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

On 08/09/2024 23:41, Jeff Newmiller via R-SIG-Mac wrote: I don't know whether MacOSX uses libiconv, It no longer does although reports compatibility with GNU libiconv 1.13. It is not at all compatible, which has caused a lot of extra work, not least as the incompatibilities have been changed/

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

On 23/08/2024 16:06, Sparapani, Rodney via R-SIG-Mac wrote: Hi Peter: I don’t know what the graph package is. But Rgraphviz is an archived package on CRAN… https://cran.r-project.org/src/contrib/Archive/Rgraphviz/ Both are current Bioconductor packages, so their software repository needs to

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

On 26/06/2024 06:41, Balamuta, James wrote: Tim, Unfortunately, there isn't a nice way of including OpenMP for macOS within a package. One potential avenue would be to use a `configure.ac` file to check for whether OpenMP headers are present on the macOS computer and, then, allow the correct

[R-SIG-Mac] FLIBS for binary R installations (was library 'quadmath' not found)

/Frameworks/R.framework/Resources/lib -lgfortran -lquadmath Until that is done, I recommend creating a ~/.R/Makevars file containing that line. On 23/05/2024 17:03, Prof Brian Ripley via R-SIG-Mac wrote: On 23/05/2024 16:00, Petar Milin wrote: I have recently updated my R (4.4.0) and all the

Re: [R-SIG-Mac] library 'quadmath' not found

On 23/05/2024 16:00, Petar Milin wrote: I have recently updated my R (4.4.0) and all the packages running on Sonoma (14.5) with Intel. When I try to install from GitHub with: install_github("zdk123/SpiecEasi") I get the error message: ld: warning: search path '/opt/gfortran/lib/gcc/x86_64-app

Re: [R-SIG-Mac] How to correct tcltk path?

On 04/04/2024 17:46, Kasper Daniel Hansen wrote: You need to install XQuartz. This is IMO stated somewhat clearly at https://cran.r-project.org/bin/macosx/ ("somewhat", because - as always - it seems pretty clear when you know what its trying to say) And definitely clear in the R-admin manua

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

You need to make clear what graphics device and R build you used: the default on a CRAN build of macOS is quartz(), which has nothing to do with XQuartz. But is this a CRAN build? AFAIK quartz() is not the default device in RStudio. And also give the information (sessionInfo()) requested in

Re: [R-SIG-Mac] Cross compilation and linking without -undefined

This is just a default. AFAICS it is set in DYLIB_LDFLAGS and you can set that as you wish - it is documented in config.site. That cross-compilation cannot test-load is a major reason not to use it and why support for packages was downplayed on Windows. On 02/01/2024 19:21, Jeroen Ooms wrote

Re: [R-SIG-Mac] Is it safe to upgrade to Somoma yet -- As far as R goes?

On 31/10/2023 18:24, Kevin Thorpe wrote: On Oct 31, 2023, at 1:46 PM, Prof Brian Ripley wrote: On 31/10/2023 13:47, Kevin Thorpe wrote: Hello. I saw that a minor release has been rolled up with binaries coming soon. My question is whether or not the issues identified (I’m thinking mainly

Re: [R-SIG-Mac] Is it safe to upgrade to Somoma yet -- As far as R goes?

On 31/10/2023 13:47, Kevin Thorpe wrote: Hello. I saw that a minor release has been rolled up with binaries coming soon. My question is whether or not the issues identified (I’m thinking mainly of a window focus issue reported on this list) after Sonoma released have been patched in this vers

Re: [R-SIG-Mac] Build / source of libRblas.vecLib.dylib

On 31/10/2023 16:08, Colin Rundel wrote: The short version of the question - does anyone know what build process is used to generate the libRblas.vecLib.dylib that is included in /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib by R-4.3.1-arm64.pkg? I have not been able to find

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

On 02/10/2023 05:41, David Winsemius wrote: Neither of you have mentioned anything about the need for reinstallation of Xquartz. Was that done? I did not need to do so when updating to Sonoma. And of course the E.app console (not 'base R') which seems to be the issue does not use X11. I al

