Re: [R-SIG-Mac] Problems with RStudio for mac

2025-07-16 Thread Simon Urbanek
7/2025, at 16:01, Ken Beath wrote: > > The problem is that it uses the Electron framework, and it isn’t supported on > earlier versions of MacOS. > > Ken > >> On 17 Jul 2025, at 1:15 pm, Simon Urbanek >> wrote: >> >> Kevin, >> >> You may

Re: [R-SIG-Mac] Problems with RStudio for mac

2025-07-16 Thread Simon Urbanek
ting >> much >>> closer to what I hope for. There are discussions on migrating (keyboard >>> shortcuts, mental assumptions, etc) from RStudio IDE to reduce the >> change, >>> and I believe there are few things one can do in RStudio that are not >> also &g

Re: [R-SIG-Mac] Problems with RStudio for mac

2025-07-16 Thread Simon Urbanek
are discussions on migrating (keyboard shortcuts, > mental assumptions, etc) from RStudio IDE to reduce the change, and I believe > there are few things one can do in RStudio that are not also feasible in > Positron. > Good luck, > Bill > On 7/15/25 18:36, Simon Urbanek wrote

Re: [R-SIG-Mac] Problems with RStudio for mac

2025-07-15 Thread Simon Urbanek
José, I agree that latest RStudio dropping support for a very large number of Macs is unfortunate. It may be worth raising it with Posit - we have very deliberately not increased the macOS version requirement of R binaries, because it would affect way too may R users based on the estimates from

Re: [R-SIG-Mac] R MacOSX FAQ Question 10.5 on BLAS changing needs update

2025-06-12 Thread Simon Urbanek
Naras, it does if you use latest version please see https://stat.ethz.ch/pipermail/r-sig-mac/2025-April/015155.html Cheers, Simon > On Jun 12, 2025, at 9:17 AM, Balasubramanian Narasimhan > wrote: > > R 4.5.0's addition of two new routines to BLAS > (https://cran.r-project.org/doc/manual

Re: [R-SIG-Mac] Need for `-headerpad_max_install_names` with `--enable-R-framework`

2025-05-16 Thread Simon Urbanek
> Clang: Apple clang version 17.0.0 (clang-1700.0.13.3) > Fortran: GNU Fortran (GCC) 8.2.0 (from > https://mac.r-project.org/tools/gfortran-14.2-universal.pkg) > SDK version: 15.4 > SDK path: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > > and could reproduce the issue

Re: [R-SIG-Mac] Need for `-headerpad_max_install_names` with `--enable-R-framework`

2025-05-15 Thread Simon Urbanek
Heather, yes, please, since we cannot reproduce it, please provide your complete configure flags, full info about your macOS version, tools used (toolchain version and SDK). We are adding -Wl,-headerpad_max_install_names for libraries (see etc/Makeconf, added by configure.ac for darwin), but th

Re: [R-SIG-Mac] Clarifying the status of OMP in CRAN binaries on Mac

2025-05-09 Thread Simon Urbanek
Philipp, the instructions (if really insist on using Xcode 16.3 - not recommended) are here: https://mac.r-project.org/openmp/ relevant part quoted: "Note: If you are using CRAN R binary and there is a potential conflict between its run-time and your run-time (which is generally a bad idea!) th

Re: [R-SIG-Mac] Clarifying the status of OMP in CRAN binaries on Mac

2025-04-25 Thread Simon Urbanek
Gavin, thanks, quick updates inline. > On Apr 25, 2025, at 9:53 PM, Gavin Simpson wrote: > > Thanks Simon, that's really helpful - I find the R manuals confusing on this > issue in part because things MacOS X related are bound up in "Unix-alike" > sections and there are often clauses and / o

Re: [R-SIG-Mac] Clarifying the status of OMP in CRAN binaries on Mac

2025-04-24 Thread Simon Urbanek
to go that route shipped their own (or linked statically) then chaos would ensue breaking all of them. Cheers, Simon > On Apr 25, 2025, at 11:38 AM, bill+rsig...@8pawexpress.com wrote: > > If it’s not compiled in, why is |libomp.dylib| distributed in R for Mac? > > Bill > >

Re: [R-SIG-Mac] Clarifying the status of OMP in CRAN binaries on Mac

2025-04-24 Thread Simon Urbanek
Gavin, > On Apr 24, 2025, at 9:58 PM, Gavin Simpson wrote: > > Dear list, > > I'm trying to clarify my understanding of what is and is not implemented / > expected in terms of openMP support in R and CRAN package *binaries* for > MacOS on apple silicon. > > I have the CRAN's R binary for Ma

