
> 
> 
> 
> Cheers,
> 
> Rainer
[...]

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[R-SIG-Mac] Homebrew

[Dr Eberhard W Lisse]

New thread :-)-O

I am wondering if I should not try to figure out how automate this.

Is there a way of (only) listing all user installed (additional) 
packages, ie not the ones that come with R?

I could then construct the below file automagically, and if I was 
really bothered and bored find out how to make Homebrew pre/post 
install scripts to automate this :-)-O

And, for the record, other than that, I can only recall one serious 
issue, when the openblas library got lost recently which was however 
fixed quite quickly. 


greetings, el

On 02/04/2020 10:17, Dr Eberhard W Lisse wrote:
> 
> I do same, including Rstudio (Cask).
> 
> Once in a while after major updates I need to reinstall all my extra
> packages, so I have written me a little script along the lines of
> 
>   #!/usr/local/bin/Rscript
>   local({
>   r <- getOption("repos")
>   r["CRAN"] <- "https://cloud.r-project.org/;
>   options(repos = r)
>   })
>   install.packages(c(
>   "RMariaDB", "rstudioapi"
>   ))
> 
> made it 0755 and can run it from the command line. Put it in my
> handbook so I don't forget and never looked back.
> 
> 
> greetings, el
> 
> On 02/04/2020 10:03 am, Rainer M Krug wrote:
>> I am using Homebrew on a Mac (two Macs - one at home, one at work)
>> instead of the official R package, and I did not have any problems
>> after upgrades - maybe I am lucky, maybe not as picky in defining
>> “problem”, but my suggestion would be to try R from homebrew to
>> install R.
>>
>> OK - no support from here - I know.
>>
>> And homebrew has also binary versions.  What is missing, is a hombrew
>> R package repository.  Maybe an idea to create one?
>>
>>
>> Cheers,
>>
>> Rainer

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e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
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Re: [R-SIG-Mac] Transitioning from Mac to LInux?

[Dr Eberhard W Lisse]

I do same, including Rstudio (Cask).

Once in a while after major updates I need to reinstall all my extra
packages, so I have written me a little script along the lines of

#!/usr/local/bin/Rscript
local({
r <- getOption("repos")
r["CRAN"] <- "https://cloud.r-project.org/;
options(repos = r)
})
install.packages(c(
"RMariaDB", "rstudioapi"
))

made it 0755 and can run it from the command line. Put it in my
handbook so I don't forget and never looked back.


greetings, el

On 02/04/2020 10:03 am, Rainer M Krug wrote:
> I am using Homebrew on a Mac (two Macs - one at home, one at work)
> instead of the official R package, and I did not have any problems
> after upgrades - maybe I am lucky, maybe not as picky in defining
> “problem”, but my suggestion would be to try R from homebrew to
> install R.
>
> OK - no support from here - I know.
>
> And homebrew has also binary versions.  What is missing, is a hombrew
> R package repository.  Maybe an idea to create one?
>
>
> Cheers,
>
> Rainer
>

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Re: [R-SIG-Mac] Transitioning from Mac to LInux?

[Eberhard W Lisse]

Actually, you can easily run Linux in Virtual Box.

But I agree, with Homebrew there is tons of unix tools available from the 
command line, and then some.

el

—
Sent from Dr Lisse’s iPad Mini 5
On 1 Apr 2020, 23:42 +0200, Simon Urbanek , wrote:
> Carl,
>
> I would argue that you won't really gain anything - if you use R the 
> Linux-way (build R from sources), it would be the same on macOS and Linux - 
> and some people do that. So for R I don't think there is a difference. I'm 
> using Linux for everything other than my desktop/laptop and the main reason 
> I'm sticking with macOS at the edge is the availability of software for 
> dealing with the rest of the world (MS Office, Adobe, Apple Mail etc.). If 
> you don't need any of it, then you may be happy with Linux. The biggest issue 
> there tends to be setting up your machine as the hardware support is far less 
> streamlined than on macOS. Some of my friends are running Linux on Mac 
> hardware - but you need the be real expert for that.
>
> Cheers,
> Simon
>
>
> > On 2/04/2020, at 7:48 AM, Carl Witthoft  wrote:
> >
> >
> > If I should ask over at r-sig-debian instead of here, please tell me. I 
> > don't wish to clog r-sig-mac with off-topic stuff.
> >
> >
> > I've been watching the massive headaches people are dealing with trying to 
> > keep R fully compatible with each MacOS X upgrade, I'm wondering whether 
> > replacing my iMac (2009) with a new Mac really makes sense from an R - user 
> > point of view, as opposed to getting some inexpensive desktop and 
> > installing Linux. I know I can run R and RStudio under Linux, for example, 
> > but don't know what limitations, if any there are when it comes to building 
> > packages from source, getting compatible compilers, and so on.
> >
> > What have some of you 'power R users' discovered when/if you tried to build 
> > , or incorporate Bioconductor or other repository's packages under Linux?
> >
> >
> > --
> > Carl Witthoft
> > c...@witthoft.com
> > resume: https://app.box.com/file/498153801347
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
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Re: [R-SIG-Mac] PACKAGES file missing