Re: [R-SIG-Mac] Rcmdr

On 01/08/2023 00:27, John Fox wrote: Hello Simon, Actually the Rcmdr *does* import (and use) the tcltk2 package, but I've had no other report of this kind of problem and haven't observed it myself. Best,  John A possible clue. tclrk2 on Linux used to do something very similar (including

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

Apple Clang 14.0.3 and its associated SDK change to MacOSX13.3.sdk broke about 25 CRAN packages (3 with segfaults) and 17 remain broken (and also with Xcode/CLT 15 beta 4 which uses a newer build of 14.0.3). But in my checks mmrm 0.2.2 is not one of them. Packages should aim to be platform-in

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

On 08/07/2023 00:41, Spencer Graves wrote: Hello, Simon Urbanek and Professor Ripley: On 7/7/23 4:21 AM, Simon Urbanek wrote: On Jul 7, 2023, at 6:54 PM, Prof Brian Ripley wrote: An alternative is not to have gfortran on the path and use a personal Makevars file, as documented at

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

An alternative is not to have gfortran on the path and use a personal Makevars file, as documented at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#macOS-packages . Reasons to do it that way include a) GCC builds have included other compilers including gcc in the same directory

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

On 17/05/2023 21:59, Simon Urbanek wrote: 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

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

On 24/04/2023 07:17, Simon Urbanek wrote: 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 Fort

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

On 18/04/2023 11:01, Göran Broström wrote: About the Fortran compiler: Den 2023-04-18 kl. 05:18, skrev Simon Urbanek: Dear Mac users, Package developers, please check the CRAN result pages for your package to make sure it passes checks. Also please note that we are now using a universal GN

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

On 04/04/2023 18:45, Tomas Kalibera wrote: On 4/4/23 18:26, Jennifer Wokaty wrote: Hi, I tried installing the x86_64 alpha available today at https://mac.r-project.org/big-sur-x86_64/R-4.3-branch/R-4.3-branch-x86_64.pkg; however, I'm getting the following error: $ sudo installer -pkg R-4.3-

Re: [R-SIG-Mac] arm downloads appear broken

On 27/02/2023 08:09, Prof Brian Ripley wrote: Your subject line is alarmist -- you only provide any evidence for 1 out of > 19000 CRAN packages (and not R itself). Package RGtk2 was archived in 2021.  The current rattle (5.5.1) does not depend on it.  A direct download is available f

Re: [R-SIG-Mac] arm downloads appear broken

Your subject line is alarmist -- you only provide any evidence for 1 out of > 19000 CRAN packages (and not R itself). Package RGtk2 was archived in 2021. The current rattle (5.5.1) does not depend on it. A direct download is available from rattle's CRAN landing page. You have not told us wh

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

Are you using R.app (you failed to say)? If so, have you acted on the documentation about 'app nap'? E.g. §4.1 of the R-admin manual. On 18/02/2023 12:31, Spencer Graves wrote: Hello:   During a long compute (in a while loop), I've asked R to report progress via: # Progress report

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

Please do read ?sessionInfo Where R was compiled under macOS 10.x (as the CRAN Intel distributions have been) but running under ‘Big Sur’ or later, macOS reports itself as ‘10.16’ (which R recognizes as ‘Big Sur ...’) and not ‘11.x’ or later. This is only an issue on Intel bi

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

On 27/01/2023 22:48, Peter West wrote: Installation of R 4.2.2 on my M1 just succeeded. Yes, that has been very widely tested. We don't know what OS you or the OP are running, though. Machines with M2 CPUs are very new (like 1-2 days old) and are presumably running 13.1 or 13.2. I have j

Re: [R-SIG-Mac] another R crash issue

well just in case. Mac OS 11.6.8 , R 4.2.2 Yes, the gmp package Mac version gives immediate seg faults. Prof Brian Ripley has already alerted the gmp package maintainer, me (a gmp package co-author, not familiar with the C++ design in there, and maintainer of dependent R package 'Rmp

Re: [R-SIG-Mac] R does not build out of the box on Ventura

On 25/10/2022 10:13, 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

Re: [R-SIG-Mac] macOS Ventura (13) Preview App Drops Support for PS/EPS File Rendering