Re: [R-SIG-Mac] R/compilers can't find libintl.h on MacOS X

2025-04-23 Thread Simon Urbanek
ar? Without exact output we can only guess ... Cheers, Simon > Duncan Murdoch > > > On 2025-04-19 5:40 p.m., Simon Urbanek wrote: >> Gavin, >> there are few issues here with different possible solutions. >> In general, you cannot mix R from Homebrew and CRAN - they

Re: [R-SIG-Mac] openmp and xcode

2025-04-22 Thread Simon Urbanek
Bill, the libomp.dylib inside R is there solely for the CRAN binaries to make sure that package binaries on CRAN can use the correct OpenMP runtime. Is it not intended to be used outside of that setup. That is also why we don’t ship the headers as anyone compiling from sources will have to do

Re: [R-SIG-Mac] R 4.5.0 and veclib version of blas

2025-04-21 Thread Simon Urbanek
Roy, Please update to R 4.5.0 Patched from https://mac.R-proejct.org as discussed here before - see https://stat.ethz.ch/pipermail/r-sig-mac/2025-April/015155.html Cheers, Simon > On Apr 21, 2025, at 1:48 PM, roy wrote: > > After executing the following: > cd /Library/Frameworks/R.framework

Re: [R-SIG-Mac] R/compilers can't find libintl.h on MacOS X

2025-04-19 Thread Simon Urbanek
Gavin, there are few issues here with different possible solutions. In general, you cannot mix R from Homebrew and CRAN - they use different toolchains and libraries so you have to pick one. 1) Despite what you said, what you are showing below is output from CRAN R, so one option (which I'd r

Re: [R-SIG-Mac] vecLib-based BLAS not working with R 4.5.0

2025-04-15 Thread Simon Urbanek
TL;DR latest R 4.5.0 Patched (r88147 or higher) from https://mac.R-project.org should work. Ulrich, Thanks for the report. Yes, the whole purpose of the R shared BLAS is that you can point it to any BLAS implementation as long as it is complete enough for R to use. Unfortunately, R 4.5.0 now r

Re: [R-SIG-Mac] update.packages() re-downloading old versions

2025-04-05 Thread Simon Urbanek
This looks like a case where an attempt is made to update with type="both" which will take into account both source and binary repositories for comparison, but packages can be installed from source only if the user has the tools and acknowledged that they really want to do that. As Peter said, i

Re: [R-SIG-Mac] install.libs error

2025-03-31 Thread Simon Urbanek
> On Mar 31, 2025, at 10:04 PM, Naresh Gurbuxani > wrote: > > Simon, > > Website mac.r-project.org/tools/ lists mandatory libraries. In the next > paragraph, it has a link to “binaries of libraries and tools for Mac OS > page”. Clicking on the link takes user to mac.r-project.org/bin. H

Re: [R-SIG-Mac] install.libs error

2025-03-30 Thread Simon Urbanek
aries. > A similar problem will arise when a new version of R uses updated versions of > liblzma and PCRE2. > The versions are quite irrelevant since they are used statically so R doesn't care which version you use in packages and vice-versa. Cheers, Simon > Thanks ever

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 264, Issue 10

2025-03-24 Thread Simon Urbanek
Please ignore this "advice" - it makes the mess even worse. As you can tell if you look closer at the output it's about 3rd party tools like homebrew messing up the build which causes the problem in the first place. BTW: the page you quote is complete nonsense: CRAN does provide binaries - that

Re: [R-SIG-Mac] install.libs error

2025-03-23 Thread Simon Urbanek
Naresh, please ignore all "advice" you go so far - most of it was wrong. From your earlier reports it looks like your system is messed up which the the core of the problem - please remove 3rd party libraries from your path (like homebrew, macports, /opt/local etc.) as that will interfere with t

Re: [R-SIG-Mac] gfortran 12 vs 14

2025-02-19 Thread Simon Urbanek
> On Feb 20, 2025, at 2:36 AM, peter dalgaard wrote: > > Do we expect to stay with gfortran 12.2.0 for 4.4.3 and then switch for > 4.5.0? > Most likely - changing version for patch releases doesn't seem necessary. Cheers, Simon > -pd > >> On 19 Fe

Re: [R-SIG-Mac] gfortran 12 vs 14

2025-02-18 Thread Simon Urbanek
Stefano, please note that the CRAN page is talking about the R 4.4.2 release and the developer tools page says "CRAN R Big Sur builds used gfortran-12.2-universal.pkg for R 4.3.0 up to 4.4.2" so they are both correct and very explicit with the corresponding links, so I’m not entirely sure w

Re: [R-SIG-Mac] R 4.5 requires gfortran 14.2

2025-01-24 Thread Simon Urbanek
Jennifer, as usual, it was announced on the mac.R-project.org webpage since it only affects the builds there. R-devel is "unstable" so it may be subject to change, but at this point gfortran 14.2 seems most likely to be the compiler we'll use for 4.5.0 unless we find any issues with that. Chee

Re: [R-SIG-Mac] Binary builds for CRAN packages for R-devel on apple silicon

2025-01-08 Thread Simon Urbanek
Kasper, TL;DR working on it should be within a week or so. The main constraint is the disk space on the package builds machines, I'll have to stop building packages for 4.3 to accommodate R-devel (yes, disk is cheap and all that, but you can't just plug in SSDs into a Mac so more involved...).

