Re: [R-SIG-Mac] Permission issues running R in terminal

[peter dalgaard]

To be precise: execute access, not write access. 

However, neither that nor deleting the dir gives the exact "Operation not 
permitted" error.

-pd

> On 19 Feb 2024, at 10:43 , Jeroen Ooms  wrote:
> 
> On Sun, Feb 18, 2024 at 11:57 PM Duncan Murdoch 
> wrote:
> 
>> I wanted to see the options to R CMD INSTALL, and was surprised to see
>> this output:
>> 
>> $ R CMD INSTALL --help
>> shell-init: error retrieving current directory: getcwd: cannot access
>> parent directories: Operation not permitted
>> shell-init: error retrieving current directory: getcwd: cannot access
>> parent directories: Operation not permitted
>> shell-init: error retrieving current directory: getcwd: cannot access
>> parent directories: Operation not permitted
>> shell-init: error retrieving current directory: getcwd: cannot access
>> parent directories: Operation not permitted
>> shell-init: error retrieving current directory: getcwd: cannot access
>> parent directories: Operation not permitted
>> shell-init: error retrieving current directory: getcwd: cannot access
>> parent directories: Operation not permitted
>> Error in tools:::.install_packages() :
>>   current working directory cannot be ascertained
>> shell-init: error retrieving current directory: getcwd: cannot access
>> parent directories: Operation not permitted
>> 
>> I installed R from CRAN, and am not running the current version:  I'm
>> still on 4.3.1, with OS also kind of old:  Monterey 12.7.3, so I was
>> surprised by this.  Is anyone else seeing it?
>> 
> 
> This happens when you don't have write access in the current dir:
> 
> mkdir /tmp/test
> cd /tmp/test
> chmod 0 .
> R CMD INSTALL --help
> 
>   [[alternative HTML version deleted]]
> 
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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
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Re: [R-SIG-Mac] Permission issues running R in terminal

[peter dalgaard]

I have the same setup, and not seeing this. That is, _unless_ I try from a 
shell running in a deleted diretory:

Peters-iMac:BUILD-dist pd$  R CMD INSTALL --help
shell-init: error retrieving current directory: getcwd: cannot access parent 
directories: No such file or directory
...

(because BUILD-dist is wiped and re-created by the automatic builds, but the 
shell still refers to the unlinked directory.)

-pd

> On 18 Feb 2024, at 23:57 , Duncan Murdoch  wrote:
> 
> I wanted to see the options to R CMD INSTALL, and was surprised to see this 
> output:
> 
> $ R CMD INSTALL --help
> shell-init: error retrieving current directory: getcwd: cannot access parent 
> directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access parent 
> directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access parent 
> directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access parent 
> directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access parent 
> directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access parent 
> directories: Operation not permitted
> Error in tools:::.install_packages() :
>  current working directory cannot be ascertained
> shell-init: error retrieving current directory: getcwd: cannot access parent 
> directories: Operation not permitted
> 
> I installed R from CRAN, and am not running the current version:  I'm still 
> on 4.3.1, with OS also kind of old:  Monterey 12.7.3, so I was surprised by 
> this.  Is anyone else seeing it?
> 
> Duncan Murdoch
> 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
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Re: [R-SIG-Mac] Rcmdr

[peter dalgaard]

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

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

- pd

> On 22 Jul 2023, at 14:20 , Sabrina Droussy  wrote:
> 
> 
>> 
>> Hello,
>> I have a big problem with R. I hope you can help me please.
>> I didn’t use R for some months and wanted to use it again to prepare an 
>> exam. I can’t open Rcmdr anymore. I tried several things : install packages, 
>> delete and reinstall R. It isn’t working.
>> 
>> Here is the message I get :
>> error reading package index file / Library/ Frameworks / R. Framework/ 
>> Versions/ 4.2/ Resources/ 
>> library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: can’t find package tile
>> error reading package index file / Library/ Frameworks / R. Framework/ 
>> Versions/ 4.2/ Resources/ 
>> library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested 
>> evaluations (infinite loop ? )  
>> 
>> Best regards 
>> 
>> Envoyé de mon iPhone
> 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] gfortran: command not found

[Peter Dalgaard]

I think the cleanest way is to diddle the /etc/paths.d structure. I have

PeterDaardsiMac:R pd$ ls /etc/paths.d
40-XQuartz  R   TeX clang8  gfortran
PeterDaardsiMac:R pd$ cat /etc/paths.d/gfortran 
/usr/local/gfortran/bin
PeterDaardsiMac:R pd$ cat /etc/paths
/usr/local/bin
/usr/bin
/bin
/usr/sbin
/sbin

and the latter would want to be /opt/gfortran/bin for 12.2 (I still have 8.2 
for now).

Two things to note:

1. The directories in paths.d/* are added to those in /etc/paths in 
alphabetical order, so careful with older versions in /usr/local/bin.

2. You (probably) need to logout and back in for the changes to take effect in 
your Terminal windows.

Alternatively, you can twiddle the shell startup files (~/.profile /etc/profile 
/etc/bashrc ) directly. The trouble I have with that, is that I never feel 
sure that I am doing it in the right place.

- Peter D.

> On 6 Jul 2023, at 19:58 , Spencer Graves  wrote:
> 
> 1.  I need to apologize to Simon:  I failed to see his reply to the original 
> post.  Then I found the instructions and installed 
> gfortran-12.2-universal.pkg, as indicated there, but it still didn't work.
> 
> 
> 2.  I'm not finding clear instructions on how to update the path on macOS 
> 11.7.8, which is the latest version available for my 2014 MacBook Pro with a 
> 2.8 GHz Quad-Core Intel Core i7.  I found several pages with differing 
> instructions.  I found one in "support.apple.com" that recommended something 
> that didn't work.[2]
> 
> 
> Further suggestions?
>   
> 
> Thanks again very much.
> Spencer Graves
> 
> 
> [2] "support.apple.com" recommended 
> "PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/ export PATH", then 
> "env".  I did "env" to get the current path, than appended 
> ":/opt/gfortran/bin" to that and executed the revised 
> "PATH=...:/opt/gfortran/bin export PATH".  However, when I checked with "env" 
> again, the change was not displayed.  I rebooted with the same result.
> 
> 
> https://support.apple.com/guide/terminal/use-environment-variables-apd382cc5fa-4f58-4449-b20a-41c53c006f8f/mac
> 
> 
> On 7/6/23 11:01 AM, Simon Urbanek wrote:
>> AFACT he didn't say so, there was no response, just double-posting of the 
>> same question after is was answered.
>> The installer says:
>> The resulting compiler will live in /opt/gfortran and can be called with
>> /opt/gfortran/bin/gfortran
>> so it's advisable to have /opt/gfortran/bin on the PATH.
>> (Side note: the arm64 build of R uses the full path, but some people have 
>> been objecting to that since they wanted to use other compilers for the 
>> legacy Intel builds, but as I suspected that causes other issues, so I'll 
>> change that for the next release).
>> Cheers,
>> Simon
>>> On Jul 6, 2023, at 11:45 PM, Peter Dalgaard >> <mailto:pda...@gmail.com>> wrote:
>>> 
>>> AFAICT, Spencer followed the implied instructions and it still didn't work.
>>> 
>>> There may also be a PATH issue when upgrading to 4.3.x, /usr/local -> 
>>> /opt/R/ Does gfortran 12.2 install to /opt/R/.../bin ?
>>> 
>>> -pd
>>> 
>>>> On 6 Jul 2023, at 07:42 , Simon Urbanek >>> <mailto:simon.urba...@r-project.org>> wrote:
>>>> 
>>>> Already answered to you and on R-pkg-devel [9 mins after you posted there 
>>>> - now more than 5h ago...]:
>>>> 
>>>> To quote from the page you downloaded R from:
>>>> 
>>>> This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish to 
>>>> compile R packages which contain Fortran code, you may need to download 
>>>> the corresponding GNU Fortran compiler from 
>>>> https://mac.R-project.org/tools <https://mac.R-project.org/tools> 
>>>> <https://mac.r-project.org/tools <https://mac.r-project.org/tools>>.
>>>> 
>>>> 
>>>> 
>>>>> On Jul 6, 2023, at 5:16 PM, Spencer Graves >>>> <mailto:spencer.gra...@prodsyse.com>> wrote:
>>>>> 
>>>>> Hello, All:
>>>>> 
>>>>> 
>>>>>  "R CMD check KFAS" under macOS 11.7.8 (the latest version that will run 
>>>>> on my aging Mac) complains "gfortran: command not found".
>>>>> 
>>>>> 
>>>>>  I just upgraded to R 4.3.1 and installed "gfortran-12.2-universal.pkg" 
>>>>> per 
>>>>> "https://cran.r-project.org/bin/macosx

Re: [R-SIG-Mac] gfortran: command not found

[Peter Dalgaard]

AFAICT, Spencer followed the implied instructions and it still didn't work. 

There may also be a PATH issue when upgrading to 4.3.x, /usr/local -> 
/opt/R/ Does gfortran 12.2 install to /opt/R/.../bin ?

-pd  

> On 6 Jul 2023, at 07:42 , Simon Urbanek  wrote:
> 
> Already answered to you and on R-pkg-devel [9 mins after you posted there - 
> now more than 5h ago...]:
> 
> To quote from the page you downloaded R from:
> 
> This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish to 
> compile R packages which contain Fortran code, you may need to download the 
> corresponding GNU Fortran compiler from https://mac.R-project.org/tools 
> <https://mac.r-project.org/tools>. 
> 
> 
> 
>> On Jul 6, 2023, at 5:16 PM, Spencer Graves  
>> wrote:
>> 
>> Hello, All:
>> 
>> 
>>"R CMD check KFAS" under macOS 11.7.8 (the latest version that will 
>> run on my aging Mac) complains "gfortran: command not found".
>> 
>> 
>>I just upgraded to R 4.3.1 and installed 
>> "gfortran-12.2-universal.pkg" per 
>> "https://cran.r-project.org/bin/macosx/tools/;.  I expected this to solve 
>> the problem.  It didn't.
>> 
>> 
>>Suggestions?
>>Thanks,
>>Spencer Graves
>> 
>> 
>> p.s.  This is my fork of KFAS, available at 
>> "https://github.com/sbgraves237/KFAS;.  "sessionInfo()" appears below.
>> 
>> 
>> ##
>> 
>> 
>> sessionInfo()
>> R version 4.3.1 (2023-06-16)
>> Platform: x86_64-apple-darwin20 (64-bit)
>> Running under: macOS Big Sur 11.7.8
>> 
>> Matrix products: default
>> BLAS: 
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
>>  
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
>>   LAPACK version 3.11.0
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> time zone: America/Chicago
>> tzcode source: internal
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_4.3.1  R6_2.5.1magrittr_2.0.3  cli_3.6.1
>> [5] tools_4.3.1 glue_1.6.2  rstudioapi_0.14 roxygen2_7.2.3
>> [9] xml2_1.3.4  vctrs_0.6.2 stringi_1.7.12  knitr_1.42
>> [13] xfun_0.39   stringr_1.5.0   lifecycle_1.0.3 rlang_1.1.1
>> [17] purrr_1.0.1
>>> 
>> 
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> 
> 
>   [[alternative HTML version deleted]]
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] Serious problem with R on macOS

[peter dalgaard]

Yes, this is consistent with the fact that R starts for you. Some other files 
seem to have gone missing though, notably the datasets and compiler package, so 
that R does not get very far before givinng up the ghost.

The pattern of recently created files disappearing is worrying, but not likely 
due to anything that R itself is doing. It is quite possible that you have a 
disk error, either physical or logical (inconsistent file system state), or it 
could be the OS error that Sarah was alluding to. You might want to try the 
First Aid option in the Disc Utility app (possibly enlist a local expert).

- Peter

> On 8 Jun 2023, at 18:37 , DePaolis, Fernando  wrote:
> 
> This is what I get after the current failure, where neither R.app nor the 
> call from the command line work.
>  
> fernandodepaolis@MacBook-Pro-2 ~ % ls -l `which R`
> lrwxr-xr-x  1 root  admin  47 Jun  5 10:23 /usr/local/bin/R -> 
> /Library/Frameworks/R.framework/Resources/bin/R
>  
> fernandodepaolis@MacBook-Pro-2 ~ % ls -l 
> /Library/Frameworks/R.framework/Resources/bin/R
> -rwxrwxr-x  1 root  admin  9196 Apr 21 14:47 
> /Library/Frameworks/R.framework/Resources/bin/R
>  
>  
> which is identical to what I got when it was working fine a couple of days 
> ago.
>  
> Thank you
>  
>  
>  
> Fernando DePaolis, Ph.D.
> Dean of Academic Operations & Integration
> Associate Professor
> Middlebury Institute of International Studies at Monterey
> --
> [Sent from Outlook for Mac –MacBook Pro]
> My working hours (US Pacific time zone) may not be your working hours. Please 
> do not feel obligated to respond outside your normal work hours, unless 
> otherwise indicated.
>  
> From: DePaolis, Fernando 
> Date: Tuesday, June 6, 2023 at 10:20 AM
> To: peter dalgaard 
> Cc: Calboli Federico (LUKE) , 
> r-sig-mac@r-project.org 
> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
> 
> Thank you!! I will do that.
>  
> PS: No, no additional or different scrubbers/antivirus/etc have been added.
>  
>  
>  
> Fernando DePaolis, Ph.D.
> Dean of Academic Operations & Integration
> Associate Professor
> Middlebury Institute of International Studies at Monterey
> --
> [Sent from Outlook for Mac –MacBook Pro]
> My working hours (US Pacific time zone) may not be your working hours. Please 
> do not feel obligated to respond outside your normal work hours, unless 
> otherwise indicated.
>  
> From: peter dalgaard 
> Date: Tuesday, June 6, 2023 at 9:50 AM
> To: DePaolis, Fernando 
> Cc: Calboli Federico (LUKE) , 
> r-sig-mac@r-project.org 
> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
> 
> [You don't often get email from pda...@gmail.com. Learn why this is important 
> at https://aka.ms/LearnAboutSenderIdentification ]
> 
> Hum...
> 
> Best I can think of is to take the hint (from Simon Urbanek) and move the 
> .pkg file from Downloads and into another folder before installing. Some 
> system cleaner-upper or virus checker could be moving stuff around. You 
> haven't perchance some virus scrubber running which might be restoring your 
> executable directories to a previous state?
> 
> You might want to make a note of the location and ownership of installed 
> files, like in
> 
> Peters-Air:R pd$ ls -l `which R`
> lrwxr-xr-x  1 root  wheel  47 Jun  6 17:41 /usr/local/bin/R -> 
> /Library/Frameworks/R.framework/Resources/bin/R
> Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R
> -rwxrwxr-x  1 root  admin  9196 Apr 21 23:47 
> /Library/Frameworks/R.framework/Resources/bin/R
> 
> and then, if/when it stops working, see if files have disappeared or changed 
> owner or permissions.
> 
> -pd
> 
> 
> > On 6 Jun 2023, at 18:05 , DePaolis, Fernando  
> > wrote:
> >
> > OS: Ventura 13.4 (22F66)
> > Downloaded R-4.3.0-x86_64.pkg from CRAN
> > Installation: Successful…everything works fine
> > Suggestion to move the installer to Trash: Declined (because I know I will 
> > need the installer again).
> > CRAN suggests reinstalling Xquartz, which I did a few times on the onset of 
> > the symptoms (I don’t do that anymore because there sems to be no point to 
> > it).
> > Use: I only use RStudio and everything works fine, until at a random time a 
> > few days later (or hours in a few instances), RStudio fails to ‘find R’, 
> > which doesn’t run on its own or from the console.
> > Possible emerging conflicts: At the beginning, I thought this could be 
> > happening because other software were install afterward, but that is

Re: [R-SIG-Mac] Serious problem with R on macOS

[peter dalgaard]

Hum...

Best I can think of is to take the hint (from Simon Urbanek) and move the .pkg 
file from Downloads and into another folder before installing. Some system 
cleaner-upper or virus checker could be moving stuff around. You haven't 
perchance some virus scrubber running which might be restoring your executable 
directories to a previous state?

You might want to make a note of the location and ownership of installed files, 
like in

Peters-Air:R pd$ ls -l `which R`
lrwxr-xr-x  1 root  wheel  47 Jun  6 17:41 /usr/local/bin/R -> 
/Library/Frameworks/R.framework/Resources/bin/R
Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R
-rwxrwxr-x  1 root  admin  9196 Apr 21 23:47 
/Library/Frameworks/R.framework/Resources/bin/R

and then, if/when it stops working, see if files have disappeared or changed 
owner or permissions.

-pd
 

> On 6 Jun 2023, at 18:05 , DePaolis, Fernando  wrote:
> 
> OS: Ventura 13.4 (22F66)
> Downloaded R-4.3.0-x86_64.pkg from CRAN
> Installation: Successful…everything works fine
> Suggestion to move the installer to Trash: Declined (because I know I will 
> need the installer again).
> CRAN suggests reinstalling Xquartz, which I did a few times on the onset of 
> the symptoms (I don’t do that anymore because there sems to be no point to 
> it).
> Use: I only use RStudio and everything works fine, until at a random time a 
> few days later (or hours in a few instances), RStudio fails to ‘find R’, 
> which doesn’t run on its own or from the console.
> Possible emerging conflicts: At the beginning, I thought this could be 
> happening because other software were install afterward, but that is not the 
> case.
> Looked for alternatives: I couldn’t find any reference online, so I suspect 
> this is quite specific to my machine and/or environment. About the 
> ‘environment’, I cannot think of anything, as no changes have been made, 
> except for routine updates (which is unlikely, but not impossible to have 
> undesirable effects).
>  
>  
> Thank you
>  
>  
>  
> Fernando DePaolis, Ph.D.
> Dean of Academic Operations & Integration
> Associate Professor
> Middlebury Institute of International Studies at Monterey
> --
> [Sent from Outlook for Mac –MacBook Pro]
> My working hours (US Pacific time zone) may not be your working hours. Please 
> do not feel obligated to respond outside your normal work hours, unless 
> otherwise indicated.
>  
> From: peter dalgaard 
> Date: Tuesday, June 6, 2023 at 8:48 AM
> To: DePaolis, Fernando 
> Cc: Calboli Federico (LUKE) , 
> r-sig-mac@r-project.org 
> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
> 
> [You don't often get email from pda...@gmail.com. Learn why this is important 
> at https://aka.ms/LearnAboutSenderIdentification ]
> 
> OK, so
> 
> - OS version?
> - What do you do to install?
> - What happens when you do it?
> 
> e.g.:
> 
> - Monterey 12.6.5
> - Downloaded R-4.3.0-x86_64.pkg from CRAN
> - As user with admin privilege, open from Downloads folder and follow 
> instructions
> - "The installation was succesful"
> - Close, move to bin.
> 
> I gather that on newer OS, you may need to move the installer out of 
> Downloads first.
> 
> 
> -pd
> 
> 
> > On 6 Jun 2023, at 17:07 , DePaolis, Fernando  
> > wrote:
> >
> > Thank you all…it is not an RStudio issue. I cannot run R from its app or 
> > the command line…It is certainly an R issue.
> > Next time it ‘uninstalls itself’ I will try to install it on another user 
> > and see what happens (although I have already tried to install it ‘just for 
> > me’ or for all users).
> >
> > Thank you again,
> >
> >
> > Fernando DePaolis, Ph.D.
> > Dean of Academic Operations & Integration
> > Associate Professor
> > Middlebury Institute of International Studies at Monterey
> > --
> > [Sent from Outlook for Mac –MacBook Pro]
> > My working hours (US Pacific time zone) may not be your working hours. 
> > Please do not feel obligated to respond outside your normal work hours, 
> > unless otherwise indicated.
> >
> > From: Calboli Federico (LUKE) 
> > Date: Tuesday, June 6, 2023 at 12:54 AM
> > To: DePaolis, Fernando , r-sig-mac@r-project.org 
> > 
> > Subject: Re: Serious problem with R on macOS
> >
> > You don't often get email from federico.calb...@luke.fi. Learn why this is 
> > important
> > If you can use R.app or R on the terminal, it is a R studio bug.  Have you 
> > tested?  Also, ‘reinstall’ works best after removing 

Re: [R-SIG-Mac] Serious problem with R on macOS

[peter dalgaard]

OK, so

- OS version?
- What do you do to install?
- What happens when you do it?

e.g.:

- Monterey 12.6.5
- Downloaded R-4.3.0-x86_64.pkg from CRAN
- As user with admin privilege, open from Downloads folder and follow 
instructions
- "The installation was succesful"
- Close, move to bin.

I gather that on newer OS, you may need to move the installer out of Downloads 
first.
 

-pd


> On 6 Jun 2023, at 17:07 , DePaolis, Fernando  wrote:
> 
> Thank you all…it is not an RStudio issue. I cannot run R from its app or the 
> command line…It is certainly an R issue.
> Next time it ‘uninstalls itself’ I will try to install it on another user and 
> see what happens (although I have already tried to install it ‘just for me’ 
> or for all users).
>  
> Thank you again,
>  
>  
> Fernando DePaolis, Ph.D.
> Dean of Academic Operations & Integration
> Associate Professor
> Middlebury Institute of International Studies at Monterey
> --
> [Sent from Outlook for Mac –MacBook Pro]
> My working hours (US Pacific time zone) may not be your working hours. Please 
> do not feel obligated to respond outside your normal work hours, unless 
> otherwise indicated.
>  
> From: Calboli Federico (LUKE) 
> Date: Tuesday, June 6, 2023 at 12:54 AM
> To: DePaolis, Fernando , r-sig-mac@r-project.org 
> 
> Subject: Re: Serious problem with R on macOS
> 
> You don't often get email from federico.calb...@luke.fi. Learn why this is 
> important
> If you can use R.app or R on the terminal, it is a R studio bug.  Have you 
> tested?  Also, ‘reinstall’ works best after removing all actual files, such 
> as the whole ~/.R, all the ~/.R* files, and whatever R studio might add.
>  
> BW
>  
> F
>  
> Federico Calboli
> Tutkija
> Genomiikka ja jalostus 
> Luonnonvarakeskus
>  
> Uwe Ligges (from CRAN sys admin) recommended that I post this to the list.
>  
> Thank you.
>  
>  
>  
> Fernando DePaolis, Ph.D.
> Dean of Academic Operations & Integration
> Associate Professor
> Middlebury Institute of International Studies at Monterey
> --
> [Sent from Outlook for Mac –MacBook Pro]
> My working hours (US Pacific time zone) may not be your working hours. Please 
> do not feel obligated to respond outside your normal work hours, unless 
> otherwise indicated.
>  
> From: DePaolis, Fernando 
> Date: Monday, June 5, 2023 at 10:19 AM
> To: cran-sysad...@r-project.org 
> Subject: Serious problem with R on macOS
> 
> Hello,
> For a few months now, I’ve been having an odd and rather annoying problem. I 
> use RStudio and it frequently cannot start R, producing the error message 
> attached below. This is clearly not the, as I worked on it the night before 
> or even just a few hours earlier. What is clear is that R is not available on 
> my system, although all the files are still there (in 
> /Library/Frameworks/R.framework). It could be that a critical file becomes 
> corrupted, or the system can’t find it. I have not been able to determine 
> whether that is the case, or which file could be affected. I might have 
> re-installed R dozens of times in the last month. This is something that 
> never happened in the previous more than 15 years of using R.
>  
> I’ve tried everything I can think of, and the problem persists…and haven’t 
> found any satisfactory feedback online either.
> Have you ever heard of a problem like this? Or do you have any suggestions?
>  
> Thank you so much for your support.
>  
>  
> 
>  
>  
>  
> Fernando DePaolis, Ph.D.
> Dean of Academic Operations & Integration
> Associate Professor
> Middlebury Institute of International Studies at Monterey
> --
> [Sent from Outlook for Mac –MacBook Pro]
> My working hours (US Pacific time zone) may not be your working hours. Please 
> do not feel obligated to respond outside your normal work hours, unless 
> otherwise indicated.
> ___
> 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 does not build out of the box on Ventura

[peter dalgaard]

Thanks for the heads-up, Brian.

Older binaries still install and run on Ventura, I hope?

I intend to hold off updating at least the office machine (which builds the 
tarballs) until 4.3.0, for platform stability. The push for Ventura doesn't 
seem to have arrived here yet, but probably will come in a few days.

By the way, I have been getting update requests for "Command Line Tools beta n 
for Xcode 14.1", even though I have no recollection of signing up for beta 
versions. I'm rather reluctant to install those. 

- Peter

> On 25 Oct 2022, at 11:13 , Prof Brian Ripley  wrote:
> 
> The problem being that devQuartz.c uses a deprecated and now removed 
> interface (ATS).
> 
> Building with --without-aqua will work.
> 
> I am sure that Simon will fix this, but not in time for 4.2.2 which is in 
> code freeze.
> 
> Note this only affects building: as the CRAN binary distributions are built 
> on much older versions of macOS they should continue to build. This is purely 
> a heads up for those building from source that they may want to delay 
> upgrading to Ventura (but someone needed to to find the issue).
> 
> For the first time for quite a while, upgrading to Ventura removes the 
> Command Line Tools which need reinstalling.
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
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Re: [R-SIG-Mac] mac.r-project.org R-devel tar.gz builds

[peter dalgaard]

Not sure what is going on here. The source tarballs at CRAN are happy enough. 