Somehow you sent HTML only, and that renders oddly in Thunderbird. Have you considered GhostScript? That used to be my viewer of choice for Postscript long ago. I think TeXShop may be a wrapper. My box has Photoshop as the default viewer for .eps and TeXShop for .ps. I almost never use Pho

Re: [R-SIG-Mac] R does not build out of the box on Ventura

r beta versions. I'm rather reluctant to install those. That's an Apple trait. As you are on macOS 12.x, I would feel free to ignore them: even those for the released CLT 14 (although (I was using that on 12.6 for a month with no issues). - Peter On 25 Oct 2022, at 11:13 , Prof

[R-SIG-Mac] R does not build out of the box on Ventura

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

Re: [R-SIG-Mac] R CMD check "HTML version of manual" NOTE/Warnings

On 25/04/2022 20:04, John Fox wrote: Dear R-sig-mac list members, When checking packages --as-cran with R 4.2.0 (and R 4.2.0 patched), I'm seeing multiple warnings (and a NOTE) concerning the HTML version of the package help-page manuals. The warning appears for every .Rd file in all of the p

Re: [R-SIG-Mac] Error identifying system version in sessionInfo()

On 13/01/2022 18:32, Rohde, Maximilian D wrote: Hello, I have encountered a bug that I have documented here: https://stackoverflow.com/questions/70690684/wrong-session-info-in-when-knitting-in-r-markdown?noredirect=1#comment124971021_70690684 In brief, the issue is that running the `sessionInf

Re: [R-SIG-Mac] .Machine differences between Intel and M1

On 21/12/2021 20:46, Simon Urbanek wrote: Matt, yes, arm64 does not support long doubles. In C the long double type is 64-bit there so has the same precision as doubles (this is allowed by the standard). And documented in ?.Machine. However, I see on my M1 Pro capabilities("long.double")

Re: [R-SIG-Mac] Strange C/C++ Compile Errors

You have not shown us the compiler command line used, nor made a reproducible example available (and we might need both). The suspicious line is > In file included from ./include/stdlib.h:36: It looks like you may have a file in the package which is masking a system header, but we don't have

Re: [R-SIG-Mac] Reverse search not working in ARM binary of R-4.1.2 (or 4.1.0) from CRAN

On 09/12/2021 17:13, Ziv Wolkowicki wrote: Team, I have an unusual issue I am only observing on specific binaries of R. I used to have ARM build of R-4.1.0 from https://cran.r-project.org/bin/macosx/ , and updated to R-4.1.2 running on my M1 Mac. Hittin

Re: [R-SIG-Mac] Nightly build segfaults

On 17/11/2021 19:32, Gábor Csárdi wrote: On Wed, Nov 17, 2021 at 8:14 PM Prof Brian Ripley wrote: [...] With the tarball I get a popup telling me “R.framework” cannot be opened because the developer cannot be verified. Interesting. I am on 12.0.1 and there is no popup, but there is a crash

Re: [R-SIG-Mac] Nightly build segfaults

On 17/11/2021 07:17, Prof Brian Ripley wrote: On 16/11/2021 22:28, Gábor Csárdi wrote: This is Monterey: ❯ uname -a Darwin Gabors-MacBook-Pro-3.local 21.1.0 Darwin Kernel Version 21.1.0: Wed Oct 13 17:33:01 PDT 2021; root:xnu-8019.41.5~1/RELEASE_ARM64_T6000 arm64 The R-devel build segfaults

Re: [R-SIG-Mac] Nightly build segfaults

On 16/11/2021 22:28, Gábor Csárdi wrote: This is Monterey: ❯ uname -a Darwin Gabors-MacBook-Pro-3.local 21.1.0 Darwin Kernel Version 21.1.0: Wed Oct 13 17:33:01 PDT 2021; root:xnu-8019.41.5~1/RELEASE_ARM64_T6000 arm64 The R-devel build segfaults: ❯ curl -O https://mac.r-project.org/monterey/R-d

Re: [R-SIG-Mac] ANSI escape weirdness on M1 (libedit issue?)