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 261, Issue 2

2024-12-11 Thread Simon Urbanek
> On Dec 12, 2024, at 10:00 AM, Duncan Murdoch wrote: > > On 2024-12-11 3:43 p.m., Michael Hall wrote: >>> >>> Message: 1 >>> Date: Wed, 11 Dec 2024 12:25:42 -0500 >>> From: Duncan Murdoch >>> To: R-SIG-Mac >>> Subject: [R-SIG-Mac] R.app not handling events >>> Message-ID: >>> Content-Type

Re: [R-SIG-Mac] Compiling BLAS with Accelerate

2024-11-30 Thread Simon Urbanek
e Internet or R admin but with no luck. > I guess some includes or other configuration is missing but I have no > experience with such huge build system. > > I am generally aiming at testing different BLASes or own implementations of > matrix operations (matmul mainly), > perf and c

Re: [R-SIG-Mac] Compiling BLAS with Accelerate

2024-11-30 Thread Simon Urbanek
Tomek, see R-admin C.3.5.1: https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Accelerate so essentially just add the following to the regular flags: --enable-BLAS-shlib --with-blas='-framework Accelerate' Cheers, Simon > On Nov 30, 2024, at 2:10 AM, Tomek Gieorgijewski > wrote:

Re: [R-SIG-Mac] What are these other 'R' processes?

2024-11-27 Thread Simon Urbanek
Carl, R itself is just a single process. However, there are plenty of ways to have multiple R processes running on your system. The "parallel" package provides various ways in which you can start more parallel R processes for parallel computing. Those will typically appear without a logo. Eve

Re: [R-SIG-Mac] Problems with R-4.4.2 in MacOS Sequoia with Intel chip

2024-11-22 Thread Simon Urbanek
Gilberto, thanks! TLDR; its a bug in the torch package - fix below. It took a while to sort out your example as it was very incomplete, here are the full required steps: --- ## sits doesn't install tests, so have the get them from sources: download.packages("sits", type='source') untar(Sys.glob

Re: [R-SIG-Mac] Problems with R-4.4.2 in MacOS Sequoia with Intel chip

2024-11-22 Thread Simon Urbanek
n96B 31 Out 22:11 pkgconfig > > > > Prof Dr Gilberto Camara > Senior Researcher > Getulio Vargas Foundation (FGV) > National Institute for Space Research (INPE), Brazil > https://gilbertocamara.org/ > = >

Re: [R-SIG-Mac] Problems with R-4.4.2 in MacOS Sequoia with Intel chip

2024-11-22 Thread Simon Urbanek
error. >>>> >>>> The problem affects only Intel-based MacMinis with R-4.4.2. Running >>>> MacMinis with R-4.2.3 work will. All is also well with R-4.4.2 in Macs >>>> with ARM, in Windows and in Lunix/Ubuntu and Linux/Fedora. >>>> >

Re: [R-SIG-Mac] GitHub Action on macOS cannot find the latest version of a package

2024-11-21 Thread Simon Urbanek
Spencer, I strongly recommend NOT selecting compilation from sources as that is non-trivial and requires a whole list of tools and libraries that you don't have - I would recommend using type="binary" in install.packages/update.packages to make sure the get the versions that haven been checked

Re: [R-SIG-Mac] Problems with R-4.4.2 in MacOS Sequoia with Intel chip

2024-11-12 Thread Simon Urbanek
Gilberto, please read https://www.r-project.org/bugs.html first, in particular about how to report a problem. Just saying "cannot execute my scripts" is not helpful at all - please provide exact output, how it differs between the versions etc. For example, the problem may be in your code or pac

Re: [R-SIG-Mac] contrib.url(type = 'mac.binary')

2024-11-12 Thread Simon Urbanek
Jeroen, yes, you're right, that is incorrect. It should read "binary" as that is the only value that automatically picks the correct binary repository for the current R build regardless of platform. Or it should say "mac.binary.big-sur-x86_64" corresponds to bin/macosx/big-sur-x86_64/contrib a