The ARM builds also fail, but that looks like a disk full condition.

-pd

> On 23 Aug 2022, at 13:41 , Brodie Gaslam via R-SIG-Mac 
>  wrote:
> 
> Just to report that the R-devel x86 tar.gz seems stuck at the 7/14 version.  
> I don't have an immediate need for the newer versions, so no rush on my 
> account.
> 
> Best,
> 
> B.
> 
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Re: [R-SIG-Mac] Problems in install some packages in R 4.2

[peter dalgaard]

We might want to circulate this in R Core, but offhand, I'd say that since the 
package ecosystem is somewhat platform dependent, it could be in the platform 
maintainers' domain to set defaults like

 options(pkgType="binary")

in the default installation's start-up files. This would make sense on Mac & 
Windows, but probably not on Linux variants. Users can always override it if 
needed.

(There's also an issue with pure R packages, which can be source-installed if 
the source is newer, but the byte-compile may still take a while and not be 
worth it for an incremental update.)

- Peter

> On 11 May 2022, at 07:56 , Simon Urbanek  wrote:
> 
> Peter,
> 
> I agree that the current behavior is not very helpful for the majority of 
> users. Personally, I'd change the default "no" so that users that don't know 
> or care what it entails can still get the package installed. Note that having 
> a compiler may not be enough, since there are often library dependencies, so 
> compiling from sources should really be attempted only by developers that do 
> it deliberately. The only argument I see for using the "both" default is for 
> cases where the package binary doesn't exist, but that is another story as 
> the user has no choice there.
> 
> Cheers,
> Simon
> 
> PS: version mismatches are in principle expected due to package sources being 
> released before binaries, but should be generally rare. However, there is 
> currently an unusual back-log of package builds for R 4.2.0 on the 
> high-sierra x86_64 system which should hopefully clear by tomorrow.
> 
> 
>> On 10/05/2022, at 9:18 PM, peter dalgaard  wrote:
>> 
>> Marginally related:
>> 
>> The "binary" bit trips up my students from time to time (with tseries 
>> recently). 
>> 
>> They get the option to install from source because it's marginally newer, 
>> answer "yes" because that'w what they always do, and then installation bombs 
>> because they don't have the compilers.  
>> 
>> Yes, they should know better, but no... 
>> 
>> We might want to consider implementing something like 
>> capabilities("compilers") so that we can condition the source installs more 
>> carefully.
>> 
>> 
>> -pd
>> 
>> 
>> 
>>> On 10 May 2022, at 04:47 , Simon Urbanek  
>>> wrote:
>>> 
>>> José,
>>> 
>>> can you be more specific as of what you did and exact output? I would 
>>> recommend using a simple
>>> 
>>> install.packages("ggplot2",type="binary")
>>> 
>>> in R.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>>> On 10/05/2022, at 12:30 PM, José Carlos Guerrero Antúnez 
>>>>  wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> When I upgraded to R version 4.2 (Platform: x86_64-apple-darwin17.0
>>>> (64-bit)), I was having problems installing certain packages (e.g. ggplot2,
>>>> Hmisc, devtools) and their dependencies.
>>>> 
>>>> I got this error message "installation of package ‘package’ had non-zero
>>>> exit status.
>>>> 
>>>> I have tried several ways to install (e.g. Package Archive file (.tgz).
>>>> 
>>>> Any ideas on how to solve this problem, thank you very much.
>>>> 
>>>> 
>>>> -- 
>>>> José Carlos Guerrero
>>>> 
>>>>[[alternative HTML version deleted]]
>>>> 
>>>> ___
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>>>> 
>>> 
>>> ___
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>> 
>> -- 
>> 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
>> 
> 

-- 
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

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

[peter dalgaard]

The button works fine (I did test it before sending), but you do need to login, 
since nobody (except possibly the list administrator) should be able to 
unsubscribe other people. 

You can ask for a password reminder, so you can unsubscribe if you have access 
to the subscribed email address.   

-pd



> On 23 Nov 2021, at 11:55 , Tony Perry  wrote:
> 
> It would also help if the "Unsubscribe" button actually worked.  Again, best 
> practice is to simply have an unsubscribe button (w/o making people scour 
> inboxes for random passwords).
> 
> Kindly remove me from this list.
> 
> Thanks
> 
> On Tue, 23 Nov 2021, 10:28 Ken Beath,  wrote:
> 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]]
>>>> 
>>>> ___
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>>> 
>>> --
>>> 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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>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

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

[peter dalgaard]

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]]
> 
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Re: [R-SIG-Mac] SHA checksum mismatch for arm64 gfortran?

[peter dalgaard]

I see this too. There were some signing issues with the R downloads recently; 
perhaps it also affected this and the SHA sum wasn't updated. You probably want 
a more authoritative answer from Simon, though.

-pd

> On 20 Nov 2021, at 22:24 , Austin Hurst  wrote:
> 
> Hi all,
> 
> Today I started trying to update the R macOS Tools installer 
> (https://github.com/rmacoslib/r-macos-rtools) to support Big Sur, Monterey, 
> and Apple Silicon. In the process, I was double-checking the SHA256 hashes of 
> the gfortran downloads on the R Mac Tools page 
> (https://mac.r-project.org/tools/) and noticed that the hash for the ARM64 
> download listed on the website 
> (86d169f9d62b2b2ddbf5fde55935fbb96729da5c47d7bf09240228cd23b664e5) doesn’t 
> match with the hash of the downloaded file 
> (e7a5272fcbe002e9e22effc18bba01c352ca95f63dc3264865d9f8020ac55821).
> 
> I checked the hash of the Intel installer and that matches fine so I’m pretty 
> sure I’m checking the hash right, and I double-checked that I was checking 
> the untouched .tar.gz and not the decompressed .tar. Is the hash on the 
> website mistaken, or is something else going on? Either way, I figured I 
> should let someone know.
> 
> Cheers,
> 
> - Austin Hurst
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Re: [R-SIG-Mac] sessionInfo on Monterey

[peter dalgaard]

Odd indeed. A local build of mine has

> sessionInfo()
R version 4.1.0 Patched (2021-05-25 r80389)
Platform: x86_64-apple-darwin20.5.0 (64-bit)
Running under: macOS Big Sur 11.5.2

(Obvsly not up-to-the minute, and my build tools are likely not either on this 
machine...)

- pd

> On 28 Aug 2021, at 08:00 , Bob Rudis  wrote:
> 
> arm64:
> 
> R version 4.1.1 Patched (2021-08-13 r80752)
> Platform: aarch64-apple-darwin20 (64-bit)
> Running under: macOS Monterey 12.0
> 
> 
> x86_64:
> 
> R version 4.1.1 Patched (2021-08-10 r80733)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Big Sur 10.16
> 
> On Fri, Aug 27, 2021 at 3:42 AM Prof Brian Ripley  
> wrote:
>> 
>> One oddity is that the CRAN Intel binary build of R (or any other built
>> under 10.x) when run on Big Sur reports
>> 
>>> sessionInfo()
>> R version 4.1.1 (2021-08-10)
>> Platform: x86_64-apple-darwin17.0 (64-bit)
>> Running under: macOS Big Sur 10.16
>> ...
>> 
>> because the system call used reports '10.16'.
>> 
>> If anyone running a beta of Monterey has the CRAN binary installed, for
>> completeness I would appreciate seeing what is reported.
>> 
>> --
>> Brian D. Ripley,  rip...@stats.ox.ac.uk
>> Emeritus Professor of Applied Statistics, University of Oxford
>> 
>> ___
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Re: [R-SIG-Mac] Corrupt R installation

[peter dalgaard]

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"
>>   ), dependencies = TRUE)
>> 
>> 
>> or similar and run it if the additional libraries disappear.
>> 
>> You can fill this with something like
>> 
>>   grep -h library *R \
>>   |awk -F 'library' '{print $2}' \
>>   |sed 's/(//g;s/)//g' \
>>   |sort -u \
>>   |awk '{print "\"" $1 "\","}'
>>   |sed '$ s/,$//'
>> 
>> or in a few lines of the language of your choice generate the whole
>> script. And of course refine to your liking with something like
>> 
>>   find ~/R -name '*.R' -exec grep -h library {} ';' \
>>   ...
>> 
>> greetings, el
>> 
>> -- 
>> To email me replace 'nospam' with 'el'
>> 
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Re: [R-SIG-Mac] R-4.0.5.pkg Bug Report

[peter dalgaard]

Eek, yes, that needs fixing. And of course only newcomers get hit because 
others will have the symlinks in place already.

I believe that instead of the grep '^1[5-9]' business you need something like

IFS=. read major minor pl << EOF
`uname -r`
EOF

and then a numeric check on $major.

-pd

> On 9 May 2021, at 01:15 , Yuri Broze  wrote:
> 
> Hi folks,
> 
> Apologies if this bug has already been noticed, but I wanted to share just
> in case it hasn't yet, and this was the best place I found.
> 
> The current CRAN-hosted MacOS installation package fails to correctly
> create symbolic links to /usr/local/bin for machines with `uname -r`
> release version of 20 or above. The faulty logic is in
> R/R-fw.pkg/Scripts/postflight; lines 6-13:
> 
> if uname -r | grep '^1[5-9]' >/dev/null; then
>## 15.0 and higher don't allow messing with /usr/bin
>## so use /usr/local/bin instead
>if [ ! -e /usr/local/bin ]; then
>mkdir -p /usr/local/bin
>fi
>cd /usr/local/bin
> fi
> 
> This seems to have resulted in some commotion on Stack Exchange and other
> places around an inability to access `R` or `Rscript` from the commandline,
> along with the usual hacky workarounds.
> 
> Hope this is helpful to bring to your attention!
> 
> Best,
> Yuri
> 
> Yuri Broze
> 314.910.3152
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] R-gui slow since last update

[peter dalgaard]

t adressés. Si vous avez reçu ce message par erreur, merci de le 
> retourner à son émetteur. Les idées et opinions présentées dans ce message 
> sont celles de son auteur, et ne représentent pas nécessairement celles de 
> l’institution ou les entités affiliées dont dépend l’auteur. La publication, 
> l'usage, la distribution, l'impression ou la copie non autorisée de ce 
> message et des attachements qu'il contient sont strictement interdits ». 
> “This email and any files transmitted with it are confidential and intended 
> solely for the use of the individual or entity to whom they are addressed. If 
> you have received this email in error please return it to the sender. The 
> ideas and views expressed in this email are solely those of its author, and 
> do not necessarily represent the views of the institution or company the 
> author is dependent from. Unauthorized publication, use, distribution, 
> printing or copying of this e-mail or any attached files is strictly 
> forbidden.
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] I'm new to R in a Mac. How do I specify the path in read.table()?

[Peter Dalgaard]

Just use forward slashes, backslashes is a Windows thing. I.e.

read.table("/Users/DFP/Desktop/Monroe319Ecoli.txt")

should do it. A generic trick is

x <- file.choose()
dd <- read.table(x)

(and then possible have a look at x)

-pd

> On 29 Jan 2021, at 21:25 , Parkhurst, David F.  wrote:
> 
> I�ve tried for over an hour to figure this out with no luck.  I�ve moved the 
> text file (created from excel) to the desktop to simplify the path.  If I 
> click on the file and ask Get Info, it lists �Where� as  iCloud Drive > 
> Desktop.  If I copy that to the clipboard and paste that into a read.table 
> command in the R interface, it comes up as /Users/DFP/Desktop.  But if I try 
> read.table("\\Users\\DFP\\Desktop\\Monroe319Ecoli.txt"), I get No such file 
> or directory.  How can I get that file into a data frame?
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Problem with dot chart examples in my Mac

[Peter Dalgaard]

R is a collaborative project, not a commercial one. You may need to look around 
or ask questions if you need something special. For the present case, someone 
was complaining about a problem, for which the solution was in the very same 
mailing list thread that he had himself contributed to. 

We have mechanisms in place for releasing updates in both source and binary 
formats. The general procedure is outlined on CRAN. For source releases, there 
is a daily snapshots link on the front page of CRAN. 

For Mac and Windows binaries, you need to go via the relevant links and for 
Windows, select links under "Other builds". 

For Mac, the link is on the Mac page, where you need to find the line saying 
"Information, tools and most recent daily builds of the R GUI, R-patched and 
R-devel can be found at http://mac.R-project.org/;. 

What we do not do is to rush out full releases for any minor problem. We run 
carefully orchestrated patch releases approximately 4 times per year, with 
alpha/beta/RC cycles every time, so as to minimize the risk of destabilizing 
the code.

- Peter D.

> On 8 Feb 2021, at 14:02 , Thomas Hopper  wrote:
> 
> Peter,
> 
> Your comment might be tongue-in-cheek, but taking it at face value, I’d like 
> to point out that if there’s a fix and users don’t know about it, that’s a 
> developer communication problem; not a user problem. Most developers deal 
> with this problem by releasing updated versions of their software, which has 
> not happened (current CRAN version is 1.73, which is what I’m using); I know 
> of no developers who have been able to solve this communication problem by 
> publishing notes about beta versions of their software to email lists that 
> have low signal to noise ratios.
> 
> Seems like there’s a better way to get updates out if the developers want to 
> avoid users repeatedly pointing out the same bugs.
> 
> Thank you,
> 
> Tom
> 
>> On Feb 8, 2021, at 5:05 AM, Peter Dalgaard  wrote:
>> 
>> If you are not aware of the fix, then you are not reading your email...
>> 
>> The NSButton message was reported to be gone in RGui v.7903, on r-help by 
>> mal...@malonequantitative.com on Jan. 18. 
>> 
>> Current patch versions (https://mac.r-project.org) are at v.7922. Next 
>> formal patch release (4.0.4) is on Feb 15, prerelease downloadable from said 
>> page.
>> 
>> - Peter Dalgaard
>> 
>> 
>> 
>>> On 8 Feb 2021, at 05:47 , Gregory Coats via R-SIG-Mac 
>>>  wrote:
>>> 
>>> Tom Hopper,
>>> On Jan 8, 2021, I first reported that R on Mac gave the error message you 
>>> reported today.
>>> We R Mac users are all getting this error. It is now a month later. I am 
>>> not aware of any fix.
>>> Greg Coats
>>> 
>>> 2021-01-07 22:58:42.997 R[8311:37566]
>>> 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.
>>> 
>>>> On Feb 7, 2021, at 2:51 PM, Tom Hopper  wrote:
>>> 
>>> 
>>> I'm also seeing the following error:
>>> 2021-02-07 14:41:15.950 R[4408:267051] 
>>> 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.
>>> 
>>> ___
>>> 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
>> 
> 
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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
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Office: A 4.23
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Re: [R-SIG-Mac] Problem with dot chart examples in my Mac

[Peter Dalgaard]

If you are not aware of the fix, then you are not reading your email...

The NSButton message was reported to be gone in RGui v.7903, on r-help by 
mal...@malonequantitative.com on Jan. 18. 

Current patch versions (https://mac.r-project.org) are at v.7922. Next formal 
patch release (4.0.4) is on Feb 15, prerelease downloadable from said page.

- Peter Dalgaard



> On 8 Feb 2021, at 05:47 , Gregory Coats via R-SIG-Mac 
>  wrote:
> 
> Tom Hopper,
> On Jan 8, 2021, I first reported that R on Mac gave the error message you 
> reported today.
> We R Mac users are all getting this error. It is now a month later. I am not 
> aware of any fix.
> Greg Coats
> 
> 2021-01-07 22:58:42.997 R[8311:37566]
> 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.
> 
>> On Feb 7, 2021, at 2:51 PM, Tom Hopper  wrote:
> 
> 
> I'm also seeing the following error:
> 2021-02-07 14:41:15.950 R[4408:267051] 
> 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.
> 
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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
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Re: [R-SIG-Mac] [External] summary() suddently producing weird NULL: values for factors and character attributes

[peter dalgaard]

6.1   
> statnet.common_4.3.0  crayon_1.3.4
> >
> 
> On 12/13/20 18:22, Richard M. Heiberger wrote:
>> please send to the list the output from both:
>> 
>> dput(head(P2))
>> 
>> utils::sessionInfo()
>> 
>> This is the Macintosh list.  Is this specifically a Macintosh problem?
>> 
>> 
>> 
>> On Sun, Dec 13, 2020 at 6:32 PM John Helly via R-SIG-Mac <
>> r-sig-mac@r-project.org> wrote:
>> 
>>> Aloha.
>>> 
>>> For the past few weeks, maybe 6 or more, I've been getting strange results
>>> from the summary() function for data.frames.  Has anyone else noticed
>>> something like this?  I don't think I've done anything to cause this but
>>> cannot find anything to attribute it to.  Example below.  It lists every
>>> row as a value in the data frame attribute DAUCO.  Similar behavior found
>>> with other read.table results using syntax below.
>>> 
>>> 
>>> PRISM=
>>> read.table(PRISM_INPUT,header=TRUE,stringsAsFactors=TRUE,sep=',',
>>> 
>>> colClasses=c('character','numeric','numeric','numeric','numeric','numeric'))
>>> 
>>> P2 is a subset of PRISM.
>>> 
>>> 
>>> 
>>> J.
>>> 
>>> --
>>> 
>>> John Helly, University of California, San Diego / San Diego Supercomputer 
>>> Center / Scripps Institution of Oceanography / 760 840 8660 mobile / 
>>> http://www.sdsc.edu/~hellyj
>>> ORCID ID: orcid.org/-0002-3779-0603
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!X3ALsWlGCDlXPERM1oTbCaxoruiXl51SE7N2G7ATqb9smiMNQuhwKEoi71_fCU8$
>>> 
> 
> -- 
> John Helly, University of California, San Diego / San Diego Supercomputer 
> Center / Scripps Institution of Oceanography / 760 840 8660 mobile / 
> http://www.sdsc.edu/~hellyj
> ORCID ID: orcid.org/-0002-3779-0603
> 
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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
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Re: [R-SIG-Mac] Some introductory questions

[peter dalgaard]

Not work how? You need to tell us what kind of errors you see, otherwise, we 
can only guess.

I'd lose the file() construct. It sets up a connection object, which can be 
less than useful when read.table reads the file several time in order to 
decipher the column structure of the file.

So plain

filepath1 <- "/Users/michaelfeher/Documents/R 
Documents/COVID19/20200906-1822-total-cases-jones.data"

should be OK, provided that the file actually exists. In particular, check that 
the space in "R Documents" really is a space and not something that just looks 
like a space (no-break space is a common culprit).

If you can read the file, but it comes out weird, then you need to diddle the 
arguments to read.table, e.g.

> filepath <- "~/tmp/R files/test.data"
> read.table(filepath)
  V1 V2
1  x  y
2  1  2
3  3  7
4  9 13
> read.table(filepath, header=TRUE)
  x  y
1 1  2
2 3  7
3 9 13


-pd


> On 8 Sep 2020, at 00:04 , Mike Feher  wrote:
> 
> Hi Peter,
> 
> Here is a snippet of the code I was trying to start with:
> 
> filepath1 <- file("/Users/michaelfeher/Documents/R 
> Documents/COVID19/20200906-1822-total-cases-jones.data")
> filepath1
> TotalCasesJones <- read.table(filepath1)
> 
> This definitely did not work for me.
> 
> Mike
> 
> On September 7, 2020 at 3:50:19 AM, peter dalgaard (pda...@gmail.com) wrote:
> 
>> 
>> 
>> > On 7 Sep 2020, at 07:09 , Ken Beath  wrote: 
>> >  
>> >> On 7 Sep 2020, at 9:31 am, Mike Feher  wrote: 
>> >  
>> [snip] 
>> >> 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.  
>> 
>> Also, how do you "read in" the data? Usually, read.table() or somesuch would 
>> be involved, although RStudio has an "Import data" functionality.  
>> 
>> -pd 
>> 
>> --  
>> 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

-- 
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

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Re: [R-SIG-Mac] Some introductory questions

[peter dalgaard]

> On 7 Sep 2020, at 07:09 , Ken Beath  wrote:
> 
>> On 7 Sep 2020, at 9:31 am, Mike Feher  wrote:
> 
[snip]
>> 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. 

Also, how do you "read in" the data? Usually, read.table() or somesuch would be 
involved, although RStudio has an "Import data" functionality. 

-pd

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
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Re: [R-SIG-Mac] Looking for help - demo() hangs R.app on 10.15.6

[peter dalgaard]

Which Rgui version is this? A somewhat similar issue with opening files on some 
platforms was fixed shortly after 4.0.2 in Rgui rev 7849. 

I forget whether this was pushed to the CRAN binary (my install has 7847). At 
any rate, if yours is older, you may want to try Rgui.app from 
https://mac.r-project.org

-pd

> On 5 Sep 2020, at 22:55 , Michael Feher  wrote:
> 
> Hello!  I am a brand-new useR and have installed R-4.0.2.pkg and XQuartz on 
> my macOS 10.15.6.  The R GUI launches fine, but when I type 'demo()', the 
> application hangs (even with XQuartz running).  However, I can run from the 
> CLI in my XQuartz window just fine.  Where can I go to get help to get up and 
> running? Thank you.
> 
> Mike
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Re: [R-SIG-Mac] plot window not showing most recent plot?

[peter dalgaard]

Works fine for me when started from R in Terminal. Cmd-leftarrow and 
Cmd-rightarrow do their thing, as listed in the menu - provided the graphics 
window has focus, otherwise they switch virtual desktops (of course). 

-pd

> On 5 Sep 2020, at 17:59 , Tim Bates  wrote:
> 
> R for R 4.0.2 GUI 1.72 Catalina build (7847)
> 
> Oops, I was going off muscle memory - I see that Quartz:Forward and Back are 
> set to "⌘ tab" and "⌘⇧ tab"  (which can't do anything as they're captured by 
> the app switcher).
> 
> What are you seeing as the keys for Quartz:Forward and Quartz:Back?
> 
> Playing around, ⌘ left-arrow works to go back one graph, but only one time, 
> and ⌘ right arrow doesn't do anything.
> 
> Clicking the actual menu items when the quartz window contains 2 graphs, back 
> take me back, but then forward doesn't take me forward...
> 
> 
> 
>> On 5 Sep 2020, at 4:29 pm, Duncan Murdoch  wrote:
>> 
>> Which front end are you using?  The cmd-] and cmd-[ don't do anything in the 
>> ones I'm using.
>> 
>> Duncan Murdoch
>> 
>> On 05/09/2020 8:23 a.m., Timothy Bates wrote:
>>> In R version: R version 4.0.2 (2020-06-22), I’m seeing the plot window not 
>>> advance when a new ggplot is drawn.
>>> calls to plot() advance the quartz window to the newest “frame”, but calls 
>>> to ggplot2::qplot() show the graph only the first time the function is 
>>> called in the quartz window’s history.
>>> For subsequent qplots, the pane does not advance to show the new plot, 
>>> instead staying on which ever “frame’ in the plot history it was at.
>>> repro
>>> plot(wt ~ mpg, data=mtcars) # displays
>>> ggplot2::qplot(mpg, wt, data=mtcars) # doesn't display
>>> close quartz window
>>> qplot(mpg, wt, data=mtcars) # displays
>>> plot(wt ~ mpg, data=mtcars) # displays
>>> qplot(mpg, wt, data=mtcars) # doesn't display
>>> try cmd-] to advance forward into current history… nothing happens (newest 
>>> plot is not in the (forward) history
>>> try cmd-[ to go back, then cmd-]  cmd-]  to go forward into current 
>>> history… newest plot displays as it should have the first time
>>> ___
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>> 
> 
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Re: [R-SIG-Mac] svn tarball

[peter dalgaard]

Not dumb. 

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

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

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

-pd

 

> On 26 Aug 2020, at 18:43 , Carl Witthoft  wrote:
> 
> Dumb question from someone who hasn't done any building in quite a while: 
> recommended director to place the svn executable?
> thanks
> Carl
> 
> On 8/26/20 6:00 AM, r-sig-mac-requ...@r-project.org wrote:
> 
>>1.  svn now available from the tools (Simon Urbanek)
>> ntent-Type: text/plain; charset="us-ascii"
>> If you want to build R from the svn repository you need svn (subversion). 
>> Xcode 10 has removed svn so it is no loner available from Apple, we are 
>> providing a binary (cmopatible with OS X 10.11 and higher) in
>> https://mac.r-project.org/tools/
>> (in "optional tools and libraries" at the bottom), direct link:
>> https://mac.r-project.org/tools/subversion-1.14.0-darwin15.6.tar.gz
>> It is a single-file signed, static build so has no dependencies and can be 
>> run from anywhere.
>> Cheers,
> 
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Re: [R-SIG-Mac] Binary R-devel Builds For OS-X

[peter dalgaard]

Simon is the one who has the full detail, but at this point, I get 

R version 4.0.1 beta (2020-05-28 r78607) -- "See Things Now"

According to mac.r-project.org, this was built at 19:29 on May 28. It's not 
really clear what time zone that is... The transition to beta was just after 
midnight CET on the 27th which is like 10AM in Auckland, so you'd expect it to 
be picked up for the May 27 build, but maybe something got stalled. Or there 
might be a delay between the SVN checkout and the .pkg build.