On 03/11/2021 12:21, Gábor Csárdi wrote: Anyone else noticed some weirdness with the arm build when the prompt has ANSI escape codes? E.g. in a terminal run this options(prompt = "\033[1m> \033[0m") and then at the new prompt type in some longer word and press CTRL+A. Longer than what? The

[R-SIG-Mac] Java 17 builds

The current version of Java is 17: this has 'long term support' and is the first to officially support M1 macs. Mac-friendly installers are now available from https://adoptium.net for Intel (which they call x64) and M1 (aarch64). Unlike builds available from jdk.java.net and Zulu these instal

Re: [R-SIG-Mac] Tcl/Tk issues in arm64 build of R 4.1.0

On 09/09/2021 19:03, John Fox wrote: Dear Simon, Philippe, and list members, I've encountered some Tcl/Tk-related issues with the Apple silicon arm64 build of R 4.1.0 for macOS. These issues affect the Rcmdr package, although they don't prevent it from working: (1) Some fonts that are availa

Re: [R-SIG-Mac] Tcl/Tk issues in arm64 build of R 4.1.0

On 09/09/2021 19:59, Prof Brian Ripley wrote: On 09/09/2021 19:03, John Fox wrote: Dear Simon, Philippe, and list members, ... (2) The Tcl/Tk Tktable package is apparently absent from the arm64 build but still present in the Intel build. The Rcmdr detects its absence and suppresses some

Re: [R-SIG-Mac] Tcl/Tk issues in arm64 build of R 4.1.0

On 09/09/2021 21:34, John Fox wrote: Dear Brian, Thank you for responding so quickly. Please see below: On 2021-09-09 2:59 p.m., Prof Brian Ripley wrote: On 09/09/2021 19:03, John Fox wrote: Dear Simon, Philippe, and list members, I've encountered some Tcl/Tk-related issues with the

Re: [R-SIG-Mac] Tcl/Tk issues in arm64 build of R 4.1.0

On 09/09/2021 19:03, John Fox wrote: Dear Simon, Philippe, and list members, I've encountered some Tcl/Tk-related issues with the Apple silicon arm64 build of R 4.1.0 for macOS. These issues affect the Rcmdr package, although they don't prevent it from working: (1) Some fonts that are availa

Re: [R-SIG-Mac] checking whether the C compiler works... no

On 06/09/2021 08:43, Naresh Gurbuxani wrote: When trying to install library reshape2, I get below messages. But I do have some other packages which depend upon C compiler (e.g., Rcpp). How can this problem be fixed? You need to look in the config.log file. The easiest way to make sure tha

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 221, Issue 14

-mac-requ...@r-project.org wrote: sessionInfo on Monterey (Prof Brian Ripley) -- Jan de Leeuw, Distinguished Professor Emeritus, UCLA Statistics https://jansweb.netlify.app https://github.com/deleeuw

[R-SIG-Mac] sessionInfo on Monterey

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

Re: [R-SIG-Mac] rgl in R version 4.1.1 Patched (2021-08-13 r80752)

On 19/08/2021 04:56, Richard M. Heiberger wrote: R version 4.1.1 Patched (2021-08-13 r80752) aarch64-apple-darwin20 library(rgl) Error in dyn.load(dynlib <- getDynlib(dir)) : unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rgl/libs/rgl

Re: [R-SIG-Mac] sf installation problem under Mac OS 11 - Big Sur

On 18/08/2021 23:52, Michal Ben-Nun wrote: Hi, I installed R 4.10 on my Mac OS 11.3.1 Presumably R 4.1.0. I am trying to install 'sf' and 'rgdal' From the mailing list I understood that this command should work: install.packages(c("rgdal","sf"),,"https://mac.R-project.org

Re: [R-SIG-Mac] R pkg 4.1.1 no longer accepted as notarized by Apple

On 13/08/2021 14:42, Eirik Thorsnes wrote: Hi, The R-4.1.1.pkg is not notarized: And that has been reported and Simon has fixed it (online, and an updated .pkg is on its way to the CRAN main site for those without Internet access). I was able to install the original .pkg on Thursday (but n