Re: [R-SIG-Mac] R-devel segmentation fault in combination RStudio/R GUI

2024-09-25 Thread Simon Urbanek
packages are not compatible between R versions. Cheers, Simon > On 26 Sep 2024, at 11:42, Simon Urbanek wrote: > > Sebastian, > > thanks, I can replicate the crash in the R GUI and it’s due to a missing > symbol detected at run-time (I’m attaching the traceback even thoug

Re: [R-SIG-Mac] R-devel segmentation fault in combination RStudio/R GUI

2024-09-25 Thread Simon Urbanek
is fully up-to-date, see >> https://www.stats.ox.ac.uk/pub/bdr/M1mac/README.txt >> >> Following the instructions in the R-admin manual and not by some third party >> is always a good idea before posting. >> >> Do please stop sending HTML, as required in t

Re: [R-SIG-Mac] R-devel segmentation fault in combination RStudio/R GUI

2024-09-24 Thread Simon Urbanek
Sebastian, if you want to replicate the CRAN builds, you have to also use the same settings, otherwise you may have a build which is not binary compatible. It is unclear from your description how you built R (there are several variants such as framework install vs "unix"-style install and they

Re: [R-SIG-Mac] Bug in reading UTF-16LE file?

2024-09-08 Thread Simon Urbanek
>From the help page: The encodings ‘"UCS-2LE"’ and ‘"UTF-16LE"’ are treated specially, as they are appropriate values for Windows ‘Unicode’ text files. If the first two bytes are the Byte Order Mark ‘0xFEFF’ then these are removed as some implementations of ‘iconv’ do not accep

Re: [R-SIG-Mac] fcaR plot not working

2024-08-28 Thread Simon Urbanek
Peter, hasseDiagram unfortunately depends on packages outside of CRAN, namely in Bioconductor, so you have to add the corresponding repositories before you install it, e.g.: setRepositories(ind=1:4) install.packages("hasseDiagram") # also installing the dependencies ‘BiocGenerics’, ‘Rgraphviz’,

Re: [R-SIG-Mac] Installing openssl package in R-devel

2024-07-21 Thread Simon Urbanek
On, and I just noticed - you appear to have some legacy Homebrew files as well in /usr/local - on a Mx Mac you should remove all from /usr/local as that is just Intel legacy that will cause a lot of problems. Cheers, Simon > On 22/07/2024, at 10:11 AM, Simon Urbanek wrote: > > Pro

Re: [R-SIG-Mac] Installing openssl package in R-devel

2024-07-21 Thread Simon Urbanek
Probably the best is to remove (aka move aside) *everything* - both /opt/R/arm64 and /opt/homebrew (or at least rename it to move it aside). The openssl package provides a fallback, but only if it doesn't detect something that gets in its way. It gets really confused if you have various various

Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package

2024-07-06 Thread Simon Urbanek
rocessor option ... > > Mikael > > On 2024-07-05 4:53 pm, Mikael Jagan wrote: >> Some thoughts in line below, not "certified" but maybe helpful. Corrections >> welcome ... >> Mikael >>> From: "Balamuta, James" >>> To: Simon Ur

Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package

2024-06-28 Thread Simon Urbanek
s/r-release/NEWS.html > [2]: https://mac.r-project.org/openmp/ > [3]: > https://github.com/RcppCore/RcppArmadillo/blob/37461ba36472305c699263afc229919d37daa5e3/configure.ac#L109 > From: Simon Urbanek > Date: Thursday, June 27, 2024 at 10:25 AM > To: Balamuta, James > Cc: Timothy Bate

Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package

2024-06-27 Thread Simon Urbanek
Most of the claims below are false - libomp is shipped with CRAN R for quite some time specifically so that packages which benefit from it significantly can enable OpenMP reasonably easily - they only need to add the flags as noted on the cited page and CRAN takes care of the rest. If there are

Re: [R-SIG-Mac] procedure to ship libomp.dylib run-time with package

2024-06-27 Thread Simon Urbanek
Tim, There is no need to worry about libomp.dylib on macOS with CRAN packages as libomp is already shipped with R. When the package its built on CRAN, it will be pointed correctly to the version inside R. However, in your output it seems that the problem may be that the user is using the wrong

Re: [R-SIG-Mac] "R CMD build" ...Error... "processing vignette ... failed with diagnostics:, Pandoc is required to build R Markdown vignettes but not available."

