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

I’m trying to use STAN which uses R CMD config to check the availability of the compilers. This works fine on my MacBook but on my iMac I have the documents on a separate hard drive. Within R CMD config it uses the location of the home folder which because of my choice of name of hard drive

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

> On 1 Sep 2016, at 5:46 PM, Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote: > > On 01/09/2016 00:43, Ken Beath wrote: >> I’m trying to use STAN which uses R CMD config to check the availability of >> the compilers. >> >> This works fine on my MacB

[R-SIG-Mac] Fortran on MacOS Sierra

I tried to build frailtypack from source using R 3.3.1 and it failed with the following message (after a ridiculous amount of warnings) gfortran-4.8 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress

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

e: > > This seems to be Sierra, which has 'tidied up' system libraries. > > > > The recommendation for El Capitan at http://coudert.name/software.html also > > works correctly on Sierra. (See the manual, preferably before posting.) > > > > There are good reasons why

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

e posting.) > > There are good reasons why the posting guide asks for 'at a minimum' the > output of sessionInfo() > > On 30/09/2016 09:31, Ken Beath wrote: > I tried to build frailtypack from source using R 3.3.1 and it failed with the > following message (after a ri

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

In the Install Packages dialog there is an Other Repository option and that seems to be permanent. It can also be changed in the Preferences. > On 29 Sep. 2016, at 8:13 am, Duncan Murdoch wrote: > > On 28/09/2016 5:26 PM, Joseph Kunkel wrote: >> I got this error

Re: [R-SIG-Mac] Recurring problem to run R with SPSS 24

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

Re: [R-SIG-Mac] Mac-only problem using readOGR(), which uses ogrInfo(), to read a shapefile from a directory on a USB pen drive

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

Re: [R-SIG-Mac] R.app crashes at startup on MacOS Sierra

I’ve had no trouble with using RStudio so it is definitely a GUI problem. I’ve also had no trouble with TeXShop so I assume that whatever LaTex editor you are using is the problem. Ken > On 1 Mar 2017, at 4:42 pm, David Diez wrote: > > Anyone have any luck with

Re: [R-SIG-Mac] Mac-only problem using readOGR(), which uses ogrInfo(), to read a shapefile from a directory on a USB pen drive

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

Re: [R-SIG-Mac] Mac OS X Yosemite 10.10.5

3.3 built for Mavericks at http://r.research.att.com should work. Ken > On 6 Sep 2018, at 4:27 am, Braden Justice wrote: > > Hello, I can’t seem to find a version that works for my mac, in the subject > line I’ve included my software. Do you know any versions of R that will work > for me??

Re: [R-SIG-Mac] R, ape, and read.nexus()

That looks like a package issue, so I would contact the author. Some authors can be very helpful. Ken > On 2 Sep 2019, at 12:05 pm, Timothy Dickinson > wrote: > > I have repeatedly been encountering a problem reading into R nexus files that > I created in PAUP* 4.0a. I use the savetrees

Re: [R-SIG-Mac] Memory Exhausted

Try this https://stackoverflow.com/questions/51295402/r-on-macos-error-vector-memory-exhausted-limit-reached and the links. Ken > On 7 Jul 2019, at 1:22 pm, Alex wrote: > > Hello all, > > I am new in R studio. I have a big data to run using RStudio. I keep > getting "Error: vector memory

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

2/11/19, 7:25 PM, "R-SIG-Mac on behalf of Manuel Spínola" > wrote: > > An update. > > Before doing the suggested installation, I updated Catalina to 10.5.2, > Xtools to 11.3 and the Command Line Tools and it works. > > Manuel > > El

Re: [R-SIG-Mac] segfault with raster package

This works fine for me using R 3.6.2 on MacOS 10.15.2 The only difference from a standard installation is that I have the setup for Rcpp, but that shouldn’t change anything. Ken > On 17 Dec 2019, at 8:34 am, Marc Girondot via R-SIG-Mac > wrote: > > When I load the last version of raster

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

What worked for me was installing the tools using https://github.com/rmacoslib/r-macos-rtools/releases and then installing rstan from source ie install.packages(“rstan”,type=“source) as suggested on one of the stan forums Ken > On 11 Dec 2019, at 11:09 am, Manuel Spínola wrote: > > Dear