-pd

> On 29 May 2020, at 00:23 , brodie gaslam  wrote:
> 
> I just installed the 4.0 patched binary, and noticed that it is still at 5/24 
> (i.e. pre Beta, although I'm guessing that's a minor distinction).  3.6 was 
> updated yesterday.  Since I'm not too familiar with this process yet, what 
> kind of update schedule should I expect for these binaries?
> 
> Best,
> 
> Brodie.
> 
> 
> 
> 
> 
> 
> On Saturday, May 16, 2020, 4:22:40 AM EDT, peter dalgaard  
> wrote: 
> 
> 
> 
> 
> 
> Yes. Simon's policy is just to use the current x.y SVN branch (say 
> R-4.0-branch) which goes through the alpha-beta-RC-(release)-Patched cycle. 
> 
> I.e. R-4.0-branch.pkg will _be_ the prerelease at the relevant stage of the 
> development cycle.
> 
> (Nerdy details: There is only x.y.0 alpha, otherwise we go directly from, 
> say, "4.0.0 Patched" to "4.0.1 beta"; or, differently put, R-patched _is_ the 
> alpha for the next version. Also, the unqualified x.y.z name is only there 
> while the relase tarball is being created, which is about 5 minutes on 
> release day so never makes it to the nightly builds.)  
> 
> -pd
> 
>> On 16 May 2020, at 02:27 , brodie gaslam  wrote:
> 
>> 
>> 
>> Presumably the alpha/RC releases are also posted to the mac.r-project.org 
>> page.
> 
> -- 
> 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
> 
> 
> 
> 
> 
> 
> 
> 

-- 
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

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

[peter dalgaard]

So you should be set. Anything more is just tidying. I have two of the three 
programs mentioned in /library/TeX xindy.mem nowhere in sight, but they are 
pretty obscure.

-pd

> On 17 May 2020, at 05:18 , Spencer Graves  wrote:
> 
> 
> 
> 
> 
>   I did "which" for all 451 executables found by "ls -l /usr/local/bin | 
> grep 'texlive/20' > texlive_20.txt".  All but 3 of them were found in 
> "/Library/TeX/texbin/".  The 3 not found were lua2dox_filter, pdfatfi, and 
> xindy.mem.  In particular, a2ping was found there.
> 
> 
>   Anything else?
>   Thanks again.
>   Spencer Graves

-- 
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Re: [R-SIG-Mac] Binary R-devel Builds For OS-X

[peter dalgaard]

Yes. Simon's policy is just to use the current x.y SVN branch (say 
R-4.0-branch) which goes through the alpha-beta-RC-(release)-Patched cycle. 

I.e. R-4.0-branch.pkg will _be_ the prerelease at the relevant stage of the 
development cycle.

(Nerdy details: There is only x.y.0 alpha, otherwise we go directly from, say, 
"4.0.0 Patched" to "4.0.1 beta"; or, differently put, R-patched _is_ the alpha 
for the next version. Also, the unqualified x.y.z name is only there while the 
relase tarball is being created, which is about 5 minutes on release day so 
never makes it to the nightly builds.)  

-pd

> On 16 May 2020, at 02:27 , brodie gaslam  wrote:
> 
> 
> Presumably the alpha/RC releases are also posted to the mac.r-project.org 
> page.

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

[peter dalgaard]

> On 15 May 2020, at 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
> 

Yup, upgrades until 2016 likely overwrote earlier links to 2015, 2014,..

The awk thing just reduces the above to the 9th field (i.e. "a2ping"), so you 
could in principle save the list to a file, say remove.me, and then

for i in `cat remove.me` ; do rm /usr/local/bin/$i ; done

(with a sudo somewhere, and do check carefully...)

> 
>   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.

Yep. That should solve things, provided there's an a2ping in 
/Library/TeX/texbin 

> 
> 
> 
>   ???
>   Thanks very much.
>   Spencer Graves
> 

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

[peter dalgaard]

TeX 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
>>> See https://tug.org/texlive/upgrade.html for details.
>>> 
>>> 
>>>   That link starts with, "By default, please get the new TL by doing
>>> a new installation instead of proceeding here."  Clicking "here" took me
>>> to where I was yesterday, when I installed MacTex-2020, which seems to
>>> have gone into "/user/local/texlive/2020".  I also found under
>>> "/user/local/texlive" subdirectories for 2014, and 2016 but not 2019.
>>> 
>>> 
>>>> tlmgr install $(cat ~/Downloads/texlive.$(date
>>>> +%Y-%m-%d).installed.txt)
>>> 
>>>   This gave me the same message as "tlmgr update --self".
>>>> and, perhaps
>>>> 
>>>> perl -i -p \
>>>> -e 's+\$SELFAUTOPARENT/+/usr/local/texlive/+' \
>>>> /usr/local/texlive/2020basic/texmf.cnf
>>>> texhash
>>> 
>>>   I have "/user/local/texlive/2020" but not "2020basic", as I
>>> indicated above.  I think I'll skip this for the moment.
>>>> :-)-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.
>>> 
>>> ls -l /usr/local/bin
>>> total 460456
>> [...]
>>>>> 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
>> [...]
>> 
> 
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Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?

[peter dalgaard]

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

> On 13 May 2020, at 14:16 , Marc Schwartz  wrote:
> 
> Spencer,
> 
> FWIW, this may be a situation where you need to remove your current/older 
> installations of TeXLive and start fresh with a clean install of TeXLive 
> 2020. It is possible that there is some conflict or corruption of the current 
> multiple installations.
> 
> That 'which pdflatex' is pointing directly to an executable in 
> /usr/local/bin, rather than to a symlink in the TeXLive tree, suggests that 
> there is something amiss with your installation.
> 
> There are two primary folder trees that would need to be removed:
> 
>  /Library/TeX
> 
> and 
> 
>  /usr/local/texlive
> 
> The former path will show in Finder, but the latter will not, unless you have 
> hidden folders set to show. If not, then you can use the Finder menu option:
> 
>  Go -> Go to Folder
> 
> and enter:
> 
>  /usr/local
> 
> That will then show you the texlive folder, which you can then right click on 
> and delete.
> 
> Both folder trees will require your Admin password to delete.
> 
> Once you do this, if you elect to do so, you will then need to re-install 
> TeXLive 2020 and hopefully start fresh.
> 
> Regards,
> 
> Marc Schwartz
> 
> 
>> On May 13, 2020, at 7:00 AM, 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 $PATH
>> /Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/sbgraves/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/opt/local/bin:/opt/local/sbin:/Users/sbgraves/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin
>> 
>> 
>>  I do find "/Library/TeX/texbin/pdflatex" on my hard drive, but "which 
>> pdflatex" doesn't find it.
>> 
>> 
>>  Thanks,
>>  Spencer Graves
>> 
>> 
>> On 2020-05-13 01:31, peter dalgaard wrote:
>>> You typically need to ensure that you have the right TeX installation in 
>>> your PATH (and not an older one earlier in the path). You should see 
>>> something like this
>>> 
>>> Peters-MacBook-Air:BUILD pd$ which pdflatex
>>> /Library/TeX/texbin/pdflatex
>>> Peters-MacBook-Air:BUILD pd$ pdflatex -version
>>> pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019)
>>> kpathsea version 6.3.1
>>> 
>>> Peters-MacBook-Air:BUILD pd$ echo $PATH
>>> /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/gfortran/bin:/usr/local/clang8/bin:/Library/TeX/texbin:/opt/X11/bin
>>> 
>>> (Notice that if I had older TeX stuff in /usr/local, I could be in similar 
>>> trouble...)
>>> 
>>> -pd
>>> 
>>> 
>>>> On 13 May 2020, at 06:15 , Spencer Graves  
>>>> wrote:
>>>> 
>>>> Hi, Ken et al.:
>>>> 
>>>> 
>>>>  Thanks for the info.  I tried to do what you suggested but still have 
>>>> the problem.
>>>> 
>>>> 
>>>>  Specifically, a web search for TexLive 2020 led me to 
>>>> "https://tug.org/texlive/;.  That invited me to download and install 
>>>> MacTex 2020 from "https://tug.org/mactex/mactex-download.html;, which I 
>>>> did.   Everything seemed to go smoothly, but when I ran "R CMD build 
>>>> Ecfun" and "R CMD check Ecfun_0.2-4.tar.gz", I got the same error.  This 
>>>> is running those commands in a Terminal.  When I invoked "r" there just 
>>>> now and requested "sessionInfo()", I got the following:
>>>> 
>>>> 
>>>> R version 4.0.0 (2020-04-24)
>>>> Pl

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

[peter dalgaard]

/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
>>> 
>>> __
>>> r-package-de...@r-project.org  mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>> 
>>> [[alternative HTML version deleted]]
>>> 
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> 
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Re: [R-SIG-Mac] Graphic problem Rcmdr

[Peter Dalgaard]

There is a generic problem with Tcl/Tk combined with other GUIs, though. 
Essentially, you need to multiplex two event loops, and there is some risk of 
race conditions. Whether such bugs actually bite can vary between platforms.

-pd

> On 30 Apr 2020, at 02:02 , Fox, John  wrote:
> 
> Dear JB,
> 
>> On Apr 29, 2020, at 1:44 PM, jean benoit TANIS  wrote:
>> 
>> This actually works well on the terminal session !! Very strange that the 
>> App GUI does not work well. I do not know if it is a general Mac problem or 
>> due to my computer settings…. 
> 
> I don't think that it could be a general Mac problem, because R.app works 
> with the Rcmdr for me and others. At least you now have a couple of solutions.
> 
> Best,
> John
> 
>> 
>> JB
>> 
>>> On 29 Apr 2020, at 18:18, Fox, John  wrote:
>>> 
>>> Dear JB,
>>> 
>>> If you use the Rcmdr with RStudio, by default it will direct output to the 
>>> RStudio console. You can change that, if you wish -- look at the Rcmdr 
>>> options in ?Commander.
>>> 
>>> Also, have you tried running R and the Rcmdr in a Terminal window, as I 
>>> suggested? If the problem is with R.app, then that might work too.
>>> 
>>> Peter: Thanks for chiming in.
>>> 
>>> Best,
>>> John
>>> 
>>>> -Original Message-
>>>> From: jean benoit TANIS 
>>>> Sent: Wednesday, April 29, 2020 1:04 PM
>>>> To: peter dalgaard 
>>>> Cc: Fox, John ; R-Sig-Mac 
>>>> Subject: Re: [R-SIG-Mac] Graphic problem Rcmdr
>>>> 
>>>> I have just tried with R studio and it works … I do not know why it does
>>>> not work with Rapp but at least I can use it now.
>>>> 
>>>> Thank you very much for your precious help !!
>>>> 
>>>> JB
>>>> 
>>>>> On 29 Apr 2020, at 16:14, peter dalgaard  wrote:
>>>>> 
>>>>> Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be
>>>> bothered to upgrade at this point). Works both from R.app and Terminal,
>>>> and even from RStudio.
>>>>> 
>>>>> One thought is a missing font, but same font is used elsewhere is it
>>>> not?
>>>>> 
>>>>> You could try playing with generic Tcl/Tk via the tcltk package and
>>>>> see if you can reproduce the problem in a simpler setting (perhaps try
>>>>> the package demos?)
>>>>> 
>>>>> -pd
>>>>> 
>>>>>> On 29 Apr 2020, at 15:07 , Fox, John  wrote:
>>>>>> 
>>>>>> Dear JB,
>>>>>> 
>>>>>> We corresponded privately about this problem, and I suggested that you
>>>> post a message to the R-SIG-Mac list when I was unable to help you solve
>>>> it. I don't experience the problem on a Mac similar to yours, but running
>>>> macOS Catalina, and no one else to my knowledge has reported a similar
>>>> problem (with blank menus).
>>>>>> 
>>>>>> I do have one additional suggestion: I assume that you're running the
>>>> Rcmdr under the standard R.app GUI. Try running R in a Terminal session.
>>>> That is open the Mac Terminal, type R  at the % command prompt and then
>>>> library(Rcmdr) at the R > prompt.
>>>>>> 
>>>>>> Perhaps others will think of additional suggestions.
>>>>>> 
>>>>>> Best,
>>>>>> John
>>>>>> 
>>>>>>> On Apr 29, 2020, at 2:18 AM, 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 iss

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

[peter dalgaard]

Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be bothered 
to upgrade at this point). Works both from R.app and Terminal, and even from 
RStudio.

One thought is a missing font, but same font is used elsewhere is it not?

You could try playing with generic Tcl/Tk via the tcltk package and see if you 
can reproduce the problem in a simpler setting (perhaps try the package demos?)

-pd

> On 29 Apr 2020, at 15:07 , Fox, John  wrote:
> 
> Dear JB,
> 
> We corresponded privately about this problem, and I suggested that you post a 
> message to the R-SIG-Mac list when I was unable to help you solve it. I don't 
> experience the problem on a Mac similar to yours, but running macOS Catalina, 
> and no one else to my knowledge has reported a similar problem (with blank 
> menus).
> 
> I do have one additional suggestion: I assume that you're running the Rcmdr 
> under the standard R.app GUI. Try running R in a Terminal session. That is 
> open the Mac Terminal, type R  at the % command prompt and then 
> library(Rcmdr) at the R > prompt.
> 
> Perhaps others will think of additional suggestions.
> 
> Best,
> John
> 
>> On Apr 29, 2020, at 2:18 AM, 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 
>> 
>> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
>> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.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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Re: [R-SIG-Mac] Problem R-4.0 beta and Rmpfr (pre-release)

[peter dalgaard]

gt;> Attaching package: 'Rmpfr'
>>>> 
>>>> The following object is masked from 'package:gmp':
>>>> 
>>>> outer
>>>> 
>>>> The following objects are masked from 'package:stats':
>>>> 
>>>> dbinom, dgamma, dnorm, dpois, pnorm
>>>> 
>>>> The following objects are masked from 'package:base':
>>>> 
>>>> cbind, pmax, pmin, rbind
>>>> 
>>>>> x <- 1400+ 0:10
>>>>> print(dpois(x, 1000), digits =18) ## standard R's double precision
>>>> [1] 1.46677334419659338e-33 1.04694742626454156e-33 7.46752800474106016e-34
>>>> [4] 5.32254312525935864e-34 3.79098513195210765e-34 2.69821005832831136e-34
>>>> [7] 1.91906832029070091e-34 1.36394336907638670e-34 9.68709779173582432e-35
>>>> [10] 6.87515812046484244e-35 4.87599866699657026e-35
>>>>> dpois(mpfr(x, 120), 1000)## more accuracy for the same
>>>> 
>>>> *** caught illegal operation ***
>>>> address 0x10a6e1c42, cause 'illegal opcode'
>>>> 
>>>> Traceback:
>>>> 1: .class1(object)
>>>> 2: as(value, dataClass)
>>>> 3: setDataPart(x, .Call(Math_mpfr, x, .Math.codes[[.Generic]]))
>>>> 4: exp(-lambda)
>>>> 5: exp(-lambda)
>>>> 6: dpois(mpfr(x, 120), 1000)
>>>> 
>>>> Possible actions:
>>>> 1: abort (with core dump, if enabled)
>>>> 2: normal R exit
>>>> 3: exit R without saving workspace
>>>> 4: exit R saving workspace
>>>> 
>>>> >>> 
>>>> Other trials seem to experience similar issues.
>>>> 
>>>> 
>>>> regards
>>>> 
>>>> Berend
>>>> 
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>>> 
>>> 
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Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 205, Issue 13

[peter dalgaard]

> On 2 Apr 2020, at 16:47 , Colin A. Smith  wrote:
> 
> tapply(rownames(installed.packages()), installed.packages()[,"LibPath"], c)

or

X <- installed.packages()
split(rownames(X), X[,"LibPath"])


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Re: [R-SIG-Mac] PCRE JIT compilation error

[peter dalgaard]

Yes, sorry:

> osVersion
[1] "macOS Mojave 10.14.6"


> On 1 Apr 2020, at 16:14 , Prof Brian Ripley  wrote:
> 
> It seems to depend on the OS version: there are known issues with PCRE JIT 
> and macOS 10.15 not just with R, but not for everyone.
> 
> Similarly, installation issues of some Rcpp-using packages is only known to 
> occur under 10.15 and not with 10.13 (which is what will be used for building 
> binary packages and has been extensively tested there).  These should go away 
> with the next Rcpp update, available pro tem via
> 
> install.packages("Rcpp", repos="https://rcppcore.github.io/drat;)
> 
> So it really is necessary to remind people to follow the posting guide and 
> include the output from sessionInfo() or at the very least
> 
> > osVersion
> [1] "macOS Catalina 10.15.4"
> 
> 
> On 01/04/2020 14:37, peter dalgaard wrote:
>> Yes, this has been happening to a number of people, including Simon 
>> Urbanek...
>> Oddly enough, I'm seeing nothing of the sort on my slightly different build 
>> setup:
>> clang8 + gfortran6.1 as per https://cran.r-project.org/bin/macosx/tools
>> PCRE2 from http://mac.r-project.org/libs/
>> $ cat config.site
>> prefix=$HOME/tmp
>> CC=clang
>> CXX=clang++
>> with_blas="-framework vecLib"
>> with_lapack=yes
>> x_includes=/opt/X11/include
>> x_libraries=/opt/X11/lib
>> CURL_CONFIG=/usr/bin/curl-config
>> (And no, it is not because JIT is off:
>>> options("PCRE_use_JIT")
>> $PCRE_use_JIT
>> [1] TRUE
>> )
>> -pd
>>> On 1 Apr 2020, at 13:30 , Bryan Hanson  wrote:
>>> 
>>> On a fresh install of the binary from mac.r-project.org, if I simply do:
>>> 
>>> library()
>>> 
>>> I see:
>>> 
>>> R > library()
>>> There were 30 warnings (use warnings() to see them)
>>> R > warnings()
>>> Warning messages:
>>> 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
>>> 'no more memory'
>>> 2: In FUN(X[[i]], ...) : PCRE JIT compilation error
>>> 'no more memory'
>>> 
>>> etc.  The usual window with installed packages does open.
>>> 
>>> Starting the conversation here on the Mac list, though it may be a bigger 
>>> problem.
>>> 
>>> Thanks, Bryan
>>> 
>>> Prof. Bryan Hanson (emeritus)
>>> Dept of Chemistry & Biochemistry
>>> DePauw University
>>> Greencastle IN 46135 USA
>>> Web: academic.depauw.edu/~hanson/index.html
>>> Repo: github.com/bryanhanson
>>> Nerdy Blog: ChemoSpec.org
>>> The Twit: @ProfBryanHanson
>>> I’m usually @ -4 GMT/UTC
>>> 
>>> R > sessionInfo()
>>> R version 4.0.0 alpha (2020-03-29 r78109)
>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>> Running under: macOS Mojave 10.14.6
>>> 
>>> Matrix products: default
>>> BLAS:   
>>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/4.0/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_4.0.0
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
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> 
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford

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Re: [R-SIG-Mac] PCRE JIT compilation error

[peter dalgaard]

Yes, this has been happening to a number of people, including Simon Urbanek...

Oddly enough, I'm seeing nothing of the sort on my slightly different build 
setup: 

clang8 + gfortran6.1 as per https://cran.r-project.org/bin/macosx/tools
PCRE2 from http://mac.r-project.org/libs/ 

$ cat config.site 
prefix=$HOME/tmp
CC=clang
CXX=clang++
with_blas="-framework vecLib"
with_lapack=yes
x_includes=/opt/X11/include
x_libraries=/opt/X11/lib
CURL_CONFIG=/usr/bin/curl-config

(And no, it is not because JIT is off:

> options("PCRE_use_JIT")
$PCRE_use_JIT
[1] TRUE

)


-pd

> On 1 Apr 2020, at 13:30 , Bryan Hanson  wrote:
> 
> On a fresh install of the binary from mac.r-project.org, if I simply do:
> 
> library()
> 
> I see:
> 
> R > library()
> There were 30 warnings (use warnings() to see them)
> R > warnings()
> Warning messages:
> 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
>   'no more memory'
> 2: In FUN(X[[i]], ...) : PCRE JIT compilation error
>   'no more memory'
> 
> etc.  The usual window with installed packages does open.
> 
> Starting the conversation here on the Mac list, though it may be a bigger 
> problem.
> 
> Thanks, Bryan
> 
> Prof. Bryan Hanson (emeritus)
> Dept of Chemistry & Biochemistry
> DePauw University
> Greencastle IN 46135 USA
> Web: academic.depauw.edu/~hanson/index.html
> Repo: github.com/bryanhanson
> Nerdy Blog: ChemoSpec.org
> The Twit: @ProfBryanHanson
> I’m usually @ -4 GMT/UTC
> 
> R > sessionInfo()
> R version 4.0.0 alpha (2020-03-29 r78109)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Mojave 10.14.6
> 
> Matrix products: default
> BLAS:   
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.0/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_4.0.0
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] R devel == 4.0.0?

[peter dalgaard]

This seems to have been resolved at this point. I think "last successful" 
actually is the expected modus operandi, something just got messed up (the 
r-devel SVN has never contained the 3.6.3 version label, it is always "x.y.0 
under development"). 

Another question is whether a failed regression test is reason enough to hold 
back the entire .pkg build, given that it is already by definition unstable. 
For source tarballs, I don't even check beyond being able to actually build the 
things, on the premise that it is often more important to get code tested in 
other areas than to fix a failing regression test.

Notice that we go to 4.0.0 alpha tomorrow so presumably an R-4-0-branch entry 
should arrive on mac.r-project.org shortly.

-pd

> On 26 Mar 2020, at 09:59 , Patrick Schratz  wrote:
> 
> Even if the R-devel build failed for a day, why does the tarball link/contain 
> the R 3.6 source then?
> 
> I update my R-devel install every few days automatically and would not notice 
> that I suddenly got R-release via that URL.
> Rather I would prefer a 404 or (better) the latest successful R-devel build?
> 
> @Simon
> Clarification would be appreciated.
> 
> Cheers, Patrick
> On 26. Mar 2020, 09:51 +0100, peter dalgaard , wrote:
>> FWIW, r-devel builds happily on my machine (MB Air '19, Mojave, clang8, 
>> gfortran 6.1.0 from CRAN), regression tests and all.
>> 
>> -pd
>> 
>>> On 25 Mar 2020, at 21:53 , Simon Urbanek  
>>> wrote:
>>> 
>>> Constantin,
>>> 
>>> no, as you can see from the log the regression tests failed for R-devel, so 
>>> it doesn't currently build. You'll have to wait until that has been fixed.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>> 
>>>> On 26/03/2020, at 4:17 AM, Constantin Ahlmann-Eltze via R-SIG-Mac 
>>>>  wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> I wanted to install R 4.0.0 on my Mac (Mojave) to test some of my packages
>>>> with the development version before it is released. I saw that
>>>> https://mac.r-project.org/ is recommended to get a pkg or tar.gz file with
>>>> the latest version. However, the R-devel version linked there points to
>>>> 3.6.3.
>>>> 
>>>> Is that the expected behavior? Am I right then, that I will have install R
>>>> 4.0.0 from source? And if so what is the recommended tool chain at the
>>>> moment for doing so?
>>>> 
>>>> Best Regards,
>>>> Constantin Ahlmann-Eltze
>>>> 
>>>> [[alternative HTML version deleted]]
>>>> 
>>>> ___
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>>>> 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
>> 
>> --
>> 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
>> 
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Re: [R-SIG-Mac] R devel == 4.0.0?

[peter dalgaard]

FWIW, r-devel builds happily on my machine (MB Air '19, Mojave, clang8, 
gfortran 6.1.0 from CRAN), regression tests and all. 

-pd

> On 25 Mar 2020, at 21:53 , Simon Urbanek  wrote:
> 
> Constantin,
> 
> no, as you can see from the log the regression tests failed for R-devel, so 
> it doesn't currently build. You'll have to wait until that has been fixed.
> 
> Cheers,
> Simon
> 
> 
> 
>> On 26/03/2020, at 4:17 AM, Constantin Ahlmann-Eltze via R-SIG-Mac 
>>  wrote:
>> 
>> Hi,
>> 
>> I wanted to install R 4.0.0 on my Mac (Mojave) to test  some of my packages
>> with the development version before it is released. I saw that
>> https://mac.r-project.org/ is recommended to get a pkg or tar.gz file with
>> the latest version. However, the R-devel version linked there points to
>> 3.6.3.
>> 
>> Is that the expected behavior? Am I right then, that I will have install R
>> 4.0.0 from source? And if so what is the recommended tool chain at the
>> moment for doing so?
>> 
>> Best Regards,
>> Constantin Ahlmann-Eltze
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
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> 
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Re: [R-SIG-Mac] R 3.6.3 for MacOS

[Peter Dalgaard]

Installed without issues on Mojave.

Reminds me that I may need some instructions on any required changes in the 
toolchain for 4.0.0 if I want to upgrade the build machine to Catalina before 
the release.