2024-06-14 Thread Simon Urbanek
Spencer, Since you already have homebrew on your PATH you can simply run "brew install pandoc". Otherwise you can just set the path while running R CMD: PATH="~/Library/Application Support/r-pandoc/3.2:$PATH" R CMD build fda As of where to set the PATH - it depends on where you run it from - i

Re: [R-SIG-Mac] M3 not working with torch

2024-05-20 Thread Simon Urbanek
Gilberto, since luz is a contributed package, you should probably start first by asking the authors. Given that the torch ecosystem is quite complex and has several layers that need to work together, even if you talk to them, you probably need to add details such as exact versions used (includi

Re: [R-SIG-Mac] R 4.4 crashes loading dplyr

2024-05-02 Thread Simon Urbanek
Carl, it shows that you apparently had some ancient version of magrittr installed way back from R 4.2.x. I have no idea why or how you got it, but update.packages(checkBuilt=TRUE) in R 4.4.0 should have fixed it. Cheers, Simon > On 1/05/2024, at 12:32 AM, Carl Witthoft wrote: > > Thanks, P

Re: [R-SIG-Mac] error when installing the robustbase package (robustbase.rdb is corrupt)

2024-03-25 Thread Simon Urbanek
Y V, as Duncan pointed out this is usually a problem with the RStudio session. Quit RStudio, re-install the package (if in doubt, use R), quit R and re-start RStudio. Cheers, Simon > On 25/03/2024, at 10:54 AM, YV B wrote: > > I'm running R 4.3.3 GUI 1.80 Big Sur Intel build (8340) and RStu

Re: [R-SIG-Mac] Graphics in R, version 4.3.2, does not work well in MacOS

2024-02-21 Thread Simon Urbanek
f doodling unrelated things on the screen is now in R-devel and R-patched (85968 and 85969 resp.) so please check R 4.3.3 beta r85969 or higher from mac.R-project.org Cheers, Simon > On 22/02/2024, at 10:57 AM, Simon Urbanek wrote: > > I can confirm that this is a bug specific to

Re: [R-SIG-Mac] Graphics in R, version 4.3.2, does not work well in MacOS

2024-02-21 Thread Simon Urbanek
I can confirm that this is a bug specific to macOS Sonoma 14.3.1, even earlier versions of Sonoma don't have that problem. Given the number of previous bugs in Sonoma chances are Apple may fix in the in the next release, but I'll see if we can do anything about it on our end in the meantime. Ch

Re: [R-SIG-Mac] Graphics in R, version 4.3.2, does not work well in MacOS

2024-02-17 Thread Simon Urbanek
Maria, can you, please, include the full output of sessionInfo() in R and system_profiler SPHardwareDataType | grep Model in Terminal? I cannot replicate it, either, but then we have no idea which hardware and macOS you are using. Thanks, Simon > On Feb 16, 2024, at 10:25 PM, María de los Án

Re: [R-SIG-Mac] Miniature plot windows

2024-01-22 Thread Simon Urbanek
Erik, thanks, this is very unusual. Can you, please, send me more details about your setup? Please run the following two lines in Terminal and send me the full output: system_profiler SPHardwareDataType | grep Model system_profiler SPDisplaysDataType Then in R run the following code and also i

Re: [R-SIG-Mac] Arm 64 Nightly Build URL Missing

2024-01-21 Thread Simon Urbanek
Brodie, thanks. There was a problem between the two build VMs where the x86_64 one could overwrite arm64's content with a stale content before they got branched. This should now be fixed - each should be supplying only its own part. Cheers, Simon > On Jan 22, 2024, at 3:09 AM, Brodie Gaslam

Re: [R-SIG-Mac] installing with remotes package

2023-12-07 Thread Simon Urbanek
Michael, remotes is a contributed package, so you should contact the author if that is what fails (you didn't say). FWIW only the latest version package binaries are available on CRAN, so if you need a specific older version of a package you need to compile it from sources - so chances are you

Re: [R-SIG-Mac] Nightly builds of R-devel?

2023-11-30 Thread Simon Urbanek
Kirill, Due to the necessary iconv workarounds for Sonoma introduced in the R 4.3.2 build, it complicates the automated nightly builds (they cannot reuse the same VM anymore) so the nightly process needs to be updated. I'm currently traveling so it will be restored when I get back later next we

Re: [R-SIG-Mac] Compiling a library with Rcpp causing many 'unknown type'/'no member named' errors

2023-11-16 Thread Simon Urbanek
Brian, you are using Anaconda so all bets are off since that is not supported by CRAN. It looks like a broken compiler/runtime combination in Anaconda so your best bet would be to contact their support as this is unrelated to R (updating Anaconda sounds like an obvious first step, hoping the co

Re: [R-SIG-Mac] R

2023-10-17 Thread Simon Urbanek
Please read the instruction on the download page - this is typically due to your system setting disallowing installation from the downloaded location so you have to move the package to a location from which you have allowed installation such as your home. Cheers, Simon > On 18/10/2023, at 1:2