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

ote: > > Thank you very much to all. > > Does Installing the macos-rtools could affect R in other ways? > > Manuel > > El mié., 11 dic. 2019 a las 6:56, Ken Beath () escribió: > What worked for me was installing the tools using > https://github.com/

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

I have Catalina and it works perfectly, as far as this goes. Ken > On 24 Oct 2019, at 9:13 am, Bryan Hanson wrote: > > Duncan… > > I’m creating a new file. The menu item is “New Document”. I called it *.R > to distinguish it from “New Rd Document”, and since when you attempt to save > it

Re: [R-SIG-Mac] damned Catalina

Try another repository. It works fine with the main CRAN and teh RStudio repositories. Ken > On 18 Dec 2019, at 10:50 pm, bruno apolloni wrote: > > Dear All > > among disasters of the new operating system Catalina, this one concerns R. > > Trying to install “regtools" the answer by Crane R

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

Your package passes checks on my machine perfectly. It has R 4.0.0 with RStudio and TexLive 2020 with updates to a week or two ago. Ken > On 13 May 2020, at 8:17 am, Spencer Graves > wrote: > > Hello, All: > > > Might "R CMD check" on Mac use obsolete LaTeX software? > > > I

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

Plus one of the duties of package managers is to make sure that they build and pass CRAN checks. Doing that with a non standard environment seems a bit risky. At the moment I can’t get anything to build on R-Devel which is making life difficult and I may raise a question if it still isn’t

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

> On 7 Sep 2020, at 9:31 am, Mike Feher wrote: > 2. Are these objects, etc. stored on disk somewhere, or are they only > accessible via the interfaces? For example, I would be interested to see > the source code for the demo examples to learn how to do certain things, if > this is possible.

Re: [R-SIG-Mac] catalina humbug

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

Re: [R-SIG-Mac] Update to versions GEOS 3.8.0, GDAL 3.0.4 and PROJ 7.0.0 in macOS Catalina

sf requires GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0) so I would assume that its full functionality is available with these. Ken > On 23 May 2020, at 10:08 am, Manuel Spínola wrote: > > Thank you very much Simon. > > I don't know much about programming so I will keep the current

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

ase or > from http://mac.r-project.org/ ) then most packages will compile with just > Xcode alone. > > Cheers, > Simon > > >> On 20/05/2020, at 12:58 PM, Ken Beath wrote: >> >> Plus one of the duties of package managers is to make sure that they build &

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

Success. I also removed everything from /usr/local then reinstalled MacTex, R and gfortran, and now I can build on both 4.0 and 4.1. Presumably something has changed in the builds between 4.0 and 4.1 and that has interacted with the accumulated nearly 6 years of mess in /usr/local. > On 20

Re: [R-SIG-Mac] Daily builds

Still missing. Ken > On 23 Jul 2020, at 11:06 pm, Gábor Csárdi wrote: > > Hi Simon, > > I wonder if the tarballs and the installers for 4.0 and 4.1 are > missing from https://mac.r-project.org/ on purpose. The logs seem to > have recent dates, but the installers or the links to them are not >

Re: [R-SIG-Mac] No labels in plots - none of the solutions that I've come across have worked

Will Restore Standard Fonts in Font Book do the same thing? Although if reinstalling the system doesn’t work I’m not certain that anything should work. Ken > On 17 Jun 2020, at 9:52 pm, Charlie D wrote: > > Had the same issue. Check your mac font book utility. In my case Arial was > missing

Re: [R-SIG-Mac] R 4 dumping tons of console messages in Big Sur

That is what happens at times with beta software, and is more likely to be Apple’s problem. Assuming that you are properly registered put a bug report into Apple. Ken > On 25 Jun 2020, at 12:49 am, Timothy Bates wrote: > > R in pretty-much unusable in Big Sur (OSX beta) - it's generating

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

Yes, I think it has happened for at least 10 years. I assume that it doesn’t get looked at unless there is some other problem. Ken > On 15 Jun 2020, at 9:06 am, Timothy Bates wrote: > > It won’t hold up submission: I believe it's just a NOTE to let the kind > people helping with submissions