[Dr Eberhard W Lisse]

You didn't give any advice. I did :-)-O And it does what the OP asked 
for :-)-O

I do some things in the command line R or even running stuff as Rscript,
but for development (and updates) an IDE such as RStudio is very helpful
even if it is not die reine Lehre :-)-O

el

On 12/02/2020 12:53, Uwe Ligges wrote:
> 
> 
> On 12.02.2020 10:51, Dr Eberhard W Lisse wrote:
[...]
> For myself, I would not use RStudio as it does what you describe: Lots
> of things I do not want to be done.  So I typically never give advise
> which editor or environment to use, as that is a matter of taste.
> 
> Best,
> Uwe Ligges
[...]


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e...@lisse.na / *  | Telephone: +264 81 124 6733 (cell)
PO Box 8421  \  /
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Re: [R-SIG-Mac] PACKAGES file missing

[Dr Eberhard W Lisse]

Joel,

This should be a temporary issue, I can reach the failed URL.

local({
+   r <- getOption("repos")
+   r["CRAN"] <- "https://cloud.r-project.org/;
+   options(repos = r)
+ })

> install.packages("tidyverse")
[...]
trying URL 
'https://cloud.r-project.org/src/contrib/tidyverse_1.3.0.tar.gz'
Content type 'application/x-gzip' length 712837 bytes (696 KB)
[...]

Did an upgrade (of packages) from within RStudio from same and that also
worked out well.

So, in the first instance, try again :-)-O

CRAN has many mirrors, but I strongly advise for using RStudio which
figures this out for themselves in addition to many other advantages
(such as sponsoring the mirroring service in the first place), so you
could try the closest mirror from https://cran.r-project.org/mirrors.html.

greetings, el

On 07/02/2020 18:54, Joel Jacobson wrote:
> Hi,
> 
> I'm a R newbie having some problems.
> 
> The special PACKAGES file seems to be missing for version 3.6:
> https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES
> 
> This is causing install.packages() to fail, which forces installation
> from source:
> 
[...]
> 
> Have I made som mistake or is this a real problem?
> 
> Many thanks for any help.
> 
> Best regards,
> 
> Joel Jacobson
[...]


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Re: [R-SIG-Mac] Using R on MacOS Catalina.....

[Dr Eberhard W Lisse]

For me it usually had to resort to the latter when there were
connectivity issues (more common in Namibia than in Potsdam :-)-O).

And maybe once or twice when I wanted to try something special.

It also has a 'cask' option with which it installs apps so I do

brew install r
brew cask install rstudio


All in all rock solid.

el

On 28/01/2020 11:43, Byron Ellis wrote:
> Homebrew is Linux-style packaging for OS X. Think of it as an
> equivalent to apt-get—either it will retrieve a binary or it will
> attempt to build one.
>

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Re: [R-SIG-Mac] Using R on MacOS Catalina.....

[Dr Eberhard W Lisse]

Matthias,

this is exactly why you should use Homebrew.

Tante Gugel is your friend :-)-O

el

On 28/01/2020 11:33, Matthias Krawutschke wrote:
[...]
> Hm, I never used "Homebrew" - I come from the UNIX - World and I like
> the command-line .
> Well, I can create the files for R via "make" - after them it breaks
> the installation ☹
[...]


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Re: [R-SIG-Mac] Using R on MacOS Catalina.....

[Dr Eberhard W Lisse]

Matthias,

A Mac with Catalina and a small hard disk?

I use the Homebrew package manager and while there is a short delay
between R and Homebrew this works out very well.  It has two options,
one with out the app, which is what I use because I for GUI I use
RStudio exclusively.

There is really no need to compile from source :-)-O XCode is huge, 
though the XCode command line tools are required.

Gruss aus dem Süden :-)-O

el

On 28/01/2020 11:05, Matthias Krawutschke wrote:
> Hello everybody,
> 
>  
> 
> I am new at this Mailinglist and I have a question about R on MacOS
> Catalina.
> 
> On your Website I had found a package for R. If I want to install it
> on my MacBook – the program told me, that I can´t install the software
> on an other volume like “system”…..  That is bad, because I had a
> small Volume on my MacBook ☹
> 
>  
> 
> If I want to compile the R-System new with GNU-C Compiler 9.2.0 – I
> can “make” the files, but “make install” return it with an ERROR.
> 
> So, did you have any ideas what kind of problems that here I had?
> 
>  
> 
> I thank you very much for your assistance and have a nice day…..
> 
>  
> 
> Herzlichst grüßt Sie das HPC - Team
> 
>  
> 
>  
> 
>  
> 
> Matthias Krawutschke
[...]
-- 
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Re: [R-SIG-Mac] update.packages() cannot install from source

[Eberhard W Lisse]

The

xcode-select —install

is required after upgrading to Catalina.