Re: [R-SIG-Mac] R 4.3.1 fails on Mac OS 14

2023-10-05 Thread Simon Urbanek
Federico, yes, you can right-click and select Open. The app is signed, but is it not notarized - we only do that for the R release packages, because that's how our process works. Cheers, Simon > On Oct 5, 2023, at 11:03 PM, Calboli Federico (LUKE) > wrote: > > “R.app” can’t be opened becau

Re: [R-SIG-Mac] R 4.3.1 fails on Mac OS X Sonoma

2023-10-04 Thread Simon Urbanek
Kevin, > On 4/10/2023, at 5:27 AM, Kevin Thorpe wrote: > > Hello. > > I am wondering if this is just an issue on M1/2 chips or does it also affect > Intel? > It is an issue with Sonoma macOS new TUI classes and not the architecture so it will affect both. > I usually hold off upgrading u

Re: [R-SIG-Mac] R 4.3.1 fails on Mac OS 14

2023-10-04 Thread Simon Urbanek
I had a look and can reproduce it. What happens is that macOS Sonoma is sending dozens of notifications that a window will close (even if no window is being closed!) and since we move the focus to the next window on close it happens every time macOS sends that notification and thus many times in

Re: [R-SIG-Mac] How can I stop my R console and other R windows "flickering" after I updated my Mac OS to Sonoma 14.0?

2023-10-01 Thread Simon Urbanek
Desmond, thanks for the report. There seem to be windows focus issue in Sonoma so I would not recommend upgrading at this point. Hopefully this will be fixed in a future macOS update (the .0 versions are notoriously flaky) - in the meantime I'll see if there is any work-around we could do in R.

Re: [R-SIG-Mac] Rebuild binaries when a LinkingTo dependency changes

2023-09-25 Thread Simon Urbanek
ackages into > '/private/var/folders/dj/yhk9rkx97wn_ykqtnmk18xvcgn/T/RtmpSL7Etm/reprex-bc8b4fff25a6-next-esok/templib' > #> (as 'lib' is unspecified) > #> > #> The downloaded binary packages are in > #> > /var/folders/dj/yhk9rkx97wn_ykqtnm

Re: [R-SIG-Mac] Rebuild binaries when a LinkingTo dependency changes

2023-09-25 Thread Simon Urbanek
Kirill, we have no way of knowing when a packages introduced a breaking change (which it really shouldn't), so the maintainers would have to inform as (Matrix authors did inform us that 1.6.0 introduces breaking change so that's why we did a manual re-bulid on that update). Also checking exact

Re: [R-SIG-Mac] Rcmdr

2023-07-31 Thread Simon Urbanek
Agreed, no problem here even with Rcmdr in older R 4.2.0. As Peter said, Rcmdr doesn't use tcltk2 so I'm sure there is a lot you're omitting here. If it doubt, make sure you don't load some old workspace and have the latest versions of all packages, e.g. via update.packages(ask=FALSE). Cheers,

Re: [R-SIG-Mac] M1+ R package test failures (local and Mac Builder)

2023-07-26 Thread Simon Urbanek
Daniel, I'm not sure I understand your question. The package mmrm 0.2.2 fails its tests for me as well. If you can reproduce the problem locally (as you indicated), then that's good as you should be in the position to fix it. Cheers, Simon > On 26/07/2023, at 1:50 AM, Sabanes Bove, Daniel via

Re: [R-SIG-Mac] Macbuilder appears down again

2023-07-24 Thread Simon Urbanek
Avi, thanks. Everything seems to work for me. 404 for the link shown in the response will occur if the job has not yet been picked up, because the system is somewhat optimistic about assuming a job will be picked up faster than you can click on the link. The result page is only generated as the

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

2023-07-07 Thread Simon Urbanek
ot a good idea since the instructions on CRAN should be fully self-sufficient *and* we want to avoid other incompatible Fortran compilers. (I have trouble reaching the x86_64 build machine from home right now, so I'll change it on Monday). Thanks, Simon > > On 07/07/2023

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

2023-07-06 Thread Simon Urbanek
> On 7/07/2023, at 10:15 AM, Spencer Graves wrote: > > Hi, Simon: > > > Thanks for this. I have more questions: > > > On 7/6/23 4:52 PM, Simon Urbanek wrote: >> In the shell: >> PATH=/opt/gfortran/bin:$PATH R CMD INSTALL ... > > >

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

2023-07-06 Thread Simon Urbanek
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. > > >

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

2023-07-06 Thread Simon Urbanek
2023, at 11:45 PM, Peter Dalgaard 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

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

2023-07-05 Thread Simon Urbanek
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