-pd

> On 6 Mar 2020, at 02:32 , Simon Urbanek  wrote:
> 
> Lori,
> 
> as posted here earlier[1], Apple has tightened notarization requirements this 
> year making it impossible for current R releases to be notarized until R 
> 4.0.0 and thus the last Apple-notarized release is R 3.6.2.
> 
> If you are on a macOS version that doesn't require notarization, then I have 
> put a binary that is not notarized in
> https://mac.R-project.org/bin/macosx/el-capitan/base/R-3.6.3.nn.pkg
> SHA1(R-3.6.3.nn.pkg)= c462c9b1f9b45d778f05b8d9aa25a9123b3557c4
> 
> I am currently investigating if we can enable the required restrictions on 
> binaries and what implications for the functionality of R that will have and 
> will keep you posted. 
> 
> Cheers,
> Simon
> 
> 
> [1] - https://stat.ethz.ch/pipermail/r-sig-mac/2019-October/013100.html
> 
> 
>> On 6/03/2020, at 6:39 AM, Shepherd, Lori  
>> wrote:
>> 
>> Is there any update on when R 3.6.3 will be available for download from  
>> https://cloud.r-project.org/bin/macosx/ ?
>> It seems like there was a release of R 3.6.3 for linux and windows on 
>> February 29th that is available but nothing yet for Mac.
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> 
>> 
>> This email message may contain legally privileged and/or confidential 
>> information.  If you are not the intended recipient(s), or the employee or 
>> agent responsible for the delivery of this message to the intended 
>> recipient(s), you are hereby notified that any disclosure, copying, 
>> distribution, or use of this email message is prohibited.  If you have 
>> received this message in error, please notify the sender immediately by 
>> e-mail and delete this email message from your computer. Thank you.
>>  [[alternative HTML version deleted]]
>> 
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Re: [R-SIG-Mac] colors from RGui in RStudio

[peter dalgaard]

project.org/bin/macosx/Mac-GUI-1.70.tar.gz.  However, I 
>>> don't understand Cocoa apps enough to know where to look for the default 
>>> colors.
>>> 
>>> Duncan Murdoch
>>> 
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>> 
> 
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Re: [R-SIG-Mac] R-latest.pkg link returning a 403 Forbidden error

[peter dalgaard]

cosx/R-latest.pkg which
>>>>> previously served the latest version of R is now returning a 403. Is
>>>>> this an intentional change, or is it an unintentional? This link is
>>>>> used by the Travis-CI build scripts for macOS, so if the link is no
>>>>> longer valid we will need to update the script.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> 
>>>> 
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>>> 
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>>> 
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>> 
> 
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Re: [R-SIG-Mac] Robust compiler toolchain for R-devel

[peter dalgaard]

Simon has recently brought up (on R-core) the related issue of what to use as 
the target platform for 4.0.0. 

I don't know whether he is ready to take his deliberations to a wider audience 
at this point.

-pd

> On 18 Feb 2020, at 09:14 , Patrick Schratz  wrote:
> 
> Hi,
> 
> I am experimenting since some days to find the “best” compiler toolchain for 
> R-devel to get R-devel package source installs on the new macOS Github 
> Actions runners work in a somewhat stable way.
> I am also on macOS locally which I use for testing as well.
> 
> I am aware of https://github.com/rmacoslib/r-macos-rtools. However, using 
> clang7 for all (CC, CXX, etc) leads to some packages failing to build 
> (sometimes due to missing OpenMP capabilities, sometimes undefined).
> 
> Therefore I decided to try out gcc (v8 and v9). While this solves most of the 
> OpenMP issues, I am running into problems for other packages regarding CC 
> compilation.
> 
> Turns out that using any clang version for CC solves most problems but not 
> all.
> However then I have a mix of gcc and clang which is most likely cause other 
> issues.
> 
> Currently Jeroen is developing a new gcc8 based toolchain for Windows.
> 
> I was reading the macOS CRAN dev pages but could not find any reasoning why
> 
> • clang7 is suggested
> • gcc is not used
> • What future plans are there for the toolchain on macOS
> 
> Could someone shine some light on this? Thanks :)
> 
> Cheers, Patrick
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] PACKAGES file missing

[peter dalgaard]

[See note from Simon Urbanek on February 7. All is related to Simon and his 
equipment being turned upside down a few weeks ago. -pd]

> On 12 Feb 2020, at 12:42 , Joel Jacobson  wrote:
> 
> The file was missing for sure from all mirrors also the main one. My guess is 
> you have a cronjob that builds the new PACKAGES file that removes the old 
> file before the new one has been created.
> 
> Best regards,
> 
> Joel
> 
> On Wed, Feb 12, 2020, at 17:01, Dr Eberhard W Lisse wrote:
>> 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
>> [...]
>> 
>> 
>> -- 
>> Dr. Eberhard W. Lisse \ / Obstetrician & Gynaecologist 
>> e...@lisse.na / * | Telephone: +264 81 124 6733 (cell)
>> PO Box 8421 \ /
>> Bachbrecht 10007, Namibia ;/
>> 
> 
> Kind regards,
> 
> Joel
> 
>   [[alternative HTML version deleted]]
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Re: [R-SIG-Mac] mac.r-project.org links are broken

[peter dalgaard]

Yes, they are on a plane to New Zealand... (more or less, anyway)

Expect things to get tidied up during next week.

-pd

> On 25 Jan 2020, at 12:08 , Jonathon Love  wrote:
> 
> hi,
> 
> in case no-one had noticed yet, the following links are broken:
> 
> http://mac.r-project.org/src/
> 
> http://mac.r-project.org/libs/
> 
> as linked from:
> 
> https://cran.r-project.org/bin/macosx/tools/
> 
> earlier today, the SSL on mac.r-project.org was broken too, but that appears 
> to be working now.
> 
> cheers
> 
> jonathon
> 
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Re: [R-SIG-Mac] set.seed

[peter dalgaard]

> On 23 Jan 2020, at 12:15 , Adrian Dușa  wrote:
> 
> Dear Peter,
> 
> Thanks, it's good to know there is a good explanation for this and also the 
> sample.kind is now more stable.
> Curiously though, I run the very same R version on both computers and I would 
> have expected RNGkind() to work the same.

The most likely explanation is that on one machine you had (like I did)

$ R

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
blablabla...

[Previously saved workspace restored]

> set.seed(12)
> sample(letters[1:10])
 [1] "a" "h" "i" "b" "g" "j" "e" "f" "d" "c"
> RNGkind()
[1] "Mersenne-Twister" "Inversion""Rounding"


...whereas

$ R --vanilla -q
> set.seed(12)
> sample(letters[1:10])
 [1] "b" "g" "c" "f" "e" "i" "d" "j" "h" "a"
> RNGkind()
[1] "Mersenne-Twister" "Inversion""Rejection"   



-pd

> 
> Best,
> Adrian
> 
> On Thu, Jan 23, 2020 at 11:18 AM peter dalgaard  wrote:
> >
> > That's the effect of RNGkind(sample.kind="Rejection") which is the new 
> > default. Unfortunately, the older and buggy "Rounding" has a tendency to 
> > linger in saved workspaces.
> >
> > -pd
> >
> > > RNGkind(sample.kind="Rejection")
> > > set.seed(12)
> > > sample(letters[1:10])
> >  [1] "b" "g" "c" "f" "e" "i" "d" "j" "h" "a"
> > > RNGkind(sample.kind="Rounding")
> > Warning message:
> > In RNGkind(sample.kind = "Rounding") : non-uniform 'Rounding' sampler used
> > > set.seed(12)
> > > sample(letters[1:10])
> >  [1] "a" "h" "i" "b" "g" "j" "e" "f" "d" "c"
> >
> >
> > > On 23 Jan 2020, at 09:51 , Adrian Dușa via R-SIG-Mac 
> > >  wrote:
> > >
> > > Dear All,
> > >
> > > I've recently acquired a new MacBook, and while transferring my files and
> > > settings I noticed something I did not expect:
> > >
> > > Old Mac:
> > >> set.seed(12)
> > >> sample(letters[1:10])
> > > [1] "a" "h" "i" "b" "g" "j" "e" "f" "d" "c"
> > >
> > >
> > > New Mac:
> > >> set.seed(12)
> > >> sample(letters[1:10])
> > > [1] "b" "g" "c" "f" "e" "i" "d" "j" "h" "a"
> > >
> > > For numbers I don't see anything different, the examples from ?set.seed
> > > producing the same results. Both R versions are the same (3.6.2) and both
> > > computers run macOS Catalina 10.15.2.
> > >
> > > I would be grateful for any advice,
> > > Adrian
> > >
> > > --
> > > Adrian Dusa
> > > University of Bucharest
> > > Romanian Social Data Archive
> > > Soseaua Panduri nr. 90-92
> > > 050663 Bucharest sector 5
> > > Romania
> > > https://adriandusa.eu
> > >
> > >   [[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
> >
> >
> >
> >
> >
> >
> >
> >
> >
> 
> 
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr. 90-92
> 050663 Bucharest sector 5
> Romania
> https://adriandusa.eu

-- 
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

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Re: [R-SIG-Mac] set.seed

[peter dalgaard]

That's the effect of RNGkind(sample.kind="Rejection") which is the new default. 
Unfortunately, the older and buggy "Rounding" has a tendency to linger in saved 
workspaces.

-pd

> RNGkind(sample.kind="Rejection")
> set.seed(12)
> sample(letters[1:10])
 [1] "b" "g" "c" "f" "e" "i" "d" "j" "h" "a"
> RNGkind(sample.kind="Rounding")
Warning message:
In RNGkind(sample.kind = "Rounding") : non-uniform 'Rounding' sampler used
> set.seed(12)
> sample(letters[1:10])
 [1] "a" "h" "i" "b" "g" "j" "e" "f" "d" "c"


> On 23 Jan 2020, at 09:51 , Adrian Dușa via R-SIG-Mac 
>  wrote:
> 
> Dear All,
> 
> I've recently acquired a new MacBook, and while transferring my files and
> settings I noticed something I did not expect:
> 
> Old Mac:
>> set.seed(12)
>> sample(letters[1:10])
> [1] "a" "h" "i" "b" "g" "j" "e" "f" "d" "c"
> 
> 
> New Mac:
>> set.seed(12)
>> sample(letters[1:10])
> [1] "b" "g" "c" "f" "e" "i" "d" "j" "h" "a"
> 
> For numbers I don't see anything different, the examples from ?set.seed
> producing the same results. Both R versions are the same (3.6.2) and both
> computers run macOS Catalina 10.15.2.
> 
> I would be grateful for any advice,
> Adrian
> 
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr. 90-92
> 050663 Bucharest sector 5
> Romania
> https://adriandusa.eu
> 
>   [[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

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Re: [R-SIG-Mac] damned Catalina

[peter dalgaard]

lease use the R-SIG-Mac 
>>>>>>>> <https://stat.ethz.ch/mailman/listinfo/r-sig-mac 
>>>>>>>> <https://stat.ethz.ch/mailman/listinfo/r-sig-mac>> mailing list.
>>>>>>>> 
>>>>>>>> Did something went wrong? Should I remove the first line of my mail?  
>>>>>>>> Actually, what I need is to run “regtools” on Cran R insalled on my 
>>>>>>>> computer. Thanks for your unsderstanding, all the best
>>>>>>>> 
>>>>>>>> Bruno
>>>>>>>> 
>>>>>>>> Bruno Apolloni
>>>>>>>> (Full Professor )
>>>>>>>> Dipartimento di Informatica
>>>>>>>> University of Milano
>>>>>>>> Via Comelico 39
>>>>>>>> 20135 Milano (Italy)
>>>>>>>> Tel. +39(0)2-50316284
>>>>>>>> Fax. +39(0)2-50316228
>>>>>>>> Mobile +39 333 7469878
>>>>>>>> e-mail: apoll...@di.unimi.it <mailto:apoll...@di.unimi.it> 
>>>>>>>> <mailto:apoll...@di.unimi.it <mailto:apoll...@di.unimi.it>>
>>>>>>>> http://homes.di.unimi.it/apolloni <http://homes.di.unimi.it/apolloni> 
>>>>>>>> <http://homes.di.unimi.it/apolloni <http://homes.di.unimi.it/apolloni>>
>>>>>>>> 
>>>>>>>> 
>>>>>>>>> Il giorno 18 dic 2019, alle ore 13:08, Ken Beath >>>>>>>> <mailto:k...@kjbeath.com.au> <mailto:k...@kjbeath.com.au 
>>>>>>>>> <mailto:k...@kjbeath.com.au>>> ha scritto:
>>>>>>>>> 
>>>>>>>>> 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 >>>>>>>>> <mailto:apoll...@di.unimi.it> <mailto:apoll...@di.unimi.it 
>>>>>>>>>> <mailto:apoll...@di.unimi.it>>> 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 
>>>>>>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6> 
>>>>>>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 
>>>>>>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6>> 
>>>>>>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 
>>>>>>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6> 
>>>>>>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 
>>>>>>>>>> <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]]
>>>>>>>>>> 
>>>>>>>>>> ___
>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> 
>>>>>>>>>> <mailto:R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org>>
>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac 
>>>>>>>>>> <https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> [[alternative HTML version deleted]]
>>>>>>> 
>>>>>>> ___
>>>>>>> R-SIG-Mac mailing list
>>>>>>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org>
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac 
>>>>>>> <https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
>>>>>> 
>>>>>> --
>>>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation 
>>>>>> Biology, UCT), Dipl. Phys. (Germany)
>>>>>> 
>>>>>> Orcid ID: -0002-7490-0066
>>>>>> 
>>>>>> Department of Evolutionary Biology and Environmental Studies
>>>>>> University of Zürich
>>>>>> Office Y34-J-74
>>>>>> Winterthurerstrasse 190
>>>>>> 8075 Zürich
>>>>>> Switzerland
>>>>>> 
>>>>>> Office:  +41 (0)44 635 47 64
>>>>>> Cell:+41 (0)78 630 66 57
>>>>>> email:  rainer.k...@uzh.ch <mailto:rainer.k...@uzh.ch>
>>>>>>  rai...@krugs.de <mailto:rai...@krugs.de>
>>>>>> Skype: RMkrug
>>>>>> 
>>>>>> PGP: 0x0F52F982
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>>> --
>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation 
>>>> Biology, UCT), Dipl. Phys. (Germany)
>>>> 
>>>> Orcid ID: -0002-7490-0066
>>>> 
>>>> Department of Evolutionary Biology and Environmental Studies
>>>> University of Zürich
>>>> Office Y34-J-74
>>>> Winterthurerstrasse 190
>>>> 8075 Zürich
>>>> Switzerland
>>>> 
>>>> Office:+41 (0)44 635 47 64
>>>> Cell:  +41 (0)78 630 66 57
>>>> email:  rainer.k...@uzh.ch <mailto:rainer.k...@uzh.ch>
>>>>rai...@krugs.de <mailto:rai...@krugs.de>
>>>> Skype: RMkrug
>>>> 
>>>> PGP: 0x0F52F982
>>>> 
>>>> 
>>>> 
>>> [[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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-- 
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

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Re: [R-SIG-Mac] Problems with rJava fir R 3.6.1

[peter dalgaard]

I try to suppress any memories of this stuff every time I have had to deal with 
it, but...

Would "R CMD javareconf" help, maybe?

-pd

> On 19 Sep 2019, at 14:09 , Thomas Knox  wrote:
> 
> I have recently installed R 3.6.1 on my MacBook running Mac OS Mojave 10.14.5 
> in order to run a custom package called MH1823 (probability of detection).  
> This package requires me to load the following packages from CRAN, tcltk, 
> tcltk2, survival and xlsx.
> 
> 
> 
> I have installed survival, xlsx and tlctk2 (i believe tcltk is embedded).  
> When I look at Package Manager i see that although the above packages are 
> installed they are not loaded.  I can load survival but when I try to load 
> “xlsx” i get the following  error message is:
> 
> 
> 
> Error: package or namespace load failed for ‘xlsx’:
> 
> .onLoad failed in loadNamespace() for 'rJava', details:
> 
>  call: dyn.load(file, DLLpath = DLLpath, ...)
> 
>  error: unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':
> 
>  
> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so,
>  6): Library not loaded: 
> /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
> 
>  Referenced from: 
> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
> 
>  Reason: image not found
> 
> starting httpd help server … done
> 
> 
> 
> 
> 
> there may be a couple of hints in here.
> 
> 
> 
> .onLoad failed in loadNamespace() for 'rJava', details  suggests the problem 
> starts with calling rJava.
> 
> 
> 
> the next line in the error:
> 
> error: unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':
> 
> I have checked this path and see no problems, everything seems to stack up 
> and I find jJava.so where it is supposed to be.  However in the next line:
> 
> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so,
>  6): Library not loaded: 
> /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
> 
> I don’t know what the number , 6 after Java.so means but have presumed 
> version number and may be why Java8 is not working.  I also note the path …. 
> /JavaVirtualMachines/jdk-11.0.1.jdk/ appears as . 
> /JavaVirtualMachines/1.6.0.jdk/
> 
> suggesting a different build
> 
> 
> 
> the same occurs when I try to load the local source package MH1823
> 
> 
> 
> When I try to load HM1823 I get the error message:
> 
> * installing *source* package ‘mh1823’ ...
> 
> ** using staged installation
> 
> ** R
> 
> ** data
> 
> ** inst
> 
> ** byte-compile and prepare package for lazy loading
> 
> Error: package or namespace load failed for ‘xlsx’:
> 
> .onLoad failed in loadNamespace() for 'rJava', details:
> 
>  call: dyn.load(file, DLLpath = DLLpath, ...)
> 
>  error: unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':
> 
>  
> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so,
>  6): Library not loaded: 
> /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
> 
>  Referenced from: 
> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
> 
>  Reason: image not found
> 
> Error: package ‘xlsx’ could not be loaded
> 
> Execution halted
> 
> ERROR: lazy loading failed for package ‘mh1823’
> 
> * removing 
> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mh1823’
> 
>> 
> 
> 
> 
> I find that the error message is substantially the same suggesting rJava 
> and/or the version of Java.  I have tried removing Java 8 from my machine and 
> installing Java 6 but don’t see any difference.  It is easy to see that Java 
> 8 has been removed but not easy to see that 6 is installed properly as the 
> path names are still the same.
> 
> 
> 
> When I try to load either tcltk or tcltk2, my instance of R stops responding 
> entirely.
> 
> 
> 
> I have also installed Xquartz as I believe this is needed for Mac OS X
> 
> 
> 
> Can anyone provide some advice on what the issue might be?  I have tried 
> reading through the FAQ’s but not found anything to point me in the right 
> direction to correct the problem.
> 
> 
> 
> Regards,
> 
> 
> 
> Tom Knox
>   [[alternative HTML version deleted]]
> 
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-- 
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

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Re: [R-SIG-Mac] Building R-devel from source (solved)

[peter dalgaard]

OK, I now got a clang7 build running on a machine here too.

Simon, if you are listening: The alternative instructions to installing SDK to 
/usr/include seems to be incomplete. With

CPPFLAGS="-isysroot 
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"

I got a succesful compile, but the link phase dies looking for -lSystem or 
somesuch. I.e., I think something needs to happen with LDFLAGS as well. This of 
course only shows up if you do not install the SDK to /usr/include.

-pd

> On 19 Aug 2019, at 11:54 , Göran Broström  wrote:
> 
> Here is the report I promised. I followed the path below:
> 
> 1. Got source from CRAN.
> 
> 2. Read instructions under "Download R for (Mac) OS X"
> (shouldn't that read "Download R for macOS" nowadays?). Especially the note 
> Important: "If you wish to compile R packages ..., see the tools directory."
> 
> 3. In the tools directory: Download and install clang-7.0.0.pkg (I see now 
> that I should have chosen clang-8.0.0 for R 3.7.0, which is R-devel?). Also 
> download and install gfortran-6.1.pkg (It says: "To be used with El Capitan 
> builds of R.", which worried me a little, since I am on High Sierra, but 
> there were no alternatives.)
> 
> With this setup I got my first reported error. Thanks to Peter, I went on to
> 
> https://cran.r-project.org/doc/manuals/r-release/Radmin.html#macOS,
> 
> where I read
> 
> --
> One way to use these builds with a binary distribution of R is to have a 
> ~/.R/Makevars file similar to (El Capitan)
> 
> 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
> 
> or (Sierra or High Sierra)
> 
> FC = /usr/local/gfortran/bin/gfortran
> FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0
>  -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
> --
> 
> I naively chose the "Sierra or High Sierra" alternative, but that was wrong 
> as you can see: It apparently refers to gfortran 6.3, so I switched to the 
> the "El Capitan" alternative.
> 
> The final error message was then something about 'unable to compile mixed C 
> and Fortran code', and that was fixed by changing
> 
> LDFLAGS="-L/usr/local/clang7/lib -L/usr/local/lib"
> 
> to
> 
> LDFLAGS="-L/usr/local/clang7/lib -L/usr/local/gfortran/lib
> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0"
> 
> and voila, ./configure run without complaints!
> 
> The later build also went smoothly (but I had to install java).
> 
> So, to sum up, there seems to be some discrepancy between the two
> instruction sets I tried to follow.
> 
> Göran
> 
> 
> 
> 
> Den 2019-08-19 kl. 00:06, skrev Göran Broström:
>> Den 2019-08-18 kl. 22:16, skrev peter dalgaard:
>>> /usr/local/clang7 is likely a better place to look. Check out Appendix C.3 
>>> of the R Inst. manual:
>>> 
>>> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS
>> That's better! After correcting some obvious(?) errors(?) in that page, 
>> ./configure run without errors! (Had only read mac.r-procject.org/tools/ so 
>> far).
>> After a night's sleep I will 'make'. I'll report back to r-sig-mac.
>> Thanks, Göran
>>> 
>>> -pd
>>> 
>>>> On 18 Aug 2019, at 21:35 , Göran Broström  wrote:
>>>> 
>>>> Update: There is a libgcc_s.1.dylib in /usr/lib, as a symlink to 
>>>> /usr/lib/libSystem.B.dylib. Is that one useful?
>>>> 
>>>> Göran
>>>> 
>>>> Den 2019-08-18 kl. 18:54, skrev Göran Broström:
>>>>> Thanks Peter,
>>>>> The tripping lines are here
>>>>> configure:24611: checking size of size_t
>>>>> configure:24616: gcc -o conftest -g -O2 -I/usr/local/include 
>>>>> -L/usr/local/lib conftest.c -ldl -lm  >\
>>>>> &5
>>>>> configure:24616: $? = 0
>>>>> configure:24616: ./conftest
>>>>> dyld: Library not loaded: /usr/local/lib/libgcc_s.1.dylib
>>>>>Referenced from: /Users/gb/R/src/R-devel/./conftest
>>>>>Reason: image not found
>>>>> so it seems as if my installation of tools is lacking an essential part 
>>>>> (/usr/local/lib/libgcc_s.1.dylib). I'll look around, but any suggestion 
>>>>> is welcome!
>>>>> Göran
>>>>> Den 2019-08-18 kl. 17:56, skrev peter dalgaard:
>>>>>> I can't claim to understand this, but on my system of same age, using 
>>>&

Re: [R-SIG-Mac] Building R-devel from source

[peter dalgaard]

/usr/local/clang7 is likely a better place to look. Check out Appendix C.3 of 
the R Inst. manual:

https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS

-pd

> On 18 Aug 2019, at 21:35 , Göran Broström  wrote:
> 
> Update: There is a libgcc_s.1.dylib in /usr/lib, as a symlink to 
> /usr/lib/libSystem.B.dylib. Is that one useful?
> 
> Göran
> 
> Den 2019-08-18 kl. 18:54, skrev Göran Broström:
>> Thanks Peter,
>> The tripping lines are here
>> configure:24611: checking size of size_t
>> configure:24616: gcc -o conftest -g -O2 -I/usr/local/include 
>> -L/usr/local/lib conftest.c -ldl -lm  >\
>> &5
>> configure:24616: $? = 0
>> configure:24616: ./conftest
>> dyld: Library not loaded: /usr/local/lib/libgcc_s.1.dylib
>>   Referenced from: /Users/gb/R/src/R-devel/./conftest
>>   Reason: image not found
>> so it seems as if my installation of tools is lacking an essential part 
>> (/usr/local/lib/libgcc_s.1.dylib). I'll look around, but any suggestion is 
>> welcome!
>> Göran
>> Den 2019-08-18 kl. 17:56, skrev peter dalgaard:
>>> I can't claim to understand this, but on my system of same age, using 
>>> system clang, configure does complete. It does get that error on line 
>>> 23748, but that, and several similar subsequent tests just end up returning 
>>> "yes".
>>> 
>>> configure:23748: checking for size_t
>>> configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c 
>>> >&5
>>> configure:23748: $? = 0
>>> configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c 
>>> >&5
>>> conftest.c:118:21: error: expected expression
>>> if (sizeof ((size_t)))
>>>  ^
>>> 1 error generated.
>>> [..snip..]
>>> configure:23748: result: yes
>>> 
>>> (as usual, configure code is nigh on unreadable, but I think the logic is 
>>> that the size_t type exists if you can do "sizeof (size_t)", but not 
>>> "sizeof ((size_t))", so the error is expected.)
>>> 
>>> The line that trips you up comes later:
>>> 
>>> configure:24611: checking size of size_t
>>> configure:24616: gcc -arch x86_64 -o conftest -g -O2 -I/usr/local/include 
>>> -L/usr/
>>> local/lib conftest.c -ldl -lm  >&5
>>> configure:24616: $? = 0
>>> configure:24616: ./conftest
>>> configure:24616: $? = 0
>>> configure:24630: result: 8
>>> 
>>> so that is where you should look for clues (or at least tell us what it 
>>> says there).
>>> 
>>> -pd
>>> 
>>>> On 18 Aug 2019, at 13:34 , Göran Broström  wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> I'm (for the first time) trying to build R-devel from source (to be able 
>>>> to check my CRAN packages on a Mac), but it breaks already after
>>>> 
>>>> gobr0002@MBP-2:~/R/src/R-devel$ ./configure
>>>> 
>>>> with
>>>> 
>>>> checking size of size_t... configure: error: in `/Users/gb/R/src/R-devel':
>>>> configure: error: cannot compute sizeof (size_t)
>>>> See `config.log' for more details
>>>> 
>>>> Some 'details' regarding size_t:
>>>> 
>>>> configure:23748: checking for size_t
>>>> configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5
>>>> configure:23748: $? = 0
>>>> configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5
>>>> conftest.c: In function 'main':
>>>> conftest.c:116:21: error: expected expression before ')' token
>>>> if (sizeof ((size_t)))
>>>>  ^
>>>> 
>>>> My MacBook Pro is old (2010), so I am stuck with MacOS 10.13.6, XCode 
>>>> 10.1. I'm using clang 7.0.0 and fortran 6.1.0.
>>>> 
>>>> Do I need to buy a new Mac?
>>>> 
>>>> Thanks, Göran
>>>> 
>>>> ___
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>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
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Re: [R-SIG-Mac] Building R-devel from source

[peter dalgaard]

I can't claim to understand this, but on my system of same age, using system 
clang, configure does complete. It does get that error on line 23748, but that, 
and several similar subsequent tests just end up returning "yes". 

configure:23748: checking for size_t
configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5
configure:23748: $? = 0
configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5
conftest.c:118:21: error: expected expression
if (sizeof ((size_t)))
^
1 error generated.
[..snip..]
configure:23748: result: yes

(as usual, configure code is nigh on unreadable, but I think the logic is that 
the size_t type exists if you can do "sizeof (size_t)", but not "sizeof 
((size_t))", so the error is expected.) 