I have several machines so I usually only need to figure out once what Apple 
has done this time :-)-O.

Once I know that, the other machines usually go without a hitch. And after a 
while one settles in and doesn’t even notice Apple being Nanny any longer. But 
I still write it into my handbook so next version I can remember :-)-O

I usually do homebrew first and when that works the other stuff usually 
compiles as well.

Or you can run

make

if that works, xcode-cli is installed properly.


el

—
Sent from Dr Lisse’s iPhone Xs
On 29 Oct 2019, 23:13 +0200, Balamuta, James Joseph , 
wrote:
> Greetings and Salutations,
>
> Note that Xcode Command Line Tools is not the same as Xcode IDE. In fact, 
> only Xcode CLI Tools are required, which are light-weight compared to the IDE.
>
> Regarding your error, this is symptomatic of an Xcode update tied to an OS 
> point-release. Note in the session information 10.15.1 (the .1 being the bump)
>
> R version 3.6.1 (2019-07-05)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Catalina 10.15.1
>
> Both of the commands highlighted are accurate. Though, the order should be 
> changed to:
>
> sudo xcode-select --reset
> sudo xcode-select --install
>
> The reset changes back to using the default command line tools path. This was 
> needed for Mojave.
>
> Sincerely,
>
> JJB
>
> On 10/29/19, 4:01 PM, "R-SIG-Mac on behalf of Spencer Graves" 
>  
> wrote:
>
> Hello, All:
>
>
> "update.packages()" fails for me on packages DescTools, digest,
> jpeg, mgcv, openxlsx, rlang, and spam. It first says:
>
>
> There are binary versions available but the
> source versions are later:
> binary source needs_compilation
> DescTools 0.99.29 0.99.30 TRUE
> digest 0.6.21 0.6.22 TRUE
> jpeg 0.1-8 0.1-8.1 TRUE
> mgcv 1.8-29 1.8-30 TRUE
> openxlsx 4.1.0.1 4.1.2 TRUE
> rlang 0.4.0 0.4.1 TRUE
> spam 2.3-0 2.3-0.2 TRUE
>
>
> It then asks, "Do you want to install from sources the packages
> which need compilation? (Yes/no/cancel)". I reply "y" or "Yes". For
> each package, it says it was
>
> ... successfully unpacked and MD5 sums checked
> ** using staged installation
> ** libs
> xcrun: error: invalid active developer path
> (/Library/Developer/CommandLineTools), missing xcrun at:
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> ERROR: compilation failed for package ‘DescTools’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’
> * restoring previous
> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’
>
>
> A web search for "xcrun: error: invalid active developer path"
> identified a couple of discussions on StackExchange that say that I need
> to have Xcode installed correctly. I think I have everything up to
> date: macOS 10.15.1 Catalina with Xcode downloaded and installed via
> the App store. RStudio 1.2.5001 with:
>
>
> sessionInfo()
> R version 3.6.1 (2019-07-05)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Catalina 10.15.1
>
> Matrix products: default
> BLAS:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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
> [6] methods base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.6.1 tools_3.6.1
>
>
> "https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a;
> recommends, "xcode-select --install", which to me seems like it should
> be equivalent to the install I just did via the App Store. This
> StackExchange discussion also said, "If the above alone doesn't do it,
> then also run: xcode-select --reset". However, before I do that, I
> thought I'd ask here if anyone else is having a problem like this. And
> if yes, and if they've fixed it, what did they do to fix it?
>
>
> Thanks,
> Spencer Graves
>
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Re: [R-SIG-Mac] R-patched installers cannot be run on Catalina

[Dr Eberhard W Lisse]

You could always issue

sudo spctl --master-disable

:-)-O

el

On 2019-10-11 19:59 , Kevin Ushey wrote:
> Hi,
> 
> I'm seeing the following when I attempt to install R-patched, as from
> http://mac.r-project.org/:
> 
> ---
> 
> “R-3.6-branch-el-capitan-signed.pkg” can’t be opened because Apple
> cannot check it for malicious software.
> 
> This software needs to be updated. Contact the developer for more information.
> 
> ---
> 
> I suspect this is pain being imposed by the requirement for notarized
> applications / installers. The dialog can be overridden through the
> Security & Privacy preferences pane, but Apple does not make this
> obvious.
> 
> The official R 3.6.1 installer is not affected; likely because it was
> grandfathered in due to its being published before Catalina was rolled
> out.
> 
> Are there plans to notarize these builds of R? (can we be helpful in
> making that happen?)
> 
> Best,
> Kevin
> 
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Re: [R-SIG-Mac] [External] Re: Xcode 10.2.1