Re: [R-SIG-Mac] macbuilder Site

2023-06-29 Thread Simon Urbanek
Roy, thanks (this is the proper place to report it). We had a power failure on one of the circuits, and it so happened that the MacBuilder was on it. I have now restarted the services so please give it a go and let me know if there are issues Thanks, Simon > On Jun 30, 2023, at 8:42 AM, Roy

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

2023-06-08 Thread Simon Urbanek
r > > 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

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

2023-06-07 Thread Simon Urbanek
Fernando, I don't think you posted the error you get when running R on the command line - can you copy/paste what you get when running R in the Terminal? Similarly, do you also get an error when running the R app (in Applications)? Cheers, Simon > On 6/06/2023, at 6:32 AM, DePaolis, Fernando

Re: [R-SIG-Mac] Identifying computer from R

2023-05-29 Thread Simon Urbanek
Dennis, PS1 is an internal shell environment variable (modifying prompt) which has nohting to do with R (and nothing to do with the computer name by default) so it won't be set in R, only in a shell. If you want the machine's hostname you'd typically use system("hostname") in R. Cheers, Simon

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Simon Urbanek
Jarrett, Duncan's suggestion was correct, but you are using older R, so I'd recommend simply upgrading R to the latest release. If you want to use old R, you have to install the older Fortran binaries that match your R version, but that's not entirely trivial so it's easier to just upgrade R i

Re: [R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical'

2023-04-30 Thread Simon Urbanek
oring previous >> �/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart� >> >>> sessionInfo() >> R version 4.3.0 Patched (2023-04-27 r84338) >> Platform: x86_64-apple-darwin20 (64-bit) >> Running under: macOS Ventura 13.2.1 >>

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-25 Thread Simon Urbanek
hat actally point to thw wrong directory. > That is not yet fixed on the master. > > Best, > Uwe > > > > On 24.04.2023 23:19, Simon Urbanek wrote: >> This has been fixed a while time ago so I suspect the culprit are outdated >> mirrors. If in doubt, please use

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Simon Urbanek
Kenneth, type="mac.binary" is not appropriate as forces is only for old High-Sierra binaries which don't exist for R 4.3.0 anymore as that build is no longer supported. You should leave type="both" (default, recommended) or type="binary". Cheers, Simon > On Apr 25, 2023, at 1:12 AM, Kenneth

Re: [R-SIG-Mac] binaries for R 4.3 x86_64

2023-04-24 Thread Simon Urbanek
This has been fixed a while time ago so I suspect the culprit are outdated mirrors. If in doubt, please use https://mac.R-project.org/bin/macosx which is the most up-to-date. Cheers, Simon > On Apr 25, 2023, at 12:51 AM, Uwe Ligges > wrote: > > > > On 24.04.2023 14:41, Kenneth Knoblauch

Re: [R-SIG-Mac] 'Default' macos (x86) download URL now gone?

2023-04-23 Thread Simon Urbanek
Dirk, thanks - the problem is that there is not a single installer package (for several years now), so that URL is ambiguous. Whether the missing link is a good or bad depends on how it is used. I would argue that any link to that URL is inherently bad, because there is no way of knowing that t

Re: [R-SIG-Mac] Problem installing RUcausal library on MAC

2023-04-23 Thread Simon Urbanek
Varin, you're missing the Fortran compiler which the package requires. To make the life a bit easier on you, upgrade to R 4.3.0 and then install GNU Fortran from https://mac.r-project.org/tools/ If you don't want to upgrade R then you'll need the Fortran from here: https://github.com/R-macos/g

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 241, Issue 5

2023-04-18 Thread Simon Urbanek
not need > >CPPFLAGS += -I/usr/local/include >LDFLAGS += -L/usr/local/lib > > just to include the header or link the shared library. > > Mikael > >> Date: Tue, 18 Apr 2023 15:18:03 +1200 >> From: Simon Urbanek >> To: R list >> Subject: [R-S

[R-SIG-Mac] Please test R 4.3.0 RC, more information below

2023-04-17 Thread Simon Urbanek
Dear Mac users, the next major R release R 4.3.0 is coming very soon so I would like to ask you to, please, test the pre-releases from https://mac.R-project.org such that any possible new issues are detected *before* the release. The upcoming release will be for macOS 11 and higher only to lev

Re: [R-SIG-Mac] typo in mac.r-project.org index?

