Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R

Yeah I **guess** so. Even though a close look at ?.Platform doesn't particularly help clarify the somewhat fuzzy concept of "default type" or "preferred setting for options('pkgType')": pkgType: character string, the preferred setting for ‘options("pkgType")’. Values ‘"source"’,

[R-SIG-Mac] GTK+ support (or rather lack thereof)

We have a fairly complete coverage of packages for R 4.0.0, but one exception is GTK+ (and thus RGtk2 and its dependencies). It seems that GTK+ has been abandoned several years ago, the documented macOS build doesn't work and there are no released binaries. To make things worse, Gnome has been s

Re: [R-SIG-Mac] OpenMP on CRAN

Patrick, you can't mix compilers - it really matters which iomp your'e using. llvm has its own modified version which may not be the same as the official Intel release. From your tests it looks like you're using the llvm one which will likely work only with that compiler. Since Apple doesn't ha

Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

Yes, to a degree - but is'a bit counter-intuitive. Unfortunately, the 4.0 installer won't keep 3.6 (not sure why, need to investigate), but vice-versa. So you have to install 4.0.0 alpha and then 3.6.3. Alternatively, you can move /Library/Frameworks/R.framework aside and then install 4.0.0 alph

Re: [R-SIG-Mac] OpenMP on CRAN

Thanks Kevin, interesting approach. However, when testing it against a few packages I get symbol pointer issues (e.g. for data.table and xgboost). Using llvm everything works. Could llvm be the best middle way? Easy installation via brew and still clang compliant. Currently my Makevars look as

Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

R versions on macOS are installed next to each other - you just need to “switch” between them during initialization. In the end R CMD * will use the R interpreter that is first in your $PATH. https://rud.is/rswitch/ helps - but you can also do so without by writing custom CLI wrappers. On 2. Apr

Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

  Is there a procedure for dual install, e.g., so I could run "R4 CMD check", etc.?   Please excuse if this has already been answered.   Thanks,   Spencer Graves On 2020-04-02 02:50, Rainer M Krug wrote: On 1 Apr 2020, at 16:07, Patrick Schratz wrote: The same goes here

Re: [R-SIG-Mac] OpenMP on CRAN

Tim, > On 3/04/2020, at 2:01 AM, BATES Timothy wrote: > > Moving to a compiler that drops support for OpenMP seems a sad choice, > especially now we’ve all climbed the learning curve of the non-Apple compiler > (the real barrier was lack of a pkg installer and that’s done now). > It has cau

Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R

Hervé, what Brian was referring to was > .Platform$pkgType [1] "mac.binary" Cheers, Simon > On 2/04/2020, at 10:20 PM, Hervé Pagès wrote: > > > > On 4/2/20 02:05, Prof Brian Ripley wrote: >> On 02/04/2020 09:34, Simon Urbanek wrote: >>> Hervé, >>> >>> "both" is a fairly recent addition an

[R-SIG-Mac] Homebrew [was: from Mac to LInux?]

> On 2/04/2020, at 9:15 PM, Patrick Schratz wrote: > > AFAIK most people on that list would vote hard against installing R via > homebrew for several reasons - maybe there should be a section about this on > the R dev / CRAN page to address this topic, @Simon? Otherwise this will come > up

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 205, Issue 13

I think I will play with this over the weekend, especially if the calm before the storm prevails. el — Sent from Dr Lisse’s iPad Mini 5 On 2 Apr 2020, 22:21 +0200, Duncan Murdoch , wrote: > That lists "base" as a package, as well as the other base and > recommended packages. That's not what Dr.

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 205, Issue 13

That lists "base" as a package, as well as the other base and recommended packages. That's not what Dr. Lisse was looking for: he wanted "all user installed (additional) packages, ie not the ones that come with R?". Duncan Murdoch On 02/04/2020 10:47 a.m., Colin A. Smith wrote: This will d

Re: [R-SIG-Mac] OpenMP on CRAN

Kevin, Simon discussed why they opted to avoid this back in June '19 when Jon Clayden brought up a similar success. https://stat.ethz.ch/pipermail/r-sig-mac/2019-June/012998.html The sentiment was using the system compiler is in manner is unsupported and works only on some systems. I'm not sur

Re: [R-SIG-Mac] OpenMP on CRAN

Hi, For what it's worth, it looks like it is still possible to use OpenMP on macOS with the system toolchain. Using the example file here: https://computing.llnl.gov/tutorials/openMP/samples/C/omp_hello.c I can compile + link + run this on macOS 10.15.4 and with: $ /usr/bin/clang -Xpreprocessor

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 205, Issue 13

> 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"]) -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 205, Issue 13

This will do it as well: package_list <- tapply(rownames(installed.packages()), installed.packages()[,"LibPath"], c) Bonus to find out which library directories are writable by the user: file.access(names(package_list), mode=2) == 0 Cheers, Colin > On Apr 2, 2020, at 10:36, Michael Hall wro

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 205, Issue 13

> On Apr 2, 2020, at 6:10 AM, r-sig-mac-requ...@r-project.org wrote: > >> Is there a way of (only) listing all user installed (additional) >> packages, ie not the ones that come with R? https://www.r-bloggers.com/list-of-user-installed-r-packages-and-their-versions/