[Dr Eberhard W Lisse]

Indeed. Thanks.

el

Sent from Dr Lisse's iPad mini 4
On 29 Apr 2019, 01:48 +0200, Bert Gunter , wrote:
> ?installed.packages
>
> (Sometimes trying the obvious works)
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and 
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> > On Sun, Apr 28, 2019 at 4:11 PM  wrote:
> > > Is there a command to list installed packages?
> > >
> > > I currently keep track manually and just run a script.
> > >
> > > el
> > >
> > > —
> > > Sent from Dr Lisse’s iPhone Xs
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > > ___
> > > 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 3.5.3 macOS binary not signed?

[Dr Eberhard W Lisse]

Marc,

the same is achieved by the hash published by CRAN.

Though, of course, if the developers have a developer account, there is
nothing wrong with using it and even less with reporting the lack of use
of it :-)-O


el

On 2019-03-14 21:49 , Marc Schwartz via R-SIG-Mac wrote:
> Hi,
> 
> I am aware of the workaround, both from the CLI and via System
> Preferences.
> 
> The question is more about confirming that the binary is valid and
> from a source that is trusted, which is the point of digitally signing
> binaries as a trusted Apple developer.
> 
> Thanks,
> 
> Marc
[...]
-- 
Dr. Eberhard W. Lisse  / Obstetrician & Gynaecologist (Saar)
e...@lisse.na/ * |   Telephone: +264 81 124 6733 (cell)
PO Box 8421  /
Bachbrecht, Namibia ;/

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Re: [R-SIG-Mac] R 3.5.3 macOS binary not signed?

[Dr Eberhard W Lisse]

Not Really.

I have been loading R binaries for almost 10 years from CRAN, if not
longer.  If the SHA is ok, I don't care about Apple's Nanny mechanism.

And, it still warns on the first run, whether you really want to run a
program downloaded from the Internet.

The correct statement wouldhave been, something like: "Be careful when
you do that and only load binaries from reputable sources such as CRAN"

I really, really, really do not understand, after almost 40 years of
doing this (sendmail anyone?), why Apple wants to make an automated
start of Postfix requiring the SIP to be disabled off of the Recovery
Boot for a simple change of the launch control files.

el

On 2019-03-14 22:37 , Simon Urbanek wrote:
> Very, very, very bad idea - never ever do that unless you're really
> happy to infest your machine with nice viruses and ransomware.
>
> Cheers,
> Simon
>
>
>> On Mar 14, 2019, at 8:43 AM, Dr Eberhard W Lisse  wrote:
>>
>> Try from the commandline
>>
>> sudo spctl --master-disable
>>
>> and then install the package
>>
>> el

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Re: [R-SIG-Mac] R 3.5.3 macOS binary not signed?

[Dr Eberhard W Lisse]

Try from the commandline

sudo spctl --master-disable

and then install the package

el

Sent from Dr Lisse's iPad mini 4
On 14 Mar 2019, 21:18 +0900, Marc Schwartz via R-SIG-Mac 
, wrote:
> Hi,
>
> I just tried to install the R 3.5.3 macOS binary from CRAN.
>
> The SHA hash matches what is on CRAN, but I get an unknown developer message 
> when I try to install.
>
> I get:
>
> pkgutil --check-signature R-3.5.3.pkg
> Package "R-3.5.3.pkg":
> Status: no signature
>
>
> I rechecked the 3.5.2 binary and do not have the issue there.
>
> Thanks,
>
> Marc Schwartz
>
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Re: [R-SIG-Mac] Disable readline echo in R for mac GUI

[Dr Eberhard W Lisse]

On my Mojave iMac

commandArgs()

returns

on RStudio

[1] "RStudio"   "--interactive"

on Mac GUI

[1] "R" "--no-save" "--no-restore-data" "--gui=aqua"

and on R command line

[1] "/Library/Frameworks/R.framework/Resources/bin/exec/R"

so maybe test for that?

el

On 15/11/2018 15:06, Jeroen Ooms wrote:
> When prompting the user for a password, we need to temporarily disable
> echo. In a tty we can call posix stty -echo (example below). The
> RStudio GUI has a native password entry function that can be triggered
> via getOption('askpass'). Is there simple method to prompt for a
> password in the R for Mac GUI (without depending on shiny or tcltk)?
> 
> readline_password <- function(prompt = "Please enter password\n"){
>   if(isatty(stdin())){
> if(system('stty -echo') == 0){
>   on.exit(system('stty echo'))
> }
>   }
>   base::readline(prompt)
> }

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