The line that trips you up comes later:

configure:24611: checking size of size_t
configure:24616: gcc -arch x86_64 -o conftest -g -O2 -I/usr/local/include 
-L/usr/
local/lib conftest.c -ldl -lm  >&5
configure:24616: $? = 0
configure:24616: ./conftest
configure:24616: $? = 0
configure:24630: result: 8

so that is where you should look for clues (or at least tell us what it says 
there).

-pd

> On 18 Aug 2019, at 13:34 , Göran Broström  wrote:
> 
> Hello,
> 
> I'm (for the first time) trying to build R-devel from source (to be able to 
> check my CRAN packages on a Mac), but it breaks already after
> 
> gobr0002@MBP-2:~/R/src/R-devel$ ./configure
> 
> with
> 
> checking size of size_t... configure: error: in `/Users/gb/R/src/R-devel':
> configure: error: cannot compute sizeof (size_t)
> See `config.log' for more details
> 
> Some 'details' regarding size_t:
> 
> configure:23748: checking for size_t
> configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5
> configure:23748: $? = 0
> configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5
> conftest.c: In function 'main':
> conftest.c:116:21: error: expected expression before ')' token
> if (sizeof ((size_t)))
> ^
> 
> My MacBook Pro is old (2010), so I am stuck with MacOS 10.13.6, XCode 10.1. 
> I'm using clang 7.0.0 and fortran 6.1.0.
> 
> Do I need to buy a new Mac?
> 
> Thanks, Göran
> 
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Re: [R-SIG-Mac] point size in svg

[peter dalgaard]

Works fine for me on 10.14.5, both with CRAN-supplied 3.6.0 and locally 
compiled  3.6.0 Patched (2019-06-23 r76734).

I suspect that you might have a font misconfiguration of sorts on your Mojave 
machine.

-pd

> On 24 Jun 2019, at 09:25 , Spencer Graves  wrote:
> 
> �� Thanks to David Winsemius for his reply.� His attachment came 
> through and displayed consistent with the R documentation.� Thus, the 
> cex.axis and cex arguments work fine with R 3.5.1 (2018-07-02) and 
> "Feather Spray" on OS X 10.11.6, but they don't work properly with the 
> current version of R under the current version of macOS.
> 
> 
> �� Spencer
> 
> 
> On 2019-06-24 00:59, David Winsemius wrote:
>>> On Jun 23, 2019, at 10:04 PM, Spencer Graves  
>>> wrote:
>>> 
>>> Hello, All:
>>> 
>>> 
>>>   I'm unable to control font size in plots created by "svg" in R 3.6.0 
>>> on macOS Mojave 10.14.5.  Consider the following:
>>> 
>>> 
>>> svg('cex-svg.svg')
>>> cex. <- 5
>>> plot(1:2, cex.axis=cex.)
>>> text(1:2, 1:2, c('as', 'DF'),
>>>   cex=cex.)
>>> dev.off()
>>> 
>>> 
>>>   When I run this in R 3.5.2 under Windows 7, it works fine.  In R 
>>> 3.6.0 under macOS 10.14.5, I get tiny fonts.  Changing "cex." has no impact 
>>> on the result.  A question about this to R-Devel generated replies from 
>>> Peter Langfelder and David Winsemius, who noted that it worked fine under 
>>> Ubuntu 18.04 (supposedly with R 3.15.2 -- probably R 3.5.2, but I'm not 
>>> sure).
>> You should be sure.
>> 
>>>  I experimented with the width, height, pointsize and family arguments for 
>>> "svg", without solving this problem.
>> With R version 3.5.1 (2018-07-02) -- "Feather Spray" on OS X 10.11.6 I am 
>> unable to reproduce. My Mac hardware is considered well past (Apple) end of 
>> life despite its functionality, so I cannot upgrade my OS. I'm attaching the 
>> file that is the result so Spencer can view it, although I suspect it will 
>> be scrubbed by the mail-server.
>> 
>> 
>> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Warning on XCode / Command Line Tools 11

[peter dalgaard]

[Forgot-to-click-send-syndrome...]

OK, I suspected that it might be retracted by Apple (auto-update is turned off 
on this machine).

Re. time frame, it seems that "Apple fall" is like late September. I recall us 
getting caught  by having a release scheduled too close to be able to fix 
Apple-induced incompatibilities. (Presumably that was 3.4.2 on Sep 28 and the 
issue was time zone file location.)

-pd

> On 6 Jun 2019, at 11:19 , Prof Brian Ripley  wrote:
> 
> On 06/06/2019 09:31, peter dalgaard wrote:
>> FWIW, no updates are suggested for the source-building machine in my office, 
>> also running Mojave. (June 5 was Constitution Day and Election Day, so I 
>> have been away from the machine until now.)
> 
> It stopping nagging me yesterday afternoon, so likely it was an Apple snafu.  
> (I heard from others who had been caught by this, and of course Apple allows 
> for 'automatic' updating so this could happen in the background.)
> 
>> We do need to keep an eye on the tools though. My current setup is an  -um- 
>> eclectic mix (*) of old and new tools, some of which are 32 bit, and this is 
>> going to be a problem in 10.15 Catalina. I did try getting the tools better 
>> in line with Simon's setup at some point, but there were hiccups and then I 
>> ran out of time and couldn't risk collateral damage.
> 
> You have a few months yet.  The residual 32-bit applications I have are from 
> Adobe, e.g. old uninstallers.
> 
>> -pd
>> (*) ="dogs dinner"
>>> On 4 Jun 2019, at 17:10 , Prof Brian Ripley  wrote:
>>> 
>>> My Mojave machine today prompted me to update to version 11 of Command Line 
>>> Tools (apparently 'beta 1', but I am not a Beta tester).
>>> 
>>> In short: don't do that (you can revert to 10.2.1 from the URL above, at 
>>> least if your Apple ID has (free) developer privileges).
>>> 
>>> CoreFoundation.framework has been removed (and its headers are used in a 
>>> couple of spots compiling R).
>>> 
>>> Further its seems that 
>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>  is no longer included and setting CPPFLAGS did not suffice.
>>> 
>>> Hopefully we will have solutions in due course, but that version is really 
>>> for 10.15 Catalina which is months away ('in the Fall', whenever that is).
>>> 
>>> -- 
>>> Brian D. Ripley,  rip...@stats.ox.ac.uk
>>> Emeritus Professor of Applied Statistics, University of Oxford
>>> 
>>> ___
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>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford

-- 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
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Re: [R-SIG-Mac] Warning on XCode / Command Line Tools 11

[peter dalgaard]

FWIW, no updates are suggested for the source-building machine in my office, 
also running Mojave. (June 5 was Constitution Day and Election Day, so I have 
been away from the machine until now.)

We do need to keep an eye on the tools though. My current setup is an  -um- 
eclectic mix (*) of old and new tools, some of which are 32 bit, and this is 
going to be a problem in 10.15 Catalina. I did try getting the tools better in 
line with Simon's setup at some point, but there were hiccups and then I ran 
out of time and couldn't risk collateral damage.

-pd


(*) ="dogs dinner"

> On 4 Jun 2019, at 17:10 , Prof Brian Ripley  wrote:
> 
> My Mojave machine today prompted me to update to version 11 of Command Line 
> Tools (apparently 'beta 1', but I am not a Beta tester).
> 
> In short: don't do that (you can revert to 10.2.1 from the URL above, at 
> least if your Apple ID has (free) developer privileges).
> 
> CoreFoundation.framework has been removed (and its headers are used in a 
> couple of spots compiling R).
> 
> Further its seems that 
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>  is no longer included and setting CPPFLAGS did not suffice.
> 
> Hopefully we will have solutions in due course, but that version is really 
> for 10.15 Catalina which is months away ('in the Fall', whenever that is).
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
> ___
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-- 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
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Re: [R-SIG-Mac] Problem with Devel version (R 3.6) for Mac OS X

[peter dalgaard]

2)
>>> Bluetooth: Version 4.4.6f4, 3 services, 19 devices, 1 incoming serial ports
>>> Network Service: AirPort, AirPort, en0
>>> Serial ATA Device: APPLE SSD SM0512G, 500.28 GB
>>> USB Device: USB 3.0 Bus
>>> USB Device: BRCM20702 Hub
>>> USB Device: Bluetooth USB Host Controller
>>> Thunderbolt Bus: MacBook Air, Apple Inc., 27.2
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> [[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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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
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Re: [R-SIG-Mac] R 3.5.3 pkg not signed

[peter dalgaard]

Your note seems to have stalled somewhere. It arrived here today (the 19th).

Anyways, this was a temporary situation, the signed package should have reached 
all of CRAN by now:

pd$ pkgutil --check-signature ~/.Trash/R-3.5.3-2.pkg
Package "R-3.5.3-2.pkg":
   Status: signed by a certificate trusted by Mac OS X
   Certificate Chain:
1. Developer ID Installer: Simon Urbanek (VZLD955F6P)
   SHA1 fingerprint: 7B 6B 81 12 E6 26 8C 16 F8 D4 0F 94 E4 3E 62 69 2E 92 
22 81
   
-
2. Developer ID Certification Authority
   SHA1 fingerprint: 3B 16 6C 3B 7D C4 B7 51 C9 FE 2A FA B9 13 56 41 E3 88 
E1 86
   
-
3. Apple Root CA
   SHA1 fingerprint: 61 1E 5B 66 2C 59 3A 08 FF 58 D1 4A E2 24 52 D1 98 DF 
6C 60

-pd


> On 14 Mar 2019, at 13:12 , Christopher Helming  wrote:
> 
> The 3.5.2 pkg was signed properly:
> $ pkgutil --check-signature ~/Downloads/R-3.5.2.pkg
> Package "R-3.5.2.pkg":
>   Status: signed by a certificate trusted by Mac OS X
>   Certificate Chain:
>1. Developer ID Installer: Simon Urbanek (VZLD955F6P)
>   SHA1 fingerprint: 7B 6B 81 12 E6 26 8C 16 F8 D4 0F 94 E4 3E 62 69 2E 92 
> 22 81
>   
> -
>2. Developer ID Certification Authority
>   SHA1 fingerprint: 3B 16 6C 3B 7D C4 B7 51 C9 FE 2A FA B9 13 56 41 E3 88 
> E1 86
>   
> -
>3. Apple Root CA
>   SHA1 fingerprint: 61 1E 5B 66 2C 59 3A 08 FF 58 D1 4A E2 24 52 D1 98 DF 
> 6C 60
> 
> But the 3.5.3 pkg has no signature:
> $ pkgutil --check-signature ~/Downloads/R-3.5.3.pkg
> Package "R-3.5.3.pkg":
>   Status: no signature
> 
> Is it possible to get 3.5.3 signed and replace the file on the download page?
> 
> Chris Helming
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] R 3.5.3 macOS binary not signed?

[peter dalgaard]

The version from mac.R-project.org installs fine. CRAN master still has the 
unsigned version (recognizable by an MD5 hash starting with fff) at this point.

-pd

> On 14 Mar 2019, at 14:36 , Simon Urbanek  wrote:
> 
> Marc,
> 
> thanks, I'm glad that at least someone pays attention and checks the 
> signature ;). I'm surprised my machine didn't raise a flag - I did test the 
> image locally from the master URL before releasing.
> 
> I have now updated the package to be signed, it is identical content, just 
> signed. You can get is from the Mac master server 
> https://mac.R-project.org/bin/macosx now and other CRAN servers will sync in 
> due time.
> 
> Thanks,
> Simon
> 
> 
> 
>> On Mar 14, 2019, at 8:18 AM, 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] R 3.5.3 macOS binary not signed?

[peter dalgaard]

[Resending - screenshot was too big]

Actually, the OS does that even if we don't pay attention, so apparently people 
just haven't gotten around to upgrade and we haven't had new Mac users 
installing 3.5.3 yet. (To a first approximation, that is - some will of course 
know how to bypass the signature check). 

-pd

> On 14 Mar 2019, at 14:36 , Simon Urbanek  <mailto:simon.urba...@r-project.org>> wrote:
> 
> Marc,
> 
> thanks, I'm glad that at least someone pays attention and checks the 
> signature ;). I'm surprised my machine didn't raise a flag - I did test the 
> image locally from the master URL before releasing.
> 
> I have now updated the package to be signed, it is identical content, just 
> signed. You can get is from the Mac master server 
> https://mac.R-project.org/bin/macosx <https://mac.r-project.org/bin/macosx> 
> now and other CRAN servers will sync in due time.
> 
> Thanks,
> Simon
> 
> 
> 
>> On Mar 14, 2019, at 8:18 AM, Marc Schwartz via R-SIG-Mac 
>> mailto:r-sig-mac@r-project.org>> 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] libcurl

[peter dalgaard]

Hmm, how did "@rpath" get in there? I don't see it anywhere in my build and 
source dirs. Looks like something that should have been substituted (by perl?) 
with the appropriate path.

Is your library (...anaconda3/lib) correctly installed? I have, for the system 
libcurl:

pd$ ls -l /usr/lib/*curl*
lrwxr-xr-x  1 root  wheel  15 Nov 14 14:36 /usr/lib/libcurl.3.dylib -> 
libcurl.4.dylib
-rwxr-xr-x  1 root  wheel  854208 Nov 30 08:37 /usr/lib/libcurl.4.dylib
lrwxr-xr-x  1 root  wheel  15 Nov 14 14:36 /usr/lib/libcurl.dylib -> 
libcurl.4.dylib

-pd


> On 25 Feb 2019, at 01:28 , robin hankin  wrote:
> 
> thanks for this Peter, my config.log file looks like this:
> 
> configure:42615: result: yes
> configure:42629: checking if libcurl is version 7 and >= 7.22.0
> configure:42658: gcc -o conftest  -g -O2
> -I/Users/rhankin/anaconda3/include -I/usr/local/include
> -I/usr/local/include  -L/usr/local/lib conftest.c
> -L/Users/rhankin/anaconda3/lib -lcurl -lssh2 -lssh2 -lssl -lcrypto
> -lssl -lcrypto -lgssapi_krb5 -lresolv -lz -L/usr\
> /local/lib -lpcre2-8 -lpcre -llzma -lbz2 -lz -licucore -ldl -lm  -liconv >&5
> configure:42658: $? = 0
> configure:42658: ./conftest
> dyld: Library not loaded: @rpath/libcurl.4.dylib
>  Referenced from: /Users/rhankin/Downloads/R-devel/./conftest
>  Reason: image not found
> ./configure: line 2254: 73408 Abort trap: 6   ./conftest$ac_exeext
> configure:42658: $? = 134
> configure: program exited with status 134
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "R"
> | #define PACKAGE_TARNAME "R"
> 
> 
> 
> Best wishes
> 
> 
> Robin
> 
> 
> hankin.ro...@gmail.com
> 
> 
> 
> hankin.ro...@gmail.com
> 
> 
> 
> 
> On Mon, Feb 25, 2019 at 11:41 AM peter dalgaard  wrote:
>> 
>> It doesn't usually happen on 10.13.6... Best guess is that somehow you are 
>> picking up an older library (e.g. in /usr/local/lib) even if you are using 
>> curl-config from a newer version.
>> 
>> The detective work needed could take off from config.log, region around this:
>> 
>> configure:39937: checking if libcurl is version 7 and >= 7.22.0
>> configure:39966: gcc -arch x86_64 -o conftest -g -O2   -I/usr/local/include  
>> -L/usr/local/lib conftest.c -lcurl -lpcre -llzma -lbz2 -lz -licucore -lm  
>> -liconv >&5
>> configure:39966: $? = 0
>> configure:39966: ./conftest
>> configure:39966: $? = 0
>> configure:39976: result: yes
>> 
>> That's for a succesful build, a failed one will usually give more info 
>> including the failing program code.
>> 
>> -pd
>> 
>>> On 24 Feb 2019, at 22:45 , robin hankin  wrote:
>>> 
>>> Hi,  macos 10.13.6, trying to compile 3.6.0, revision 76152.
>>> 
>>> ./configure
>>> [snip]
>>> 
>>> checking for curl-config... /Users/rhankin/anaconda3/bin/curl-config
>>> checking libcurl version ... 7.63.0
>>> checking curl/curl.h usability... yes
>>> checking curl/curl.h presence... yes
>>> checking for curl/curl.h... yes
>>> checking if libcurl is version 7 and >= 7.22.0... no
>>> configure: error: libcurl >= 7.22.0 library and headers are required
>>> with support for https
>>> 
>>> if we have libcurl 7.63, as it says in the output, why the error?  How
>>> to proceed?
>>> 
>>> hankin.ro...@gmail.com
>>> 
>>> ___
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>>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 

-- 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
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Re: [R-SIG-Mac] libcurl

[peter dalgaard]

It doesn't usually happen on 10.13.6... Best guess is that somehow you are 
picking up an older library (e.g. in /usr/local/lib) even if you are using 
curl-config from a newer version.

The detective work needed could take off from config.log, region around this:

configure:39937: checking if libcurl is version 7 and >= 7.22.0
configure:39966: gcc -arch x86_64 -o conftest -g -O2   -I/usr/local/include  
-L/usr/local/lib conftest.c -lcurl -lpcre -llzma -lbz2 -lz -licucore -lm  
-liconv >&5
configure:39966: $? = 0
configure:39966: ./conftest
configure:39966: $? = 0
configure:39976: result: yes

That's for a succesful build, a failed one will usually give more info 
including the failing program code.

-pd

> On 24 Feb 2019, at 22:45 , robin hankin  wrote:
> 
> Hi,  macos 10.13.6, trying to compile 3.6.0, revision 76152.
> 
> ./configure
> [snip]
> 
> checking for curl-config... /Users/rhankin/anaconda3/bin/curl-config
> checking libcurl version ... 7.63.0
> checking curl/curl.h usability... yes
> checking curl/curl.h presence... yes
> checking for curl/curl.h... yes
> checking if libcurl is version 7 and >= 7.22.0... no
> configure: error: libcurl >= 7.22.0 library and headers are required
> with support for https
> 
> if we have libcurl 7.63, as it says in the output, why the error?  How
> to proceed?
> 
> hankin.ro...@gmail.com
> 
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Re: [R-SIG-Mac] Different performance with different R versions

[Peter Dalgaard]

I don't think there has been anything mentioned about slowdowns of that 
magnitude, but it's been 3.5 years since 3.1.3.

Would it be possible to narrow down what kind of code has become slow? 

Since the OS version is different, I assume the first timing is historical and 
not easily redone, but if it is now using like 70 times as long as before, 
chances are that it is spending 69/70 of the time in the same few places.

One generic frequent cause of grief with simulations is to keep onto the fitted 
models in entirety, including model frames etc., causing massive memory 
build-up.

-pd

> On 12 Dec 2018, at 17:39 , Cowan, R (MERIT)  
> wrote:
> 
> I am running a small simulation, and getting very different run times when I 
> use different versions of R. 
>   Two set-ups using the same machine (MacBook Pro 2013 vintage)
> 
>   1. R version 3.1.3  running on system OS X 10.9.5
> 
>> system.time(source("simulationR-R.R"))
> 
> user  system elapsed 
> 3.890   0.061   3.965 
> 
>   Compared to
> 
>   2. R version 3.5.1  running on system OS X 10.12.6
> 
>> system.time(source("simulationR-R.R"))
> 
> user  system elapsed 
>   277.924   2.087 280.841 
> 
> The source code is identical. This is a pretty big difference running the 
> same code on the same hardware.
> Before submitting the code, is this a known issue?
> 
> 
> Thanks,
> Robin Cowan
> _______
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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
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Re: [R-SIG-Mac] Blank help window

[Peter Dalgaard]

What? Are they born that way, or does Migration Assistent bungle things up? Or 
maybe OpenVPN does?

Anyways, try adding a line saying

127.0.0.1   localhost

-pd

> On 19 Oct 2018, at 00:34 , Ben Tupper  wrote:
> 
> Hi,
> 
> 
> ben@gale ~ $ ping localhost
> ping: cannot resolve localhost: Unknown host
> 
> Here's /etc/hosts in its entirety.
> 
> ben@gale ~ $ more /etc/hosts
> # BEGIN section for OpenVPN Client SSL sites
> 127.94.0.1  client.openvpn.net
> 127.94.0.2  openvpn-client.vpn.bigelow.org
> # END section for OpenVPN Client SSL sites
> 
> I'm not currently using VPN.
> 
> 
>> On Oct 18, 2018, at 6:29 PM, peter dalgaard  wrote:
>> 
>> Cannot _find_ localhost?? Can you do this (in a Terminal window) ?
>> 
>> Peter-Dalgaards-MacBook-Air:STAT pd$ ping localhost
>> PING localhost (127.0.0.1): 56 data bytes
>> Request timeout for icmp_seq 0
>> Request timeout for icmp_seq 1
>> ^C
>> --- localhost ping statistics ---
>> 3 packets transmitted, 0 packets received, 100.0% packet loss
>> 
>> If not, what is in the first couple of lines in /etc/hosts?
>> 
>> -pd
>> 
>>> On 19 Oct 2018, at 00:09 , Ben Tupper  wrote:
>>> 
>>> Just a little followup.  Switching the default browser from Firefox to 
>>> Safari yields a similar message in the browser after...
>>> 
>>> Browse[2]> browseURL(x)
>>> 
>>> 'Safari can't open the page "localhost:29682/library/utils/html/help.html"
>>> because Safari can't find the server "localhost".'
>>> 
>> 
>> -- 
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
> 
> Ecological Forecasting: https://eco.bigelow.org/
> 
> 
> 
> 
> 

-- 
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

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Re: [R-SIG-Mac] Blank help window

[peter dalgaard]

Cannot _find_ localhost?? Can you do this (in a Terminal window) ?

Peter-Dalgaards-MacBook-Air:STAT pd$ ping localhost
PING localhost (127.0.0.1): 56 data bytes
Request timeout for icmp_seq 0
Request timeout for icmp_seq 1
^C
--- localhost ping statistics ---
3 packets transmitted, 0 packets received, 100.0% packet loss

If not, what is in the first couple of lines in /etc/hosts?

-pd

> On 19 Oct 2018, at 00:09 , Ben Tupper  wrote:
> 
> Just a little followup.  Switching the default browser from Firefox to Safari 
> yields a similar message in the browser after...
> 
> Browse[2]> browseURL(x)
> 
> 'Safari can't open the page "localhost:29682/library/utils/html/help.html"
> because Safari can't find the server "localhost".'
> 

-- 
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

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Re: [R-SIG-Mac] Blank help window

[Peter Dalgaard]

 by Brew which I 
>>>> installed manually.
>>>> 
>>>> An issue with R arose I can't solve.  The help systen opens with a blank 
>>>> window.
>>>> 
>>>> Help works when I run R from the terminal so I know the files are 
>>>> installed.  Help works fine on the Macintosh I used a the source for the 
>>>> migration so it isn't a problem I inherited.  Re-installing R (see 
>>>> sessionInfo below) didn't solve the problem.
>>>> 
>>>> Anyone have any suggestions how I can get help to work?
>>>> 
>>>> 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
>>>> 
>>>> Matrix products: default
>>>> BLAS: 
>>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>>> LAPACK: 
>>>> /Library/Frameworks/R.framework/Versions/3.5/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 
>>>> 
>>>> other attached packages:
>>>> [1] HANDLS_0.34 zUtil_0.121
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
>>>> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
>>>> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
>>>> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
>>>> [17] Matching_4.9-3  bit64_0.9-7 foreign_0.8-70  bit_1.1-14 
>>>> [21] compiler_3.5.1  maptools_0.9-2  memoise_1.1.0  
>>>> 
>>>> ___
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>>>> R-SIG-Mac@r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
> 
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
> 
> Ecological Forecasting: https://eco.bigelow.org/
> 
> 
> 
> 
> 

-- 
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

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Re: [R-SIG-Mac] Blank help window

[Peter Dalgaard]

Hum, it's not like it cannot work (on iMac running High Sierra):

> help("help") # works fine

You might want to check if anything is non-TRUE here:

> capabilities()
   jpeg pngtiff   tcltk X11aqua
http/ftp sockets 
   TRUETRUETRUETRUETRUETRUE
TRUETRUE 
 libxmlfifo  cledit   iconv NLS profmem   
cairo ICU 
   TRUETRUETRUETRUETRUETRUE
TRUETRUE 
long.double libcurl 
   TRUETRUE 

And you seem to have more than the defaults attached, I only have compiler and 
tools. Perhaps check ~/.RData and config files?:

> sessionInfo()
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

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.5/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   base 

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1   


-pd

> On 17 Oct 2018, at 01:11 , zListserv  wrote:
> 
> 
> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
> Assistant.  Everything went well, though there are always a few things that 
> don't transfer such as applications installed by Brew which I installed 
> manually.
> 
> An issue with R arose I can't solve.  The help systen opens with a blank 
> window.
> 
> Help works when I run R from the terminal so I know the files are installed.  
> Help works fine on the Macintosh I used a the source for the migration so it 
> isn't a problem I inherited.  Re-installing R (see sessionInfo below) didn't 
> solve the problem.
> 
> Anyone have any suggestions how I can get help to work?
> 
> 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
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/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 
> 
> other attached packages:
> [1] HANDLS_0.34 zUtil_0.121
> 
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
> [17] Matching_4.9-3  bit64_0.9-7 foreign_0.8-70  bit_1.1-14 
> [21] compiler_3.5.1  maptools_0.9-2  memoise_1.1.0  
> 
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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
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Re: [R-SIG-Mac] pasting from the clipboard

[peter dalgaard]

read.table(text=my_str,) saves you the dangling open connection.