Re: [R-SIG-Mac] In svg("tst.svg") : failed to load cairo DLL

Install (or re-install) XQuartz. As the R-admin manual §4 says Various parts of the build require XQuartz to be installed: see https://www.xquartz.org/releases. These include the tcltk package and the X11 device: attempting to use these without XQuartz will if possible remind you. This is al

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"

On 17/07/2021 21:38, Duncan Murdoch wrote: On 17/07/2021 3:39 a.m., Lindsay Foreman wrote: To whom it may concern, I am so sorry for being such a dunce.  I have been trying and trying to get the R App to work on my MacBook Air running Big Sur V11.4, and am just not making any progress.  It sa

Re: [R-SIG-Mac] [External] Re: [External] Re: Mac M1 emacs

On 08/03/2021 17:59, Richard M. Heiberger wrote: I updated the OS to 11.2.2, again redownloaded the app https://mac.r-project.org/libs-arm64/emacs-27.1-app-arm64-darwin20.dmg and still get the damaged app message. How did you download it? That page and R-admin recommend using curl and when I

Re: [R-SIG-Mac] BWidget (external software)

On 09/02/2021 23:59, Manuel Spínola wrote: Dear list members, How can I install the external package BWidget in R for macOS? I believe you are asking about a Tcl/Tk package (not an R package): that is discussed in the R manuals and https://cran.r-project.org/doc/manuals/r-release/R-exts.ht

Re: [R-SIG-Mac] [External] Behaviour or Quartz windows

The quartz() device has nothing to so with XQuartz. Quartz is part of macOS: https://en.wikipedia.org/wiki/Quartz_(graphics_layer) Using XQuartz betas is not supported: it is very unfortunate that they are persuading users to install a beta version. You have not followed the posting guide an

Re: [R-SIG-Mac] XQuartz now supports Apple Silicon

On 30/01/2021 09:46, Bob Rudis wrote: Announcement and d/l links: — https://www.mail-archive.com/xquartz-dev@lists.macosforge.org/msg01027.html — https://www.xquartz.org/releases/XQuartz-2.8.0_beta1.html Folks who use it should get prompted to install it next time you open it. And now beta3 w

Re: [R-SIG-Mac] Missing R and RScript on /usr/bin/ on Big Sur

On 17/01/2021 23:01, Luis Puerto wrote: Hey! I was and I realized after sending the email. But that path doesn't have also any R symbolic link either. Can anyone tell me how many symbolic links to R binaries are there? From the manual 'The installer puts links to R and Rscript in /usr/local

Re: [R-SIG-Mac] M1 mid-January update

à 08:41, Prof Brian Ripley a écrit : For native builds - nothing to report for x86_64 builds running under Rosetta which almost all the time 'just work' (and work fast). The goal remains to release a native binary distribution with R 4.1.0 ca April: all but the intrepid are advi

[R-SIG-Mac] M1 mid-January update

For native builds - nothing to report for x86_64 builds running under Rosetta which almost all the time 'just work' (and work fast). The goal remains to release a native binary distribution with R 4.1.0 ca April: all but the intrepid are advised to use x86_64 until then. - There is an experim

Re: [R-SIG-Mac] is there an M1 virtual machine image available for linux?

On 15/12/2020 03:26, Simon Urbanek wrote: To my best knowledge the only way to test anything on M1 is to buy one. As far as I know there is no virtual solution yet. If you see one, let me know. As for CRAN there is no official arm64 build yet - the hardware just arrived and I need to setup the

[R-SIG-Mac] CRAN package checks on M1 Mac

We have managed a fairly complete check run with natively-compiled R and packages, and a full one with x86_64 R and packages running under Rosetta (mainly using CRAN binary distributions). The bottom line is that running under Rosetta works really well. Although relative speeds vary widely, us

Re: [R-SIG-Mac] vecLib BLAS and LAPACK on Mac OS 11.01 and Xcode 12.2

ock BLAS. I believe that had already changed (in R-devel and R-patched): your R was not current. (Please do re-read the R lists' posting guide and update before posting.) Best, Anirban On 26 Nov 2020, at 4:22 AM, Prof Brian Ripley wrote: A few comments: 1) Do you really want to be using