Re: [R-SIG-Mac] Homebrew

Rainer, I am definitively interested. But, as a disclaimer, I am an elderly Gynecologist only dabbling in R and a little in Perl :-)-O. el On 02/04/2020 12:43, Rainer M Krug wrote: > > >> On 2 Apr 2020, at 12:17, Duncan Murdoch >> wrote: >> >> On 02/04/2020 5:58 a.m., Dr Eberhard W Lisse wr

[R-SIG-Mac] OpenMP on CRAN

Moving to a compiler that drops support for OpenMP seems a sad choice, especially now we’ve all climbed the learning curve of the non-Apple compiler (the real barrier was lack of a pkg installer and that’s done now). Losing OpenMP for the CRAN version of OpenMx/umx (our SEM packages) would be a

Re: [R-SIG-Mac] Homebrew

Argument for homebrew: brew upgrade which will figure out what needs to be upgraded so I don't have manually keep track of it. BTW, it usually pulls the binary, and these have worked without any issues for many years, the last time something went wrong on the Download and it pulled t

Re: [R-SIG-Mac] Homebrew

> On 2 Apr 2020, at 12:56, Hervé Pagès wrote: > > Just for a minute let's ignore the fact that installing R via Homebrew is not > considered a good option by the competent authorities (which sounds like a > good enough reason to stay away from it). I'm still wondering: what's the > benefit

Re: [R-SIG-Mac] Homebrew

Just for a minute let's ignore the fact that installing R via Homebrew is not considered a good option by the competent authorities (which sounds like a good enough reason to stay away from it). I'm still wondering: what's the benefit vs installing the official CRAN binary? Just curious. Than

Re: [R-SIG-Mac] Homebrew

> On 2 Apr 2020, at 12:17, Duncan Murdoch wrote: > > On 02/04/2020 5:58 a.m., Dr Eberhard W Lisse wrote: >> New thread :-)-O >> I am wondering if I should not try to figure out how automate this. >> Is there a way of (only) listing all user installed (additional) >> packages, ie not the ones t

Re: [R-SIG-Mac] Homebrew

On 02/04/2020 5:58 a.m., Dr Eberhard W Lisse wrote: New thread :-)-O I am wondering if I should not try to figure out how automate this. Is there a way of (only) listing all user installed (additional) packages, ie not the ones that come with R? Look at the "Priority" column in installed.pack

[R-SIG-Mac] Homebrew

New thread :-)-O I am wondering if I should not try to figure out how automate this. Is there a way of (only) listing all user installed (additional) packages, ie not the ones that come with R? I could then construct the below file automagically, and if I was really bothered and bored find out

Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R

On 4/2/20 02:05, Prof Brian Ripley wrote: On 02/04/2020 09:34, Simon Urbanek wrote: Hervé, "both" is a fairly recent addition and my guess would be that it has been guarded specifically since it is the default and installing binaries only works for the CRAN version. I didn't look at the ne

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

> On 2 Apr 2020, at 10:15, Patrick Schratz wrote: > > AFAIK most people on that list would vote hard against installing R via > homebrew for several reasons - maybe there should be a section about this on > the R dev / CRAN page to address this topic, @Simon? Otherwise this will come > up a

Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R

On 02/04/2020 09:34, Simon Urbanek wrote: Hervé, "both" is a fairly recent addition and my guess would be that it has been guarded specifically since it is the default and installing binaries only works for the CRAN version. I didn't look at the new "both" code to see how it knows that it's th

Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R

Thanks. Only seeing this after I sent my other email about also getting crashes when I use your conf.high-sierra-x86_64 settings. But of course I'm not on Catalina so my setting is not exactly the same as yours. Therefore I should conclude that the CRAN binaries are not meant for me. H. On 4/

Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R

FWIW I also get the same thing (i.e. R crashes on loading CRAN binary packages) if I configure R 4.0 alpha like here https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4/conf.high-sierra-x86_64, that is, if all the compilers use -mmacosx-version-min=10.13 and I set --build=x86_64-apple-darwin1

Re: [R-SIG-Mac] Installing CRAN binary packages with R 4.0 installed from source crashes R

Hervé, "both" is a fairly recent addition and my guess would be that it has been guarded specifically since it is the default and installing binaries only works for the CRAN version. I didn't look at the new "both" code to see how it knows that it's the CRAN version - there is really no special

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

I do same, including Rstudio (Cask). Once in a while after major updates I need to reinstall all my extra packages, so I have written me a little script along the lines of #!/usr/local/bin/Rscript local({ r <- getOption("repos") r["CRAN"] <- "http

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

AFAIK most people on that list would vote hard against installing R via homebrew for several reasons - maybe there should be a section about this on the R dev / CRAN page to address this topic, @Simon? Otherwise this will come up again and again. Anyhow, this is also not relating to the initial

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

I am using Homebrew on a Mac (two Macs - one at home, one at work) instead of the official R package, and I did not have any problems after upgrades - maybe I am lucky, maybe not as picky in defining “problem”, but my suggestion would be to try R from homebrew to install R. OK - no support fro

Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

> On 1 Apr 2020, at 16:07, Patrick Schratz wrote: > > The same goes here regarding support. > > I am (co-)maintaining a package on ropensci focusing on provider-agnostic CI > approaches for R (tic) and have quite some experience with all the little > culprits there. > > Since you mentioned

Re: [R-SIG-Mac] R 4.0 toolchain

Thanks Simon. Branching off here to discuss the toolchain in general. I see the danger posting not 100% correct scripts and in blog posts in general because they might get outdated and not always reflect the official documentation. On the other side: What is the middle way? Arguably installing a