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

ative -arch x86_64 -ftemplate-depth-256 > > Does it seem to mean anything relevant? > >> On Nov 8, 2020, at 11:24 PM, Ken Beath wrote: >> >> It is actually Makevars. If it is there it will be in the .R directory of >> your home folder. >> >> Unles

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

t change anything. I > wanted to try it again now, but I am not finding a .MakeVars file anywhere on > my computer. Where should it be? > > Thanks, > > Gonçalo > >> On Nov 8, 2020, at 8:04 PM, Ken Beath wrote: >> >> Guessing here. Possibly schoo

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

Guessing here. Possibly schools.stan has a problem, that is what teh first error is suggesting. The remaining is a possible problem with .MakeVars which is no longer needed with R. I would also check that files aren’t being saved with a strange encoding. Ken > On 9 Nov 2020, at 7:25 am, Roy

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

With RStudio I just quit, restart and then update the packages. Ken > On 11 Jun 2021, at 8:07 am, Simon Urbanek wrote: > > > Those errors come from packages that you didn't re-install - anything that > uses /usr/local is not from CRAN. So check > /Users/Misha/Library/R/4.0/library/ > Best

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

According to RStudio support for ARM R is only available in the RStudio daily builds https://dailies.rstudio.com which are very unstable. Ken > On 19 May 2021, at 7:33 pm, Renato Morais > wrote: > > Hi all, > > I'm new here, so please forgive my clumsy error

Re: [R-SIG-Mac] more rgl problems

RStudio have a page for reporting bugs at https://github.com/rstudio/rstudio/issues/ You may be the first M! bug. They haven’t progressed my fairly serious bug report about Windows (if you plot a graph and the screen hasn’t updated when you start

Re: [R-SIG-Mac] Unable to change some members of a vector

This question is not related to Macs, but here is the answer anyway. First up, anyone who uses R should understand what a factor is. Find an introductory text on R and read the section on factors. Even better, read the whole book. It seems that it has been decided that R will not automatically

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

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

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

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

Re: [R-SIG-Mac] https://mac.r-project.org/benchmarks/

I ran some tests using my packages and a bootstrapped linear model, and the results were that my M1 MacBook Air was faster than my iMac 8-core 2020, and that included using 4 parallel cores on the M1 versus 8 on the iMac. Ken > On 1 Nov 2021, at 8:11 am, Simon Urbanek wrote: > > > Tim, >

Re: [R-SIG-Mac] r-sig-mac@r-project.org - "You can’t open the application “R” because this application is not supported on this Mac"

You could try the Intel version until the problem with ARM is sorted. It should run fine but will require Rosetta 2. Ken > On 17 Jul 2021, at 5:39 pm, Lindsay Foreman <19038...@brookes.ac.uk> wrote: > > To whom it may concern, > > I am so sorry for being such a dunce. I have been trying and

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

Less than 30 seconds on my iMac, so something is very wrong with your fonts or file system. Ken > On 6 Jun 2022, at 2:34 pm, Richard M. Heiberger wrote: > > I am in the middle of validating fonts. The machine has been running for > about 12 hours, the Activity Monitor CPU > time for the Font

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

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

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

A random sample of packages linking to Rcpp shows that many have NOTEs for installed package size. I would avoid using special compiler flags, as this is something that may cause problems in the future. Ken > On 19 Mar 2023, at 8:27 am, Gilberto Camara > wrote: > > Hi Simon > > Many

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

The problem seems to be with the Electron framework they switched to in the current version. >From https://dailies.rstudio.com/version/2022.07.1+554.pro3/ the previous >version works, but not the Electron version. For those that are interested >Electron is a newer framework that has the

Re: [R-SIG-Mac] List of unnecessary messages when I plot something in R from Terminal

What may be important is that you are running R 4.2.1 which was replaced by 4.2.2 on 31 October 2022, and may know a lot more about Ventura. Also if you are on Ventura it would probably be best to make sure that you are upgraded to 13.2 which hopefully has a lot of the bugs fixed. Ken > On 12