-pd

> On 8 Oct 2018, at 02:43 , Tom Hopper  wrote:
> 
> Another approach that should work cross-platform is to paste the data into
> a string, then read the string using read.table():
> 
> my_str <- ""
> my_df <- read.table(textConnection(object = my_str),
>header = TRUE,
>sep = "",
>stringsAsFactors = FALSE)
> 
> The pasted data should have line breaks so each row is on its own line in
> your script, and you'll want to adjust the parameters header and sep to
> suit your data.
> 
> An example of suitable data would be:
> 
> my_str <- "T_/K Density_g/mL D2O
> 273 0.999841 1.10469
> 274 0.00 NA
> 275 0.41 NA"
> 
> Regards,
> 
> Tom
> 
> On Wed, Oct 3, 2018 at 10:10 AM Marc Schwartz via R-SIG-Mac <
> r-sig-mac@r-project.org> wrote:
> 
>> 
>>> On Oct 3, 2018, at 9:22 AM, Robert Baer  wrote:
>>> 
>>> My memory is that  on the Mac
>>> 
>>> dat = read.table(file = pipe("pbpaste"), header = TRUE)  # should
>> allow me to paste a dataframe copied from a spreadsheet into R.
>>> 
>>> When I try that in RStudio 1.1.456 with R 3.5.1 on OSX 10.13.1
>>> 
>>> I get the message:
>>> 
>>>  incomplete line found by readTableHeader on 'pbpaste'
>>> 
>>> Could anyone explain this message to me,  and more importantly, tell me
>> the proper way to paste a dataframe copied to the clipboard from Excel on
>> the Mac?
>>> 
>>> 
>> 
>> 
>> Hi,
>> 
>> The default cell (field) delimiter with Excel is the TAB character, so you
>> want to use something like:
>> 
>>  read.table(pipe("pbpaste"), sep = "\t", header = TRUE)
>> 
>> Note that you will likely get a warning along the lines of what you got
>> above, which I believe is due to Excel not having an EOL for the final row
>> in the clipboard.
>> 
>> Regards,
>> 
>> Marc Schwartz
>> 
>> 
>> 
>> 
>>[[alternative HTML version deleted]]
>> 
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>> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)

[peter dalgaard]

[Oops. Forgot to copy this back to R-sig-mac, it seems...]

Thanks, Brian,

Yes, we have previously learned the hard way that timing R releases too close 
to MacOS updates is a bad idea...

The manual updates haven't made it to CRAN yet, you need to look in the 
sources. 

For those who might be curious, but lazy:

>>>> 
As from macOS 10.14 (‘Mojave’) an additional step is needed to install the 
headers to /usr/include: from a Terminal run

sudo installer -pkg \
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
 \
-target /

Alternatively, change the include path via

CPPFLAGS="-isystem 
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
<<<<


Incidentally, probably unrelated, I discovered that the R-patched snapshots had 
stalled since Sep 13 due to an SVN database error. This should be cleared up 
now.

-pd 

> On 25 Sep 2018, at 08:59 , Prof Brian Ripley  wrote:
> 
> A heads up:
> 
> The Mojave update removes /usr/include and (re)installing the Command Line 
> Tools does not put the standard system headers there.  Workarounds are now 
> described in the R-admin manual for R-devel and R-patched.
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
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Re: [R-SIG-Mac] SHA-1 Hash for R-3.5.0.pkg Incorrect

[peter dalgaard]

For whatever it is worth, I am using shasum -a 256 for the source release 
announcements.

-pd

> On 25 Apr 2018, at 22:37 , Marc Schwartz <marc_schwa...@me.com> wrote:
> 
> Hi Simon,
> 
> Thanks for the explanation.
> 
> It did not occur to me that SHA-0 was being used, since it was withdrawn as a 
> standard circa early 90's, after significant flaws were identified.
> 
> Apple (and others) either have or are moving away from SHA-1 to SHA-2, at 
> least for TLS/PKI security:
> 
>  https://support.apple.com/en-us/HT207459 
> <https://support.apple.com/en-us/HT207459>
> 
> recognizing the differences between session specific TLS/PKI trust uses and 
> longer term file integrity checking. I know Linus is more "relaxed" regarding 
> SHA-1 and the implications for Git, or at least was last year, albeit 
> indicating a path away from it in time.
> 
> I guess the question boils down to, if we are going to provide hashes of the 
> files under the premise that it should offer a high level of comfort to useRs 
> that the file has not been modified/replaced since generation, presuming that 
> the published hash value itself was not altered, I would put forth for 
> further discussion, moving to SHA-2 and away from both MD5 and SHA-1 
> (certainly moving away from SHA-0), depending upon a more broad assessment of 
> the implications of doing so.
> 
> Thanks!
> 
> Marc
> 
> 
>> On Apr 25, 2018, at 2:54 PM, Simon Urbanek <simon.urba...@r-project.org> 
>> wrote:
>> 
>> Marc,
>> 
>> thanks, the issue is:
>> 
>> hagal:R-3.5.0$ openssl sha R-3.5.0-el-capitan-signed.pkg
>> SHA(R-3.5.0-el-capitan-signed.pkg)= 9f5f3365afee54d3fe3148a60c1405955916f076
>> 
>> hagal:R-3.5.0$ openssl sha1 R-3.5.0-el-capitan-signed.pkg
>> SHA1(R-3.5.0-el-capitan-signed.pkg)= 6e90d38892bb366630ae30c223a898e8af84dff7
>> 
>> so either we change the label to SHA (or SHA-0?) or change the checksum. In 
>> the root we actually provide both, even if that may or may not be relevant. 
>> For now I did the latter in the index.html.
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>> 
>> 
>>> On Apr 25, 2018, at 7:57 AM, Marc Schwartz <marc_schwa...@me.com> wrote:
>>> 
>>> Hi All,
>>> 
>>> Last month:
>>> 
>>> https://stat.ethz.ch/pipermail/r-sig-mac/2018-March/012691.html
>>> 
>>> there was a report that the SHA-1 hash of the R-3.4.4.pkg, as listed on 
>>> CRAN, was not correct, even though the MD5 hash and the digital signature 
>>> appeared to be correct.
>>> 
>>> The same phenomenon is the case with R-3.5.0.pkg.
>>> 
>>> The MD5 hash on CRAN is:
>>> 
>>> MD5-hash: 414029c9c9f706d3d04baa887ccffbc4 
>>> 
>>> and I get:
>>> 
>>> md5 R-3.5.0.pkg
>>> MD5 (R-3.5.0.pkg) = 414029c9c9f706d3d04baa887ccffbc4
>>> 
>>> from the CLI on my Mac.
>>> 
>>> However, the SHA-1 hash on CRAN is:
>>> 
>>> SHA-hash: 9f5f3365afee54d3fe3148a60c1405955916f076 
>>> 
>>> and I get:
>>> 
>>> shasum R-3.5.0.pkg
>>> 6e90d38892bb366630ae30c223a898e8af84dff7  R-3.5.0.pkg
>>> 
>>> from the CLI on my Mac.
>>> 
>>> It would seem that there is a lingering issue with the generation of the 
>>> SHA-1 hash value on CRAN.
>>> 
>>> Thanks,
>>> 
>>> Marc Schwartz
>>> 
>>> ___
>>> 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] package building

[peter dalgaard]

Or at the very least at 3.5.0 alpha, which happens a couple of weeks further 
down the line (schedule pending). 

-pd

> On 13 Mar 2018, at 08:24 , Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote:
> 
> In any case, package support for R-oldrel (3.3.x) officially finishes once 
> the following series (3.4.x) is signed off, which is on Thursday this week.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
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Re: [R-SIG-Mac] help: change of e-mail address

[peter dalgaard]

Um, no we can't! 

You are writing to all subscribers of the list and we cannot mess with 
eachother's subscriptions. 

In case of administrative trouble, you need 

>  r-sig-mac-ow...@r-project.org

However, are you _sure_ that it didn't work to follow the instructions at 
https://stat.ethz.ch/mailman/listinfo/r-sig-mac ?

Notice in particular that the system cannot retroactively change recipients on 
things that have already been sent, and that mails can sit in mailer queues for 
some time. I.e., you may recieve mails to the old address for a while until the 
new address takes effect.

-pd

> On 1 Feb 2018, at 08:39 , Hagens, M. (Mathilde) <m.hag...@uu.nl> wrote:
> 
> To whom it may concern,
> 
> I've been trying to change my e-mail address unsuccessfully via the World 
> Wide Web. Could you please change my e-mail address to 
> mathilde.hag...@wur.nl? 
> 
> Thank you,
> Mathilde
> 
> Dr. M. (Mathilde) Hagens | Assistant Professor | Department of Soil Quality | 
> Wageningen University & Research | Droevendaalsesteeg 4, 6708 PB Wageningen, 
> the Netherlands | tel. +31 317 487 775 | 
> www.wur.nl/en/Persons/Mathilde-dr.-M-Mathilde-Hagens.htm | Please note new 
> e-mail address: mathilde.hag...@wur.nl
> 
> 
> 
> From: R-SIG-Mac [r-sig-mac-boun...@r-project.org] on behalf of 
> r-sig-mac-requ...@r-project.org [r-sig-mac-requ...@r-project.org]
> Sent: Thursday, February 01, 2018 06:22
> To: r-sig-mac@r-project.org
> Subject: R-SIG-Mac Digest, Vol 180, Issue 1
> 
> Send R-SIG-Mac mailing list submissions to
>r-sig-mac@r-project.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> or, via email, send a message with subject or body 'help' to
>r-sig-mac-requ...@r-project.org
> 
> You can reach the person managing the list at
>r-sig-mac-ow...@r-project.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of R-SIG-Mac digest..."
> _______
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> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
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Re: [R-SIG-Mac] R 3.4.3 binaries

[peter dalgaard]

I would guess that either Uwe/CRAN is swamped or Simon is traveling to NZ, or 
both... 

-pd

> On 6 Dec 2017, at 10:26 , Federico Calboli <federico.calb...@helsinki.fi> 
> wrote:
> 
> Hi All,
> 
> I know that I can get the latest and greatest binaries from 
> http://r.research.att.com/ but I am puzzled why there are still no OSX R 
> 3.4.3 binaries on CRAN.  The Windows installer has been up a few days 
> already.  Is there anything I am missing concerning this delay?  
> 
> Cheers
> 
> F
> 
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-- 
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Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] Xcode 9

[peter dalgaard]

> On 27 Sep 2017, at 08:43 , Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote:
> 
> On 27/09/2017 03:28, Kasper Daniel Hansen wrote:
>> I don't see this with
>>   Xcode 9
>>   OS X Sierra (10.12.6)
>> and either
>> R Under development (unstable) (2017-09-26 r73351) -- "Unsuffered
>> Consequences"
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin16.7.0 (64-bit)
>> or
>> R version 3.4.2 RC (2017-09-26 r73351) -- "Short Summer"
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin16.7.0 (64-bit)
>> Specifically I can compile R and it passes make check.  Perhaps it got
>> fixed since the post.
> 
> It did (look at the logs for r73347 and r73351), but also we have discovered 
> that not all upgrades to Xcode 9 had the problem.
> 

Yes. My home desktop machine updated command line tools only and didn't see the 
problem. The laptop wants to upgrade the full Xcode (no idea how that came to 
be...) but claims to need another 1.66GB of disk to upgrade, so it is probably 
not in the cards to check a build there just now. The work machine had the 
problem until I downgraded to Xcode 8.3.3, but as this is the machine building 
the actual release, I'm not touching it until some weeks after the 3.4.2 
release.

Right now, we just override the configure detected utimensat() declaration on 
all Macs, which should be harmless (also on High Sierra, although we wouldn't 
claim to support an OS which was unreleased at the code freeze). We'll think of 
a better fix --- it looks like the Curl developers have fixed a similar issue, 
so we can copy their approach.

> While we are at it, there is a problem with finding the default time zone on 
> High Sierra.  This is worked around already in R-devel and will be in 3.4.2 
> patched: until then setting TZ is a good workaround (and that is in the 
> R-admin manual for 3.4.2 RC).
> 
>> On Fri, Sep 22, 2017 at 4:47 AM, peter dalgaard <pda...@gmail.com> wrote:
>>> Just a quick note: Xcode 9 will not presently create a working R on Sierra
>>> or earlier.
> 
> (I don't believe Xcode 9 is available for 'earlier'.)

You're probably right. I wasn't sure when I wrote that (& also not sure whether 
one could cross-compile.)

-pd

> 
>>> 
>>> This is because it ships with an SDK for 10.13 (unreleased) and defines an
>>> entry for utimensat(), which is not actually in the system library for
>>> earlier versions.
>>> 
>>> There is no way we can fix this reliably for the upcoming 3.4.2 release,
>>> so if you intend to build R from sources, either
>>> 
>>> - just do not upgrade, stay on Xcode 8.3.3
>>> 
>>> or
>>> 
>>> - manually remove the line from config.h saying
>>> 
>>> #define HAVE_UTIMENSAT 1
>>> 
>>> 
>>> 
>>> 
>>> The slightly longer story is that Apple decided to have their include
>>> files generate a _warning_ that utimensat() is only available in 10.13,
>>> like this:
>>> 
>>> gcc -I../../../R/src/extra  -I. -I../../src/include
>>> -I../../../R/src/include  -I/usr/local/include -I../../../R/src/nmath
>>> -DHAVE_CONFIG_H -g -O2  -c ../../../R/src/main/platform.c -o platform.o
>>> ../../../R/src/main/platform.c:2474:5: warning: 'utimensat' is only
>>> available on
>>>   macOS 10.13 or newer [-Wunguarded-availability-new]
>>> utimensat(AT_FDCWD, to, times, 0);
>>> ^
>>> /Applications/Xcode.app/Contents/Developer/Platforms/
>>> MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
>>> note:
>>>   'utimensat' has been explicitly marked partial here
>>> int utimensat(int __fd, const char *__path, const struct timespec __...
>>> ^
>>> ../../../R/src/main/platform.c:2474:5: note: enclose 'utimensat' in a
>>>   __builtin_available check to silence this warning
>>> utimensat(AT_FDCWD, to, times, 0);
>>> ^
>>> ../../../R/src/main/platform.c:2890:11: warning: 'utimensat' is only
>>> available
>>>   on macOS 10.13 or newer [-Wunguarded-availability-new]
>>> res = utimensat(AT_FDCWD, fn, times, 0) == 0;
>>>   ^
>>> /Applications/Xcode.app/Contents/Developer/Platforms/
>>> MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
>>> note:
>>>   'utimensat' has been explicitly marked partial here
>>> int utimensat(int __fd, const char 

[R-SIG-Mac] Xcode 9

[peter dalgaard]

Just a quick note: Xcode 9 will not presently create a working R on Sierra or 
earlier.

This is because it ships with an SDK for 10.13 (unreleased) and defines an 
entry for utimensat(), which is not actually in the system library for earlier 
versions. 

There is no way we can fix this reliably for the upcoming 3.4.2 release, so if 
you intend to build R from sources, either 

- just do not upgrade, stay on Xcode 8.3.3 

or 

- manually remove the line from config.h saying

#define HAVE_UTIMENSAT 1




The slightly longer story is that Apple decided to have their include files 
generate a _warning_ that utimensat() is only available in 10.13, like this: 

gcc -I../../../R/src/extra  -I. -I../../src/include -I../../../R/src/include  
-I/usr/local/include -I../../../R/src/nmath -DHAVE_CONFIG_H -g -O2  -c 
../../../R/src/main/platform.c -o platform.o
../../../R/src/main/platform.c:2474:5: warning: 'utimensat' is only available on
  macOS 10.13 or newer [-Wunguarded-availability-new]
utimensat(AT_FDCWD, to, times, 0);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
 note: 
  'utimensat' has been explicitly marked partial here
int utimensat(int __fd, const char *__path, const struct timespec __...
^
../../../R/src/main/platform.c:2474:5: note: enclose 'utimensat' in a
  __builtin_available check to silence this warning
utimensat(AT_FDCWD, to, times, 0);
^
../../../R/src/main/platform.c:2890:11: warning: 'utimensat' is only available
  on macOS 10.13 or newer [-Wunguarded-availability-new]
res = utimensat(AT_FDCWD, fn, times, 0) == 0;
  ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
 note: 
  'utimensat' has been explicitly marked partial here
int utimensat(int __fd, const char *__path, const struct timespec __...
^
../../../R/src/main/platform.c:2890:11: note: enclose 'utimensat' in a
  __builtin_available check to silence this warning
res = utimensat(AT_FDCWD, fn, times, 0) == 0;
  ^
2 warnings generated.

Because of dynamic linking, we do not see the effect of this until we actually 
try running the binary:

begin installing recommended package MASS
dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
  Expected in: /usr/lib/libSystem.B.dylib

/Users/pd/r-release-branch/BUILD-dist/bin/INSTALL: line 34: 59149 Done  
  echo 'tools:::.install_packages()'
 59150 Abort trap: 6   | R_DEFAULT_PACKAGES= LC_COLLATE=C 
"${R_HOME}/bin/R" $myArgs --slave --args ${args}


Same warning also happens during the configure checks, but as it is not an 
error the test program compiles and links OK (but is never run), and we get

checking whether utimensat exists and is declared... yes

Ugh!...


- Peter D.


-- 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
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Re: [R-SIG-Mac] Sys.timezone == NA?

[peter dalgaard]

> On 20 Jul 2017, at 19:29 , BATES Timothy <tim.ba...@ed.ac.uk> wrote:
> 
> Hi,
> On R 3.40, I've been getting some Warnings about timezone, e.g.
> 
> Warning message: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 
> 'default/Europe/London'
> 
> But also Sys.timezone returns NA Is this a bug? was there a change in tz 
> moving to 3.4.0?

No, but there seems to have been a bug introduced in MacOS 10.13 _beta_ (!!). 
We might have to work around it if it persists in the final release, but until 
then we assume that it is Apple's problem. See also PR#17307.

-pd


> 
> Sys.timezone()
> [1] NA
> 
> R version: R version 3.4.0 Patched (2017-05-02 r72651)
> Platform: x86_64-apple-darwin15.6.0 
> MacOS: 10.13
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
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Re: [R-SIG-Mac] Poor plotting performance on Mac OS X

[peter dalgaard]

Thanks Don,

Can you perhaps make that a little closer to being reproducible for people who 
might want to try it on newer hardware? (packages, location of input file).

(And by the way, xterm? What did Terminal.app do to you?)

This, along with a thread from 2014 that Google dug up, strongly suggests that 
quartz() is the culprit. It might not be our fault though, as it seems that 
"matplotlib" (Python) has had similar problems. In the latter case, it seems to 
have worked to "switch to the agg backend", whatever that means. (AGG is 
AntiGrain Geometry, which is apparently so stable that it hasn't changed since 
2006. Its author died suddenly in 2013, it seems.)

-pd


> On 10 Jul 2017, at 19:59 , MacQueen, Don <macque...@llnl.gov> wrote:
> 
> For what it's worth, here is my experience on a late 2013 Mac Pro.
> (I normally run R from an xterm shell within an X Windows context)
> 
> The best performance for displaying the image on-screen uses cairographics 
> and Polypath. It's the only one fast enough to be satisfactory for 
> interactive use, in my opinion [though x11(type='Xlib') could be tolerated]. 
> pdf() is even faster.
> 
> -Don
> 
>> nsw <- readOGR('data','SA3_2016_AUST', stringsAsFactors=FALSE)
> OGR data source with driver: ESRI Shapefile 
> Source: "data", layer: "SA3_2016_AUST"
> with 358 features
> It has 9 fields
> Warning message:
> In readOGR("data", "SA3_2016_AUST", stringsAsFactors = FALSE) :
>  Dropping null geometries: 93, 94, 161, 162, 245, 246, 275, 276, 311, 312, 
> 328, 329, 339, 340, 351, 352, 357, 358
> 
> ## The "original" X windows device (does not support Polypath)
>> x11(type='Xlib')
>> system.time( plot(nsw, usePolypath=FALSE) )
>   user  system elapsed 
>  0.882   0.512  99.618 
> 
> ## a more "modern" version of the X windows device
>> x11(type='cairo')
>> system.time( plot(nsw, usePolypath=FALSE) )
>   user  system elapsed 
>  2.233   5.007  68.410 
> 
> 
> ## Polypath gives large improvement
>> x11(type='cairo')
>> system.time( plot(nsw, usePolypath=TRUE) )
>   user  system elapsed 
>  1.772   0.461   5.785 
> 
> ## Same R session as above, but using the quartz device
>> quartz()
>> system.time( plot(nsw) )
>user   system  elapsed 
> 1135.6061.556 1137.445 
> 
>> pdf('test.pdf')
>> system.time( plot(nsw) )
>   user  system elapsed 
>  2.029   0.200   2.248 
>> dev.off()
> 
> 
>> sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base 
> 
> other attached packages:
> [1] rgdal_1.2-8 sp_1.2-5   
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.4.1  tools_3.4.1 grid_3.4.1  lattice_0.20-35
> 
> 
> -- 
> Don MacQueen
> 
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
> 
> 
> On 7/10/17, 4:40 AM, "R-SIG-Mac on behalf of Ashley Betts" 
> <r-sig-mac-boun...@r-project.org on behalf of 
> ashley.be...@saltbushsoftware.com> wrote:
> 
>Hi Peter, outputting to PDF made a huge difference! It ran for only 15 
> seconds and there was no trailing unresponsive prompt. The PDF ended up being 
> around 2Mb and opened and displayed almost immediately in Preview.
> 
>I did watch the system when I was outputting to the quartz device last 
> time and the process was steadily consuming a single core. When I watched it 
> on the Windows machines I saw it use most of the cores but not to capacity. 
> After seeing this I read up on multithreading libraries on Mac and finally 
> setup R to use the Accelerate library. I’ve verified this library is being 
> loaded by sampling the process. It make zero difference however and the 
> print(plt) still only consumes a single core.
> 
>Regards,
> 
>Ashley
> 
>> On 10 Jul 2017, at 6:21 PM, peter dalgaard <pda...@gmail.com> wrote:
>> 
>> Pretty clear that the process is getting stuck in Apple-graphics land, then. 
>> This could be inefficiency of the device driver, but also just ... Apple. 
>> Could you try running the same thing to a PDF (AFAIR, just open the device 
>> with pdf(file="myplot.pdf"), then print(plt), then dev.off()). It would

Re: [R-SIG-Mac] Poor plotting performance on Mac OS X

[peter dalgaard]

Pretty clear that the process is getting stuck in Apple-graphics land, then. 
This could be inefficiency of the device driver, but also just ... Apple. Could 
you try running the same thing to a PDF (AFAIR, just open the device with 
pdf(file="myplot.pdf"), then print(plt), then dev.off()). It would be good to 
know if this is fast, and also whether viewing the resulting PDF in Preview is 
slow (in which case it is Not Our Problem).

Also, does running the Activity Monitor give any clues? Like, perhaps you are 
running out of memory. 