2023-04-14 Thread Simon Urbanek
Mikael, the SDK version (=system libraries) is independent of the Xcode version (=toolchain version). We are using macOS 11 SDK, because we want the binaries to run on macOS 11. R packages typically don't use run-time weak symbol guards, so they would likely crash when compiled against higher S

Re: [R-SIG-Mac] Symbol not found: _timespec_get

2023-04-04 Thread Simon Urbanek
Jennifer, that build in only for macOS 11 (Big Sur) and higher, older versions are no longer supported (neither by Apple nor by us). I'll update the installer to disallow installation on older macOS version to avoid confusion. Thanks, Simon > On Apr 5, 2023, at 6:04 AM, Jennifer Wokaty > wr

Re: [R-SIG-Mac] Install error for gmm package

2023-04-02 Thread Simon Urbanek
Hasan, packages shouldn't be using gomp as it is not supported - it seems that gmm is hard-coding -lgomp even if it is not enabled by R. Although this is a bug in gmm (which the authors should fix), you can try to work around it by installing the GNU Fortran compiler as follows: open the Termi

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

2023-03-27 Thread Simon Urbanek
Nicolas, we can't tell unless you post the error log and you didn't even tell us your macOS version, but in recent versions security settings prevent the installation from the Downloads folder, so make sure you move it away from there to some safe location (home, Desktop or /tmp). Otherwise, su

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

2023-03-18 Thread Simon Urbanek
Gilberto, Please note that size checks are not really relevant for binary packages - it is normal for binaries to be large as they may include static libraries (e.g., rgdal has 273Mb). Also note that 4.8Mb is rather small for a library since it also includes debugging symbols (CRAN packages are

Re: [R-SIG-Mac] R , RCPP unsing MACOS ventura

2023-03-14 Thread Simon Urbanek
don't see that problem myself, but I don't use Homebrew (at least not on the default PATH). Cheers, Simon > On 15/03/2023, at 9:45 AM, Michael Hall wrote: > > > >> On Mar 14, 2023, at 3:32 PM, Simon Urbanek >> wrote: >> >> If that is the case, c

Re: [R-SIG-Mac] R , RCPP unsing MACOS ventura

2023-03-14 Thread Simon Urbanek
Federico, given that Homebrew is likely the cause for the mess, advising to install a custom installation seems like a very bad idea. It is likely very dependent on the versions of the tools from Homebrew which is what breaks. Therefore I would strongly advise against it (unless you know what y

Re: [R-SIG-Mac] R , RCPP unsing MACOS ventura

2023-03-14 Thread Simon Urbanek
If that is the case, can you actually post what the issue is? The original post had no details and did not follow up when asked for details. When googling the issue seems to arise in Homebrew, not the Apple tools so as I noted removing Homebrew should work. Cheers, Simon > On 15/03/2023, at

Re: [R-SIG-Mac] R , RCPP unsing MACOS ventura

2023-03-13 Thread Simon Urbanek
Andrea, Make sure you don't have any outdated tools or flags overrides (e.g. in ~/.R). If it doubt clean /usr/local and uninstall Homebrew. The error suggests your are using compilers that don't support your system. If you cleaned out those and still needs help, please post the full output of

Re: [R-SIG-Mac] Can R on a Mac use the GPU

2023-02-21 Thread Simon Urbanek
Bill, to answer the general part of you question, there are quite a few packages that allow you to use your GPU. At the low level you can use OpenCL which allows you to write code directly on the GPU and turn it into R functions. At a higher level there are frameworks like Torch and Tensorflow

Re: [R-SIG-Mac] macOS may not give R much time in a long compute

2023-02-18 Thread Simon Urbanek
> On Feb 19, 2023, at 3:50 AM, Spencer Graves > wrote: > > On 2/18/23 6:40 AM, Prof Brian Ripley wrote: >> Are you using R.app (you failed to say)? > > > I'm "using the newest version of RStudio" [Version 2022.12.0+353 > (2022.12.0+353)]. This means I am running R.app? > No, it

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

2023-02-11 Thread Simon Urbanek
Christofer, yes, unfortunately this is a known bug in macOS Ventura affecting a lot of command-line programs that use GUI. Do not upgrade to Ventura (usually a good advice given the long list of known bugs in Ventura) or wait for a fix from Apple. Cheers, Simon > On Feb 11, 2023, at 11:28 P

[R-SIG-Mac] Ventura users: do not install R from the Downloads folder

2023-02-08 Thread Simon Urbanek
Apparently there is a bug in Ventura that prevents software installation from the Downloads folder. Once the installer package is moved someplace else - the home or Desktop - it works. So if you see "Installation failed", make sure you move the package (typically that would be the R-4.2.2-arm64.

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

2023-02-06 Thread Simon Urbanek
t; Head of Biostatistics, Applied Health Research Centre (AHRC) > Li Ka Shing Knowledge Institute of St. Michael’s Hospital > Assistant Professor, Dalla Lana School of Public Health > University of Toronto > email: kevin.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 > &

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