Re: [R-SIG-Mac] vecLib BLAS and LAPACK on Mac OS 11.01 and Xcode 12.2

A few comments: 1) Do you really want to be using an old and buggy LAPACK? For that is what --with-lapack gives you, and the manual does warn you. 2) With Xcode 12.2 you will not see the .dylibs you are used to seeing: linking to system resources is done using .tbd files and although the dy

Re: [R-SIG-Mac] Apple Silicon aka M1 Macs

R-admin manual (the version on CRAN is as usual a few days behind). On 17/11/2020 14:57, Prof Brian Ripley wrote: Mine (a 8GB MBA) arrived today, so I have started doing some comparisons. For the CRAN build of R 4.0.3, §2.8 of R-admin recommends checking the installation with pdf("tes

Re: [R-SIG-Mac] Unable to use vecLib BLAS and LAPACK in Mac OS 11.0.1

Which version of Xcode/Command Line Tools are you using? If >= 12 (and perhaps earlier) Apple have set default C options which violate the C99/C11 standard, so you need -Wno-implicit-function-declaration. If you have a configure issue, do read and report the relevant parts of config.log file:

Re: [R-SIG-Mac] sf installation problem under Mac OS 11 - Big Sur

On 19/11/2020 11:22, GilbertoCamara wrote: Dear all, Mac users that have upgraded to Mac OS 11 BigSur have reported having problems with “rgdal” and “sf”. The same happened to me when I upgraded my Mac. What problems are those? You report nothing, and make reference to no reports here nor o

[R-SIG-Mac] Apple Silicon aka M1 Macs

Mine (a 8GB MBA) arrived today, so I have started doing some comparisons. For the CRAN build of R 4.0.3, §2.8 of R-admin recommends checking the installation with pdf("tests.pdf") ## optional, but prevents flashing graphics windows Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en") t

Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS

On 29/09/2020 12:27, Kasper Daniel Hansen wrote: To use veclib you need --with-blas="-framework Accelerate" Details are in the R-admin manual, including that R fails one of its checks. Simon's calling this vecLib is a bit misleading. 'vecLib' was a vectorized library for PPC Macs, and th

Re: [R-SIG-Mac] svn location

A couple more points on this 1) Apple's svn is 1.10.4, Simon's is 1.14.0 so you probably should not mix checkouts done with the different versions. 2) Digging amongst the versions available on developer.apple.com, CLT 11.3.1 contained svn etc, 11.5 did not (but did not remove existing tools,

Re: [R-SIG-Mac] bzip2 configure error

On 29/08/2020 19:38, Duncan Murdoch wrote: I seem to have got past this error by reinstalling Xcode.  I'm not sure what went wrong with the old install; I'm pretty sure I did an R-devel build since installing Catalina. This seems to come from a CLT update: my Catalina box updated to 12.0 beta

Re: [R-SIG-Mac] Running R with lldb

One of the suggestions in https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Debugging-on-macOS should help. Both worked for my build of R-devel yesterday On 05/08/2020 14:25, Duncan Murdoch wrote: I'm now successfully building R-devel in /Users/murdoch/R/R-devel.  If I run it f

Re: [R-SIG-Mac] Link-Time Optimization (LTO)

On 15/07/2020 09:50, Jeroen Ooms wrote: On Tue, Jul 14, 2020 at 4:22 PM Prof Brian Ripley wrote: This is a rather technical post about how libraries of compiled code can be further optimized. LTO generally produces smaller[*] and faster code (typically by a few percent) at the expense of

[R-SIG-Mac] Link-Time Optimization (LTO)

This is a rather technical post about how libraries of compiled code can be further optimized. LTO generally produces smaller[*] and faster code (typically by a few percent) at the expense of increased installation time and is being used for large projects such as browsers and soon for some Li