-pd

> On 10 Jul 2017, at 00:05 , Ashley Betts <ashley.be...@saltbushsoftware.com> 
> wrote:
> 
> Oh yes, sorry about that. I originally had screen shots attached showing the 
> timings but the email ended up being too large. All of the time is in the 
> print. Nearly all other commands run within seconds. Oddly, after 
> approximately half hour the prompt returns which I get one Sys.time() to 
> execute but then the prompt hangs when I enter the second Sys.time() for the 
> best part of an hour and half.
> 
> I tried to profile but that failed. I tried sampling the process a number of 
> times and every time I sampled execution was buried in CGContextDrawPath
> GEPolygon  (in libR.dylib) + 127  [0x101cb54df]  engine.c:0
> + 
>   
> 2502 clipPolygon  (in libR.dylib) + 571  
> [0x101cb574b]  engine.c:1080
> + 
>   
>   2502 CGContextDrawPath  (in CoreGraphics) + 181  
> [0x7fff8d433e59]
> + 
>   
> 2502 ripc_DrawPath  (in libRIP.A.dylib) + 417  
> [0x7fff8ec631a3]
> + 
>   
>   2502 ripc_Render  (in libRIP.A.dylib) + 380  
> [0x7fff8ec4f750]
> + 
>   
> 2502 RIPRenderCoverage  (in libRIP.A.dylib) + 
> 1844  [0x7fff8ec4ff84]
> 
> 
> Regards,
> 
> Ashley
> 
> 
> 
> 
>> On 9 Jul 2017, at 9:35 PM, peter dalgaard <pda...@gmail.com> wrote:
>> 
>> Hmm, you're not telling us much about where the time is being spent. Some 
>> more detailed timing using system.time() could be useful.
>> 
>> If it is a graphics device issue, I would expect almost everything in the 
>> final print(plt). You could try switching graphics device, e.g. to pdf() 
>> which should be pretty much the same on all platforms. You might also try 
>> creating PDF files on one machine and displaying on the other. 
>> 
>> -pd 
>> 
>>> On 9 Jul 2017, at 12:45 , Ashley Betts <ashley.be...@saltbushsoftware.com> 
>>> wrote:
>>> 
>>> Hi All,
>>>  I'm quite new to R and recently started investigating the geospatial 
>>> plotting capabilities of R via ggplot2. I started by using some of the 
>>> publicly available datasets from the Australian Bureau of Statistics. 
>>> Plotting the Level 3 Statistical Area boundaries took over 2 hours on my 
>>> 2012 Mac Book Pro. As there were over 3M rows in the fortify’ed data frame 
>>> I initially thought this was just how long it must take. I then ran the 
>>> exact same script on my work laptop which is similarly spec’ed and it ran 
>>> in approximately 30 seconds. This now has me extremely disappointed in the 
>>> performance on the Mac which is where I use R the most. I changed my BLAS 
>>> library to the Accelerate library in a whim that this might make a 
>>> difference. It did not. Whilst I primarily use RStudio I also ran the same 
>>> script in R.app and if there was any improvement it was not noticeable. I 
>>> did notice in the Windows run that it seemed to use multiple cores (which 
>>> is what made me investigate the BLAS change) whilst the Mac seems to stay 
>>> bound to a single core. My initial thoughts were that it must be something 
>>> to do with ggplot but after sampling the rsession process a number of times 
>>> (see attached Sample of rsession.txt) it appears to be s

Re: [R-SIG-Mac] Poor plotting performance on Mac OS X

[peter dalgaard]

Hmm, you're not telling us much about where the time is being spent. Some more 
detailed timing using system.time() could be useful.

If it is a graphics device issue, I would expect almost everything in the final 
print(plt). You could try switching graphics device, e.g. to pdf() which should 
be pretty much the same on all platforms. You might also try creating PDF files 
on one machine and displaying on the other. 

-pd 

> On 9 Jul 2017, at 12:45 , Ashley Betts <ashley.be...@saltbushsoftware.com> 
> wrote:
> 
> Hi All,
>   I'm quite new to R and recently started investigating the geospatial 
> plotting capabilities of R via ggplot2. I started by using some of the 
> publicly available datasets from the Australian Bureau of Statistics. 
> Plotting the Level 3 Statistical Area boundaries took over 2 hours on my 2012 
> Mac Book Pro. As there were over 3M rows in the fortify’ed data frame I 
> initially thought this was just how long it must take. I then ran the exact 
> same script on my work laptop which is similarly spec’ed and it ran in 
> approximately 30 seconds. This now has me extremely disappointed in the 
> performance on the Mac which is where I use R the most. I changed my BLAS 
> library to the Accelerate library in a whim that this might make a 
> difference. It did not. Whilst I primarily use RStudio I also ran the same 
> script in R.app and if there was any improvement it was not noticeable. I did 
> notice in the Windows run that it seemed to use multiple cores (which is what 
> made me investigate the BLAS change) whilst the Mac seems to stay bound to a 
> single core. My initial thoughts were that it must be something to do with 
> ggplot but after sampling the rsession process a number of times (see 
> attached Sample of rsession.txt) it appears to be spending most of it’s time 
> in CGContextDrawPath in Apples CoreGraphics so I assume it is a Graphics 
> related issue. I’m running R 3.4 on my Mac and 3.3.2 on the Windows machine. 
> I’ve attached the script and have screen dumps of the process sample text and 
> a number of others which I can supply if helpful in analysing the issue. 
> Could someone possibly let me know if this is PEBCAK issue or an actual 
> problem with R. If the later how do I go about getting the issue resolved?
> 
> The SA3 boundary data is available here:
> 
> http://www.abs.gov.au/AUSSTATS/abs@.nsf/DetailsPage/1270.0.55.001July%202016?OpenDocument
> 
> as 'Statistical Area Level 3 (SA3) ASGS Ed 2016 Digital Boundaries in ESRI 
> Shapefile Format’
> 
> Regards,
> 
> Ashley
> 
> 
> 
> 
> 
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Re: [R-SIG-Mac] R 3.4.0 problem

[peter dalgaard]

t;>>> 
>>>> * installing *source* package ‘gmp’ ...
>>>> ** package ‘gmp’ successfully unpacked and MD5 sums checked
>>>> creating cache ./config.cache
>>>> checking for __gmpz_ui_sub in -lgmp... no
>>>> configure: error: GNU MP not found, or not 4.1.4 or up, see
>>>> http://gmplib.org
>>>> ERROR: configuration failed for package ‘gmp’
>>>> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
>>>> Resources/library/gmp’
>>>> Warning in install.packages :
>>>> installation of package ‘gmp’ had non-zero exit status
>>>> ERROR: dependency ‘gmp’ is not available for package ‘dplR’
>>>> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
>>>> Resources/library/dplR’
>>>> Warning in install.packages :
>>>> installation of package ‘dplR’ had non-zero exit status
>>>> 
>>>> The downloaded source packages are in
>>>> ‘/private/var/folders/c5/6g4vbk5x55586m8ky2v_6pbcgn/T/RtmprYzSE8/
>>>> downloaded_packages’
>>>> 
>>>> 
>>>> All the other packages work in good conditions.
>>>> Please help me to solve this annoying situation.
>>>> 
>>>> Best regards!
>>>> 
>>>> CR
>>>> 
>>>> 
>>>> -- 
>>>> 
>>>> -
>>>> -
>>>> Catalin-Constantin ROIBU
>>>> ​
>>>> Lecturer PhD, Forestry engineer
>>>> Forestry Faculty of Suceava
>>>> Str. Universitatii no. 13, Suceava, 720229, Romania
>>>> office phone  +4 0230 52 29 78, ext. 531
>>>> mobile phone+4 0745 53 18 01
>>>> FAX:+4 0230 52 16 64
>>>> silvic.usv.ro <http://www.usv.ro/>
>>>> 
>>>> 
>>>> 
>>>> <https://mailtrack.io/> Sent with Mailtrack
>>>> <https://mailtrack.io/install?source=signature=en=catalinro...@gmail.com=22>
>>>> <#>
>>>> 
>>>>[[alternative HTML version deleted]]
>>>> 
>>>> ___
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>>> 
>>> David Winsemius
>>> Alameda, CA, USA
>>> 
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>> 
> 
> David Winsemius
> Alameda, CA, USA
> 
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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

[peter dalgaard]

[Christofer seemed to have fallen off the cc: list, now included]

> On 24 May 2017, at 00:18 , David Winsemius <dwinsem...@comcast.net> wrote:
> 
> What version of the Java Runtime Environment is available? What do you get 
> for:
> 
> system('javac -version')
> #I get:
> #javac 1.8.0_65
> 
> I think that version was working with rJava, but I followed the "critical" 
> advice on the Java SDK webpage ...
> 
> ... and after updating I now  get
> #javac 1.8.0_131
> 
> And rJava still loads without error. I'm not on Sierra, however.
> 

I am, and rJava doesn't load here either. However after

sudo R CMD javareconf

it seems happy as a clam.


> Good luck;
> David,

-- 
Peter Dalgaard, Professor,
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Re: [R-SIG-Mac] R is taking too long to load

[peter dalgaard]

Most easily by typing "R --vanilla" the command line of Terminal.app. Dunno if 
you can do it with R.app. 

-pd


> On 19 May 2017, at 00:58 , Christofer Bogaso <bogaso.christo...@gmail.com> 
> wrote:
> 
> Thanks,
> 
> How can I start R with --vanilla in Mac? Sorry if this question is very 
> trivial.
> 
> On Fri, May 19, 2017 at 3:11 AM, Hervé Pagès <hpa...@fredhutch.org> wrote:
>> Hi,
>> 
>> First thing I would do is make sure you don't have any startup file
>> or .Rhistory in the way. If starting R with --vanilla is fast, then
>> that's probably the case.
>> 
>> H.
>> 
>> 
>> On 05/18/2017 12:44 PM, Christofer Bogaso wrote:
>>> 
>>> Hi,
>>> 
>>> It just started happening recently that R is taking too long to load
>>> and entire system freezes during its loading.
>>> 
>>> Have anyone experienced something similar? Previously my R was
>>> completely okay, however it just started recently.
>>> 
>>> Any solution for this? I have reinstalled R and now it is the latest
>>> version 3.4.0. I am using Sierra iOS.
>>> 
>>> Appreciate for any pointer.
>>> 
>>> Thanks,
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=m7VSPPECqAsFryKwwUO-q8QiizXtbiWc-kj9qtPO2h0=cSQVI4BrFUKhUyo5ZPrQMQOwu-ZSCMWpxh5IJ8y9L6s=
>>> 
>> 
>> --
>> Hervé Pagès
>> 
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>> 
>> E-mail: hpa...@fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:(206) 667-1319
> 
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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[peter dalgaard]

The culprit seems to have been in Xcode 8.3.1, see this Ticket 

http://core.tcl.tk/tk/tktview/3f323bf2b42b668a5678

This was found and fixed little more than a month ago, so I was being unfair to 
ActiveState in a previous note (which may or may not make its way through 
moderation).

The Ticket also contains a two-line patch for the Tk sources, so I suppose this 
provides a way for us to build at least the framework format, with Xft support. 

-pd

> On 17 May 2017, at 21:21 , Peter Dalgaard <pda...@gmail.com> wrote:
> 
> And a bit more. The Rcmdr crash happens here:
> 
> debugging in: .Tcl.objv(.Tcl.args.objv(...))
> debug: structure(.External(.C_dotTclObjv, objv), class = "tclObj")
> Browse[2]> objv
> [[1]]
>  wm 
> 
> [[2]]
>  protocol 
> 
> [[3]]
>  .1 
> 
> [[4]]
>  WM_DELETE_WINDOW 
> 
> [[5]]
>  R_call 0x7fedc1987ff8 
> 
> Browse[2]> 
> Abort trap: 6
> 
> and I can make the same thing happen in wish, so it is Not Our Fault:
> 
> Peter-Dalgaards-iMac:BUILD pd$ /usr/local/bin/wish
> % toplevel .1
> .1
> % wm protocol .1 WM_DELETE_WINDOW {puts hi}   
> /usr/local/bin/wish: line 2: 32765 Abort trap: 6   "$(dirname 
> $0)/../../../Library/Frameworks/Tk.framework/Versions/8.6/Resources/Wish.app/Contents/MacOS/Wish"
>  "$@"
> 
> 
> -pd
> 
>> On 17 May 2017, at 20:51 , Peter Dalgaard <pda...@gmail.com> wrote:
>> 
>> A few more data points:
>> 
>> I tried building Tcl/Tk 8.6.6 from the sources from sourceforge. Contrary to 
>> what it says on the package, it insists on building Tcl and Tk as 
>> frameworks, which in turn requires that R's configure needs special 
>> instructions. This works reasonably well for simple tcltk stuff (demos, the 
>> CRAN selection menu), but unfortunately, library(Rcmdr) causes an "Abort 
>> trap: 6" almost immediately. (I get a sense of deja vu about this... Did 
>> Brian try something similar years ago?)
>> 
>> It does actually seem to work to build R against the system-supplied v.8.5 
>> frameworks. However, this is Aqua-based, and the fonts are a bit weird 
>> (smooth, but way too small) and the Rcmdr menus get moved to the top bar.
>> 
>> I am pretty sure by now that all this stuff is a generic tcltk build problem 
>> and way out of John's domain. (Thanks for posting the font code, John. I 
>> hope I can get around to having a closer look at it at some point. Those 
>> .Tcl(paste()) constructs make me cringe a bit, but not all are easily 
>> eliminated.)
>> 
>> -pd
>> 
>>> On 16 May 2017, at 23:52 , peter dalgaard <pda...@gmail.com> wrote:
>>> 
>>> 
>>>> On 16 May 2017, at 21:03 , peter dalgaard <pda...@gmail.com> wrote:
>>>> 
>>>> I don't think the config flags for R matter in this regard. The behaviour 
>>>> is completely paralleled by wish8.6: 
>>> 
>>> Hmmm, not sure the wish ::tk::pkgconfig thing proves anything, after I 
>>> tried some of the ActiveState installs and a source build. This stuff is 
>>> making my head spin!
>>> 
>>> However, I discovered that it is possible to install R-3.4.0.pkg as usual, 
>>> and then a customized install of (say) R-3.3-branch-mavericks.pkg, omitting 
>>> everything except the Tcl/Tk stuff. That gives you R 3.4.0 and Rcmdr with 
>>> antialiased fonts.
>>> 
>>> -- 
>>> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
>> -- 
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> 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
> 
> 
> 
> 
> 
> 
> 
> 
> 

-- 
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

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[Peter Dalgaard]

And a bit more. The Rcmdr crash happens here:

debugging in: .Tcl.objv(.Tcl.args.objv(...))
debug: structure(.External(.C_dotTclObjv, objv), class = "tclObj")
Browse[2]> objv
[[1]]
 wm 

[[2]]
 protocol 

[[3]]
 .1 

[[4]]
 WM_DELETE_WINDOW 

[[5]]
 R_call 0x7fedc1987ff8 

Browse[2]> 
Abort trap: 6

and I can make the same thing happen in wish, so it is Not Our Fault:

Peter-Dalgaards-iMac:BUILD pd$ /usr/local/bin/wish
% toplevel .1
.1
% wm protocol .1 WM_DELETE_WINDOW {puts hi}   
/usr/local/bin/wish: line 2: 32765 Abort trap: 6   "$(dirname 
$0)/../../../Library/Frameworks/Tk.framework/Versions/8.6/Resources/Wish.app/Contents/MacOS/Wish"
 "$@"


-pd

> On 17 May 2017, at 20:51 , Peter Dalgaard <pda...@gmail.com> wrote:
> 
> A few more data points:
> 
> I tried building Tcl/Tk 8.6.6 from the sources from sourceforge. Contrary to 
> what it says on the package, it insists on building Tcl and Tk as frameworks, 
> which in turn requires that R's configure needs special instructions. This 
> works reasonably well for simple tcltk stuff (demos, the CRAN selection 
> menu), but unfortunately, library(Rcmdr) causes an "Abort trap: 6" almost 
> immediately. (I get a sense of deja vu about this... Did Brian try something 
> similar years ago?)
> 
> It does actually seem to work to build R against the system-supplied v.8.5 
> frameworks. However, this is Aqua-based, and the fonts are a bit weird 
> (smooth, but way too small) and the Rcmdr menus get moved to the top bar.
> 
> I am pretty sure by now that all this stuff is a generic tcltk build problem 
> and way out of John's domain. (Thanks for posting the font code, John. I hope 
> I can get around to having a closer look at it at some point. Those 
> .Tcl(paste()) constructs make me cringe a bit, but not all are easily 
> eliminated.)
> 
> -pd
> 
>> On 16 May 2017, at 23:52 , peter dalgaard <pda...@gmail.com> wrote:
>> 
>> 
>>> On 16 May 2017, at 21:03 , peter dalgaard <pda...@gmail.com> wrote:
>>> 
>>> I don't think the config flags for R matter in this regard. The behaviour 
>>> is completely paralleled by wish8.6: 
>> 
>> Hmmm, not sure the wish ::tk::pkgconfig thing proves anything, after I tried 
>> some of the ActiveState installs and a source build. This stuff is making my 
>> head spin!
>> 
>> However, I discovered that it is possible to install R-3.4.0.pkg as usual, 
>> and then a customized install of (say) R-3.3-branch-mavericks.pkg, omitting 
>> everything except the Tcl/Tk stuff. That gives you R 3.4.0 and Rcmdr with 
>> antialiased fonts.
>> 
>> -- 
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> 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
> 
> 
> 
> 
> 
> 
> 
> 
> 

-- 
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

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[Peter Dalgaard]

A few more data points:

I tried building Tcl/Tk 8.6.6 from the sources from sourceforge. Contrary to 
what it says on the package, it insists on building Tcl and Tk as frameworks, 
which in turn requires that R's configure needs special instructions. This 
works reasonably well for simple tcltk stuff (demos, the CRAN selection menu), 
but unfortunately, library(Rcmdr) causes an "Abort trap: 6" almost immediately. 
(I get a sense of deja vu about this... Did Brian try something similar years 
ago?)

It does actually seem to work to build R against the system-supplied v.8.5 
frameworks. However, this is Aqua-based, and the fonts are a bit weird (smooth, 
but way too small) and the Rcmdr menus get moved to the top bar.

I am pretty sure by now that all this stuff is a generic tcltk build problem 
and way out of John's domain. (Thanks for posting the font code, John. I hope I 
can get around to having a closer look at it at some point. Those .Tcl(paste()) 
constructs make me cringe a bit, but not all are easily eliminated.)

-pd

> On 16 May 2017, at 23:52 , peter dalgaard <pda...@gmail.com> wrote:
> 
> 
>> On 16 May 2017, at 21:03 , peter dalgaard <pda...@gmail.com> wrote:
>> 
>> I don't think the config flags for R matter in this regard. The behaviour is 
>> completely paralleled by wish8.6: 
> 
> Hmmm, not sure the wish ::tk::pkgconfig thing proves anything, after I tried 
> some of the ActiveState installs and a source build. This stuff is making my 
> head spin!
> 
> However, I discovered that it is possible to install R-3.4.0.pkg as usual, 
> and then a customized install of (say) R-3.3-branch-mavericks.pkg, omitting 
> everything except the Tcl/Tk stuff. That gives you R 3.4.0 and Rcmdr with 
> antialiased fonts.
> 
> -- 
> 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
> 
> 
> 
> 
> 
> 
> 
> 
> 

-- 
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

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[peter dalgaard]

> On 16 May 2017, at 21:03 , peter dalgaard <pda...@gmail.com> wrote:
> 
> I don't think the config flags for R matter in this regard. The behaviour is 
> completely paralleled by wish8.6: 

Hmmm, not sure the wish ::tk::pkgconfig thing proves anything, after I tried 
some of the ActiveState installs and a source build. This stuff is making my 
head spin!

However, I discovered that it is possible to install R-3.4.0.pkg as usual, and 
then a customized install of (say) R-3.3-branch-mavericks.pkg, omitting 
everything except the Tcl/Tk stuff. That gives you R 3.4.0 and Rcmdr with 
antialiased fonts.

-- 
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

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[peter dalgaard]

Mystery solved after looking into the actual .pkg files. They simply contain a 
full Tcl/Tk which installs into /usr/local, which obviously affects anything 
that links it dynamically. I somehow thought that they would install somewhere 
separate. (Stop grinning, Simon!)

Anyways, the way forward must be to get Tcl/Tk compiled exactly as they were in 
3.3.x.

-pd




> On 16 May 2017, at 15:18 , peter dalgaard <pda...@gmail.com> wrote:
> 
> Double-checked: Indeed, installing 3.3-branch-mavericks.pkg enables xft on my 
> local builds of R-patched and R-devel. H..
> 
> -pd 
> 
>> On 16 May 2017, at 14:55 , peter dalgaard <pda...@gmail.com> wrote:
>> 
>> Curiouser and curiouser, now my local build of R-devel stopped using xft 
>> _without any recompile_ I swear that it worked before I installed 
>> R-3.4.0.pkg
>> 
>> I have both /opt/local/ and /usr/local variants of Tcl/Tk 8.6 and only the 
>> former has wish8.6 understanding the tk::pkgconfig stuff, so there is plenty 
>> of room for confusion. The latter seems to be from Simon's site; the other 
>> one could be a MacPorts relic...
>> 
>> -pd
>> 
>>> On 16 May 2017, at 13:28 , peter dalgaard <pda...@gmail.com> wrote:
>>> 
>>> It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
>>> something slightly weird[*] with the fonts too, but this seems to be 
>>> orthogonal to the ugly-font issue).
>>> 
>>> To see the issue quickly, try 
>>> 
>>> library(tcltk)
>>> .Tcl("::tk::pkgconfig get fontsystem")
>>> 
>>> With CRAN 3.3.3, I get 
>>> 
>>>  xft 
>>> 
>>> and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says
>>> 
>>>> .Tcl("::tk::pkgconfig get fontsystem")
>>> Error in .Tcl("::tk::pkgconfig get fontsystem") : 
>>> could not find function ".Tcl"
>>> 
>>> as does a local build of R-patched (???!!!). 
>>> 
>>> This is pretty weird. I'll see if I can dig up some more about where the 
>>> difference is.
>>> 
>>> -pd
>>> 
>>> 
>>> 
>>> [*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the font 
>>> change in the tkfaq window.
>>> 
>>> 
>>>> On 15 May 2017, at 23:17 , Fox, John <j...@mcmaster.ca> wrote:
>>>> 
>>>> Dear Jose,
>>>> 
>>>> It's a bit difficult to respond to your latest messages because you sent 
>>>> so many of them.
>>>> 
>>>> I'm not entirely sure what's producing your font problems -- perhaps Simon 
>>>> will have some additional ideas -- but you should be aware that you can't 
>>>> load the Rcmdr package -- or, more generally, the tcltk package -- without 
>>>> XQuartz (or another X11 system). Normally, XQuartz should start 
>>>> automatically when the Rcmdr (or tcltk) package is loaded. That is, you 
>>>> should not have to start it separately.
>>>> 
>>>> It may help to know that the Rcmdr package selects its default dialog font 
>>>> by querying the default Tk font, via the command
>>>> 
>>>>tclvalue(.Tcl("font actual TkDefaultFont -family"))
>>>> 
>>>> and sets the font for commands and output by querying the default Tk 
>>>> fixed-width font:
>>>> 
>>>>tclvalue(.Tcl("font actual TkFixedFont -family"))
>>>> 
>>>> On my Macs, these are respectively the helvetica and courier fonts.
>>>> 
>>>> In any event, I'm glad that you seem to have solved your problem.
>>>> 
>>>> John
>>>> 
>>>>> -Original Message-
>>>>> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
>>>>> Sent: Monday, May 15, 2017 3:18 PM
>>>>> To: Simon Urbanek <simon.urba...@r-project.org>; Fox, John
>>>>> <j...@mcmaster.ca>; r-sig-mac@r-project.org
>>>>> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
>>>>> 
>>>>> When I run R without XQuartz, the text from the help screen renders
>>>>> well. I think the problem seems to be related to XQuartz.
>>>>> 
>>>>> José
>>>>> 
>>>>> 
>>>>> José G. Conde, MD, MPH
>>>>> Professor, School of Medicine
>>>>> Director, CentIT2
>>>>> UPR Medical Sciences C

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[peter dalgaard]

Double-checked: Indeed, installing 3.3-branch-mavericks.pkg enables xft on my 
local builds of R-patched and R-devel. H..

-pd 

> On 16 May 2017, at 14:55 , peter dalgaard <pda...@gmail.com> wrote:
> 
> Curiouser and curiouser, now my local build of R-devel stopped using xft 
> _without any recompile_ I swear that it worked before I installed 
> R-3.4.0.pkg
> 
> I have both /opt/local/ and /usr/local variants of Tcl/Tk 8.6 and only the 
> former has wish8.6 understanding the tk::pkgconfig stuff, so there is plenty 
> of room for confusion. The latter seems to be from Simon's site; the other 
> one could be a MacPorts relic...
> 
> -pd
> 
>> On 16 May 2017, at 13:28 , peter dalgaard <pda...@gmail.com> wrote:
>> 
>> It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
>> something slightly weird[*] with the fonts too, but this seems to be 
>> orthogonal to the ugly-font issue).
>> 
>> To see the issue quickly, try 
>> 
>> library(tcltk)
>> .Tcl("::tk::pkgconfig get fontsystem")
>> 
>> With CRAN 3.3.3, I get 
>> 
>>  xft 
>> 
>> and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says
>> 
>>> .Tcl("::tk::pkgconfig get fontsystem")
>> Error in .Tcl("::tk::pkgconfig get fontsystem") : 
>> could not find function ".Tcl"
>> 
>> as does a local build of R-patched (???!!!). 
>> 
>> This is pretty weird. I'll see if I can dig up some more about where the 
>> difference is.
>> 
>> -pd
>> 
>> 
>> 
>> [*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the font 
>> change in the tkfaq window.
>> 
>> 
>>> On 15 May 2017, at 23:17 , Fox, John <j...@mcmaster.ca> wrote:
>>> 
>>> Dear Jose,
>>> 
>>> It's a bit difficult to respond to your latest messages because you sent so 
>>> many of them.
>>> 
>>> I'm not entirely sure what's producing your font problems -- perhaps Simon 
>>> will have some additional ideas -- but you should be aware that you can't 
>>> load the Rcmdr package -- or, more generally, the tcltk package -- without 
>>> XQuartz (or another X11 system). Normally, XQuartz should start 
>>> automatically when the Rcmdr (or tcltk) package is loaded. That is, you 
>>> should not have to start it separately.
>>> 
>>> It may help to know that the Rcmdr package selects its default dialog font 
>>> by querying the default Tk font, via the command
>>> 
>>> tclvalue(.Tcl("font actual TkDefaultFont -family"))
>>> 
>>> and sets the font for commands and output by querying the default Tk 
>>> fixed-width font:
>>> 
>>> tclvalue(.Tcl("font actual TkFixedFont -family"))
>>> 
>>> On my Macs, these are respectively the helvetica and courier fonts.
>>> 
>>> In any event, I'm glad that you seem to have solved your problem.
>>> 
>>> John
>>> 
>>>> -Original Message-
>>>> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
>>>> Sent: Monday, May 15, 2017 3:18 PM
>>>> To: Simon Urbanek <simon.urba...@r-project.org>; Fox, John
>>>> <j...@mcmaster.ca>; r-sig-mac@r-project.org
>>>> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
>>>> 
>>>> When I run R without XQuartz, the text from the help screen renders
>>>> well. I think the problem seems to be related to XQuartz.
>>>> 
>>>> José
>>>> 
>>>> 
>>>> José G. Conde, MD, MPH
>>>> Professor, School of Medicine
>>>> Director, CentIT2
>>>> UPR Medical Sciences Campus
>>>> 
>>>> Tel  (787) 763-9401 Fax (787) 758-5206
>>>> 
>>>> Email: jose.con...@upr.edu
>>>> 
>>>> URL: http://rcmi.rcm.upr.edu
>>>> 
>>>>> On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
>>>> <jose.con...@upr.edu> wrote:
>>>>> 
>>>>> … and the same I get the same issue with R “help” screens in my iMac.
>>>> I cannot reproduce this in the macBook.
>>>>> 
>>>>> José
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> José G. Conde, MD, MPH
>>>>> Catedrático, Escuela de M

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[peter dalgaard]

Curiouser and curiouser, now my local build of R-devel stopped using xft 
_without any recompile_ I swear that it worked before I installed 
R-3.4.0.pkg

I have both /opt/local/ and /usr/local variants of Tcl/Tk 8.6 and only the 
former has wish8.6 understanding the tk::pkgconfig stuff, so there is plenty of 
room for confusion. The latter seems to be from Simon's site; the other one 
could be a MacPorts relic...

-pd

> On 16 May 2017, at 13:28 , peter dalgaard <pda...@gmail.com> wrote:
> 
> It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
> something slightly weird[*] with the fonts too, but this seems to be 
> orthogonal to the ugly-font issue).
> 
> To see the issue quickly, try 
> 
> library(tcltk)
> .Tcl("::tk::pkgconfig get fontsystem")
> 
> With CRAN 3.3.3, I get 
> 
>  xft 
> 
> and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says
> 
>> .Tcl("::tk::pkgconfig get fontsystem")
> Error in .Tcl("::tk::pkgconfig get fontsystem") : 
>  could not find function ".Tcl"
> 
> as does a local build of R-patched (???!!!). 
> 
> This is pretty weird. I'll see if I can dig up some more about where the 
> difference is.
> 
> -pd
> 
> 
> 
> [*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the font 
> change in the tkfaq window.
> 
> 
>> On 15 May 2017, at 23:17 , Fox, John <j...@mcmaster.ca> wrote:
>> 
>> Dear Jose,
>> 
>> It's a bit difficult to respond to your latest messages because you sent so 
>> many of them.
>> 
>> I'm not entirely sure what's producing your font problems -- perhaps Simon 
>> will have some additional ideas -- but you should be aware that you can't 
>> load the Rcmdr package -- or, more generally, the tcltk package -- without 
>> XQuartz (or another X11 system). Normally, XQuartz should start 
>> automatically when the Rcmdr (or tcltk) package is loaded. That is, you 
>> should not have to start it separately.
>> 
>> It may help to know that the Rcmdr package selects its default dialog font 
>> by querying the default Tk font, via the command
>> 
>>  tclvalue(.Tcl("font actual TkDefaultFont -family"))
>> 
>> and sets the font for commands and output by querying the default Tk 
>> fixed-width font:
>> 
>>  tclvalue(.Tcl("font actual TkFixedFont -family"))
>> 
>> On my Macs, these are respectively the helvetica and courier fonts.
>> 
>> In any event, I'm glad that you seem to have solved your problem.
>> 
>> John
>> 
>>> -Original Message-
>>> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
>>> Sent: Monday, May 15, 2017 3:18 PM
>>> To: Simon Urbanek <simon.urba...@r-project.org>; Fox, John
>>> <j...@mcmaster.ca>; r-sig-mac@r-project.org
>>> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
>>> 
>>> When I run R without XQuartz, the text from the help screen renders
>>> well. I think the problem seems to be related to XQuartz.
>>> 
>>> José
>>> 
>>> 
>>> José G. Conde, MD, MPH
>>> Professor, School of Medicine
>>> Director, CentIT2
>>> UPR Medical Sciences Campus
>>> 
>>> Tel  (787) 763-9401 Fax (787) 758-5206
>>> 
>>> Email: jose.con...@upr.edu
>>> 
>>> URL: http://rcmi.rcm.upr.edu
>>> 
>>>> On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
>>> <jose.con...@upr.edu> wrote:
>>>> 
>>>> … and the same I get the same issue with R “help” screens in my iMac.
>>> I cannot reproduce this in the macBook.
>>>> 
>>>> José
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> José G. Conde, MD, MPH
>>>> Catedrático, Escuela de Medicina
>>>> Director, CentIT2
>>>> Recinto de Ciencias Médicas, UPR
>>>> 
>>>> Tel  (787) 763-9401  Fax (787) 758-5206
>>>> 
>>>> Correo electrónico: jose.con...@upr.edu
>>>> 
>>>> URL: http://rcmi.rcm.upr.edu
>>>> 
>>>>> On May 15, 2017, at 2:14 PM, Jose G Conde Santiago
>>> <jose.con...@upr.edu> wrote:
>>>>> 
>>>>> This is the actual resolutions.
>>>>> 
>>>>> José
>>>>> 
>>>>> 
>>>>> José G. Conde, MD, MPH
>>>>> Professor, S

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[peter dalgaard]

It's a build issue relating to Tcl/Tk, not specifically Rcmdr (Rcmdr does 
something slightly weird[*] with the fonts too, but this seems to be orthogonal 
to the ugly-font issue).

To see the issue quickly, try 

library(tcltk)
.Tcl("::tk::pkgconfig get fontsystem")

With CRAN 3.3.3, I get 

 xft 

and likewise with a local nightly build of R-devel, but CRAN 3.4.0 says

> .Tcl("::tk::pkgconfig get fontsystem")
Error in .Tcl("::tk::pkgconfig get fontsystem") : 
  could not find function ".Tcl"

as does a local build of R-patched (???!!!). 

This is pretty weird. I'll see if I can dig up some more about where the 
difference is.

-pd



[*] Try library(tcltk); demo(tkfaq)  then library(Rcmdr) and watch the font 
change in the tkfaq window.


> On 15 May 2017, at 23:17 , Fox, John <j...@mcmaster.ca> wrote:
> 
> Dear Jose,
> 
> It's a bit difficult to respond to your latest messages because you sent so 
> many of them.
> 
> I'm not entirely sure what's producing your font problems -- perhaps Simon 
> will have some additional ideas -- but you should be aware that you can't 
> load the Rcmdr package -- or, more generally, the tcltk package -- without 
> XQuartz (or another X11 system). Normally, XQuartz should start automatically 
> when the Rcmdr (or tcltk) package is loaded. That is, you should not have to 
> start it separately.
> 
> It may help to know that the Rcmdr package selects its default dialog font by 
> querying the default Tk font, via the command
> 
>   tclvalue(.Tcl("font actual TkDefaultFont -family"))
> 
> and sets the font for commands and output by querying the default Tk 
> fixed-width font:
> 
>   tclvalue(.Tcl("font actual TkFixedFont -family"))
> 
> On my Macs, these are respectively the helvetica and courier fonts.
> 
> In any event, I'm glad that you seem to have solved your problem.
> 
> John
> 
>> -Original Message-
>> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
>> Sent: Monday, May 15, 2017 3:18 PM
>> To: Simon Urbanek <simon.urba...@r-project.org>; Fox, John
>> <j...@mcmaster.ca>; r-sig-mac@r-project.org
>> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
>> 
>> When I run R without XQuartz, the text from the help screen renders
>> well. I think the problem seems to be related to XQuartz.
>> 
>> José
>> 
>> 
>> José G. Conde, MD, MPH
>> Professor, School of Medicine
>> Director, CentIT2
>> UPR Medical Sciences Campus
>> 
>> Tel  (787) 763-9401 Fax (787) 758-5206
>> 
>> Email: jose.con...@upr.edu
>> 
>> URL: http://rcmi.rcm.upr.edu
>> 
>>> On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
>> <jose.con...@upr.edu> wrote:
>>> 
>>> … and the same I get the same issue with R “help” screens in my iMac.
>> I cannot reproduce this in the macBook.
>>> 
>>> José
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> José G. Conde, MD, MPH
>>> Catedrático, Escuela de Medicina
>>> Director, CentIT2
>>> Recinto de Ciencias Médicas, UPR
>>> 
>>> Tel  (787) 763-9401  Fax (787) 758-5206
>>> 
>>> Correo electrónico: jose.con...@upr.edu
>>> 
>>> URL: http://rcmi.rcm.upr.edu
>>> 
>>>> On May 15, 2017, at 2:14 PM, Jose G Conde Santiago
>> <jose.con...@upr.edu> wrote:
>>>> 
>>>> This is the actual resolutions.
>>>> 
>>>> José
>>>> 
>>>> 
>>>> José G. Conde, MD, MPH
>>>> Professor, School of Medicine
>>>> Director, CentIT2
>>>> UPR Medical Sciences Campus
>>>> 
>>>> Tel  (787) 763-9401 Fax (787) 758-5206
>>>> 
>>>> Email: jose.con...@upr.edu
>>>> 
>>>> URL: http://rcmi.rcm.upr.edu
>>>> 
>>>>> On May 15, 2017, at 12:31 PM, Jose G Conde Santiago
>> <jose.con...@upr.edu> wrote:
>>>>> 
>>>>> 
>>>> 
>>> 
> 
> ___
> R-SIG-Mac mailing list
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> 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

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Re: [R-SIG-Mac] R3.4.0 Upgrade from R3.3.3

[peter dalgaard]

Yes, especially this time, since the toolchain has been updated.

My favourite procedure for this goes like

(pkgs <- .libPaths())
(pkgs.old <- sub("3.4", "3.3", pkgs, fixed=TRUE))
(pkgs.new <- setdiff(list.files(pkgs.old), list.files(pkgs)))

Check for sanity(!), then install.packages(pkgs.new). Things may need 
modification if yor setup involves personalized libraries, multiple repos, etc.

Just copying the entire directory followed by update.packages(checkBuilt=TRUE) 
will overwrite packages from the installation of 3.4 and not all of those are 
CRAN based.

[To tell the truth, I don't usually practice what I preach. I just install the 
missing packages when it turns out that I need them...] 

-pd

> On 23 Apr 2017, at 05:49 , Roy Mendelssohn - NOAA Federal 
> <roy.mendelss...@noaa.gov> wrote:
> 
> I keep forgetting.  So if I jump from R3.3.3 to R3.4.0 is it necessary (or at 
> least advisable) to re-install packages?
> 
> Thanks,
> 
> -Roy
> 
> **
> "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: http://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

-- 
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

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Re: [R-SIG-Mac] R patched version for Mac

[Peter Dalgaard]

Simon,

I seem to recall someone already poked you on this matter, but I can't find a 
record of it, so maybe not...

The symptoms are pretty clear, the log indicates a successful recent build, but 
apparently the packages have not been built since Oct 27, so 
R-3.3-branch-mavericks.pkg contains the version from the and is actually older 
than the current release. (I checked the contents with pkgutils, and it is not 
just a labeling issue; the Payload files are time-stamped Oct 27 05:15)

-pd

> On 28 Dec 2016, at 11:59 , Prof Brian Ripley  wrote:
> 
> On 27/12/2016 19:19, Watson, David W. (MSFC-ES62) wrote:
>> I have been trying to download the “patched” version of 3.3.2 for Mac from 
>> CRAN,
> 
> What makes you think there is a patched version on CRAN?  Did you follow the 
> link on https://cran.r-project.org/bin/macosx/
> to 
> http://r.research.att.com/mavericks/R-3.3-branch/R-3.3-branch-mavericks.pkg?  
> That is Simon Urbanek's site, so you need to ask him.
> 
> but the version that gets delivered is actually the October Release Candidate 
> version,
>> (R version 3.3.2 RC (2016-10-26 r71594). It has been doing this since 3.3.2 
>> has been released. Is there a real patched version somewhere?
>> 
>> David Watson
>> NASA - MSFC
>> Mail Code ES62
>> Phone 256-544-1300
>> FAX   256-544-2964
>> david.w.wat...@nasa.gov
> 
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
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Re: [R-SIG-Mac] Download data from Internet contained in a Zip file

[peter dalgaard]

Things happened with HTTPS in 3.2.2, so upgrade... 

With 3.3.2 on Mavericks, I see

> temp <- tempfile()
> download.file("https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip",temp)
trying URL 
'https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip'
Content type 'application/octet-stream' length 1228 bytes
==
downloaded 1228 bytes

-pd

> On 26 Dec 2016, at 12:19 , Christofer Bogaso <bogaso.christo...@gmail.com> 
> wrote:
> 
> $version.string
> [1] "R version 3.2.1 (2015-06-18)"

-- 
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

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Re: [R-SIG-Mac] Problem running TOBIT for R 3.2 at SPSS 24 Interface MAC Sierra 10.12.1

[Peter Dalgaard]

It really should be SPSS's responsibility to track these issues. They are 
sponging off our work, precariously close to overstepping the license 
conditions, creating new problems, then expecting us to come and fix them.

As for the concrete issue, you seem to be bitten by what was a major annoyance 
in the 3.2 series: pbkrtest requiring R >= 3.2.3 and hence all packages 
depending on it (like car) doing so as well. 

If SPSS hardcodes the R version, you are up the proverbial creek... You might 
get away with hacking the DESCRIPTION file for pbkrtest to make it install (not 
work, but you likely won't use it anyway) under 3.2.0. Of course, if it breaks 
you can keep both pieces.

I'd probably be more inclined to save out the data set, fire up an appropriate 
version of R (or RStudio), do

library(foreign)
d <- read.spss("myfile.sav", to.data.frame=TRUE)
library(AER)


and so forth.

You may need to study the R syntax a little. Achim and Christian wrote an 
inexpensive book called "Applied Econometrics with R"

-pd

> On 8 Dec 2016, at 10:34 , Andreas Schröder  
> wrote:
> 
> Dear R-SIG-Mac members, 
> 
> This is my first post and I would like to thank you first of all for helping 
> out fellow users of R!
> 
> I am currently doing my master thesis and struggle with making the TOBIT 
> regression run on my SPSS 24, operated with Mac (OS Sierra 10.12.1). 
> 
> I use SPSS 24 and have the installer plugin-in for R successfully  installed. 
> I installed the correct R version 3.2 and also XQuartz but if I try to 
> execute the TOBIT regression (I can choose it in my SPSS menu now) I get 
> constantly dialogues showing that certain packages would be missing (CAR, AED 
> etc.). (Pic 1). Apparently, those packages have been added later to R (higher 
> r version than the one mandated by my spss 24 version). I downloaded the 
> versions R 3.2.5 that is referred to in the first picture but once I try 
> installing it, I get displayed another error message by SPSS that the version 
> of R was incorrect. Also manually installing the AER package on R 3.2. did 
> not work for me because I do not know where to find and executable file 
> within the AER package. (Pic 3)
> 
> 
> I already spent yesterday and partly the day before to find my mistake but I 
> couldn’t resolve the issue.
> I am glad to receive any kind of input!
> 
> Best, 
> 
> Andreas
> 
> 
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Re: [R-SIG-Mac] R error

[peter dalgaard]

> On 16 Nov 2016, at 21:13 , Bryan Hanson <han...@depauw.edu> wrote:
> 
> Kirk this has been reported previously but apparently doesn't affect many 
> users. You can ignore it safely. Bryan

It should probably be fixed at some point. For one thing, the method might 
actually disappear in a future version of the OS, but there are also some hints 
that it might misbehave on Retina displays (haven't seen it actually do that, 
though). It's one of those things that has lingered on while we supported Snow 
Leopard.

-pd

> 
> Sent from an undisclosed location - check with the NSA.
> 
>> On Nov 16, 2016, at 1:56 PM, Kirk Steyer <kirkl...@mac.com> wrote:
>> 
>> I have been using R for the last five years and is my favorite platform for 
>> computations and simulations. My question:
>> 
>> I am an Apple user and since the upgrade to 10.8, I am now using 10.12.1 
>> (16B2555) macOS Sierra, i have been getting this error message when I try to 
>> execute a command from the document editor.
>> 
>> 2016-11-16 10:32:52.467 R[10235:1165417] *** WARNING: Method 
>> convertPointFromBase: in class NSView is deprecated on 10.7 and later. It 
>> should not be used in new applications. 
>> 
>> Is there something I could do, or have not done to avoid this error.
>> 
>> Thanks
>> 
>> 
>> Kirk Steyer
>> Principal Engineer
>> Pharmaceutical & Medical Devices
>> 2306 Lava Drive
>> San Jose, CA 95133
>> O: 408.937.5807
>> C: 408.833.9102
>> kirkl...@mac.com
>> 
>> 
>>   [[alternative HTML version deleted]]
>> 
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> 
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Re: [R-SIG-Mac] Writing R package that calls Fortran on Mac os X El Capitan Error

[peter dalgaard]

> On 16 Jun 2016, at 22:53 , Kodalore Vijayan, Vineetha W <vwk...@mun.ca> wrote:
> 
> Perfect! Its working now. Thanks a lot for your patience and help.
> 
> Just curious, what did I do wrong in the previous case?
> 

Tried to use a dynamic library that wasn't there:

>> useDynLib(randomepi)


but you never built a randomepi.so. You built randomepi.o, but that is an 
object file not a dynamic library. It was eventually linked into Nepidemic.so, 
which is the thing that you do want to useDynLib() on.

-pd

(Incidentally, watch your casing, you use "Nepidemic" and "NEpidemic" every 
other time. Sooner or later you'll find yourself in a situation where the case 
actually matters and gives you a mysterious malfunction.)

> -Vineetha
> 
> On Thu, Jun 16, 2016 at 2:48 PM, Eduardo M. A. M.Mendes <
> emammen...@gmail.com> wrote:
> 
>> Please rename your NAMESPACE to something else and create a new one with
>> 
>> useDynLib(NEpidemic,.registration = TRUE)
>> export(randomepi)
>> 
>> It is worth a try.
>> 
>> On Jun 16, 2016, at 5:40 PM, Kodalore Vijayan, Vineetha W <vwk...@mun.ca>
>> wrote:
>> 
>> Yes. My package name is "Epidemic" and namespace contains the following:
>> 
>> useDynLib(randomepi)
>> useDynLib(Nepidemic, .registration = TRUE)
>> 
>> exportPattern("^[[:alpha:]]+")
>> export(randomepi)
>> import(graphics,grDevices,stats, utils)
>> 
>> 
>> I could see Nepidemic.so and randomepi.o files in the src folder.
>> 
>> -V
>> 
>> 
>> 
>> 
>> On Thu, Jun 16, 2016 at 2:28 PM, Eduardo M. A. M.Mendes <
>> emammen...@gmail.com> wrote:
>> 
>>> Dear Vennetha
>>> 
>>> I am running R on a mac too.
>>> 
>>> Please see if my comments below helps.
>>> 
>>> 
>>> On Jun 16, 2016, at 5:00 PM, Kodalore Vijayan, Vineetha W <vwk...@mun.ca>
>>> wrote:
>>> 
>>> I'm trying to write an R package that calls a Fortran subroutine on my
>>> Mac
>>> os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.
>>> 
>>> I couldn't  build the library with my current namespace commands.
>>> I get the following error:
>>> 
>>> 
>>> * installing *source* package ‘Nepidemic’ ...
>>> ** libs
>>> gfortran  -fPIC -Wall -g -O2  -c  randomepi.f95 -o randomepi.o
>>> gfortran -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
>>> Nepidemic.so randomepi.o -F/Library/Frameworks/R.framework/.. -framework R
>>> -Wl,-framework -Wl,CoreFoundation
>>> 
>>> 
>>> The name of the library created by r cmd shlib is Nepidemic.so.
>>> 
>>> installing to
>>> /Users/Vineetha/myrlibrary/myrpackages/Nepidemic.Rcheck/Nepidemic/libs
>>> ** R
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** testing if installed package can be loaded
>>> Error in library.dynam(lib, package, package.lib) :
>>> shared object ‘randomepi.so’ not found
>>> 
>>> 
>>> Note that the r cmd check is looking for randomepi.so so it means that it
>>> is calling the wrong library (it should be Nepidemic.so).  Are you sure
>>> that the NAMESPACE contains the following lines?
>>> 
>>> useDynLib(NEpidemic,.registration = TRUE)
>>> export(randomepi)
>>> 
>>> in all the examples I have those lines would suffice.
>>> 
>>> Error: loading failed
>>> Execution halted
>>> ERROR: loading failed
>>> * removing
>>> ‘/Users/Vineetha/myrlibrary/myrpackages/Nepidemic.Rcheck/Nepidemic’
>>> 
>>> 
>>> My package name is "NEpidemic" and source code file in src folder is
>>> "randomepi.f95"
>>> 
>>> Any help would be much appreciated. I'm vey new to both R
>>> and Fortran coding, especially in package building.
>>> 
>>> Thanks in advance!
>>> Vineetha
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
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>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>>> 
>> 
>> 
> 
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> 
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-- 
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

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Re: [R-SIG-Mac] Writing R package that calls Fortran on Mac os X El Capitan Error

[peter dalgaard]

The most obvious thing is that you build Nepidemic.so but the error talks about 
randomepi.so.  Could it be as simple as putting the wrong thing in 
useDynLib(...)?

-pd


> On 16 Jun 2016, at 22:00 , Kodalore Vijayan, Vineetha W <vwk...@mun.ca> wrote:
> 
> I'm trying to write an R package that calls a Fortran subroutine on my  Mac
> os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.
> 
> I couldn't  build the library with my current namespace commands.
> I get the following error:
> 
> 
> * installing *source* package ‘Nepidemic’ ...
> ** libs
> gfortran  -fPIC -Wall -g -O2  -c  randomepi.f95 -o randomepi.o
> gfortran -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
> Nepidemic.so randomepi.o -F/Library/Frameworks/R.framework/.. -framework R
> -Wl,-framework -Wl,CoreFoundation
> installing to
> /Users/Vineetha/myrlibrary/myrpackages/Nepidemic.Rcheck/Nepidemic/libs
> ** R
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Error in library.dynam(lib, package, package.lib) :
>  shared object ‘randomepi.so’ not found
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing
> ‘/Users/Vineetha/myrlibrary/myrpackages/Nepidemic.Rcheck/Nepidemic’
> 
> 
> My package name is "NEpidemic" and source code file in src folder is
> "randomepi.f95"
> 
> Any help would be much appreciated. I'm vey new to both R
> and Fortran coding, especially in package building.
> 
> Thanks in advance!
> Vineetha
> 
>   [[alternative HTML version deleted]]
> 
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> 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

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Re: [R-SIG-Mac] R commander installation problem (Mac OSX Capitan)

[peter dalgaard]

Please avoid sending in HTML. It comes out barely readable (at best).

I don't see a problem with Rcmdr on Mavericks with R 3.3.0.

The error message points to a problem with the Tcl/Tk installation, probably 
not Rcmdr per se. 

To isolate the issue, you could try 

library(tcltk)
demo(tkfaq)

(or some of the other demos).

-Peter D

 
On 01 Jun 2016, at 13:31 , Candice Chan <aurorasea...@hotmail.com> wrote:

> 
> 
> 
> Hello, I am completely new to using R and I'm trying to install it onto my 
> laptop (Mac Capitan 10.11.5). I have downloaded R commander, and also ensured 
> I installed the latest X Quartz. I then run "library(Rcmdr)", but received 
> the following message: Loading required package: splinesLoading required 
> package: RcmdrMiscLoading required package: carLoading required package: 
> sandwichError : .onLoad failed in loadNamespace() for 'Rcmdr', details:  
> call: structure(.External(.C_dotTclObjv, objv), class = "tclObj")  error: 
> [tcl] invalid command name "tk_messageBox".Error: package or namespace load 
> failed for �Rcmdr�I searched for help and some previous posts suggested 
> running X quartz in the background and restarting R, and try again. However 
> that failed to solve the problem. I would really appreciate your help and 
> advice on this. Thank you very much Candice NUS Student 
> 
>   [[alternative HTML version deleted]]
> 
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-- 
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

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