Re: [R-SIG-Mac] Advise on building R on OSX without optimization for debugging

On 13/07/2020 11:14, Simon Urbanek wrote: On Jul 13, 2020, at 7:59 PM, Prof Brian Ripley wrote: On 08/07/2020 21:38, Simon Urbanek wrote: Dmitriy, due to permissions and the various limitations on passing environment variables across processes it is often easier to simply run R and attach

Re: [R-SIG-Mac] Advise on building R on OSX without optimization for debugging

On 08/07/2020 21:38, Simon Urbanek wrote: Dmitriy, due to permissions and the various limitations on passing environment variables across processes it is often easier to simply run R and attach the debugger to it: $ R [...] Sys.getpid() [1] 89955 $ sudo lldb Password: (lldb) attach 8995

[R-SIG-Mac] Timezone databases on macOS

I have tweaked the selection of this in R-devel. For a long time the handling of timedates in macOS was 32-bit, and that included the zoneinfo compiler (/usr/sbin/zic) and hence the shipped timezone database. The latter is now 64-bit on High Sierra (the earliest we support) but there must stil

[R-SIG-Mac] Packages with updated spatial libraries.

I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2. Install with (e.g.) options(repos="https://www.stats.ox.ac.uk/pub/RWin";) install.packages('rgdal', type = 'binary') (This needed a development version of the rgdal sources.) This

Re: [R-SIG-Mac] R CMD check warning in 4.0.0 RC

On 20/04/2020 16:51, Duncan Murdoch wrote: I've just installed R version 4.0.0 RC (2020-04-18 r78249) and am checking a package on MacOS High Sierra (10.13.6).  I can't install the recommended version of Xcode on this MacOS version.  I'm currently using Xcode 9.2.  (I think Xcode 10.x is suppos

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

On 04/04/2020 05:15, Tom Elliott wrote: Simon, Hence this is a call to the R community to see if anyone actually cares. I (and Chris Wild and quite a few of our mac users) care and would greatly appreciate working GTK+ CRAN packages! I don't have any knowledge re source etc, but just to remi

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] Please test R 4.0.0 pre-releases!

On 01/04/2020 22:02, Simon Urbanek wrote: JJB, 1. correct, there was too much trouble in this. But please feel free to start a new thread about this here if you have strong opinions. Also note that it is possible (and not hard) to install packages from source with an OpenMP-supporting compil

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

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 pac

[R-SIG-Mac] Xcode/CLT 11

As a test (I would not recommend it), I installed Command Line Tools 11 on my Mojave machine. 1) As expected, it does not contain any macOS_SDK_headers_for_macOS package, so the second approach in https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Recommended-C_002fC_002b_002b-compile

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

On 19/08/2019 15:00, peter dalgaard wrote: 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.s

Re: [R-SIG-Mac] RGtk2 segfaulting on macOS

On 22/07/2019 03:47, Tom Elliott wrote: Hi, The macOS binaries were recently built for macOS, however they're still not quite right. Runing the following ... It is likely that the segfault is in the Gtk2 libraries: which OS version and which Gtk2 installation? I have not managed to get Gt

Re: [R-SIG-Mac] Apple Clang does support OpenMP (if libomp is available)

On 06/06/2019 16:39, Simon Urbanek wrote: Jon, some time ago Apple's clang has silently dropped -fopenmp so we were able to at least keep it in the flags even if it wasn't actually using it. Still, it was only dropping it, it wasn't actually generating any parallel code, so there was real poi

Re: [R-SIG-Mac] Warning on XCode / Command Line Tools 11

2-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 te

[R-SIG-Mac] Warning on XCode / Command Line Tools 11

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 b

Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)

On 04/04/2019 22:37, Kevin Ushey wrote: I also recall after updating to Xcode 10.2 on my Mojave machine that the system headers normally installed at /usr/include had vanished, and re-installing the headers with the aforementioned package at /Library/Developer/CommandLineTools/Packages/macOS_SDK_

Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

BTW, reading the manual (in this case 'R Installation and Administration') often helps, and would have here. On 16/11/2018 19:10, Jonathan Greenberg wrote: I'm hoping to get some insight into seeing if I can get "rj" working again in Mojave/R 3.5.1 -- this is a requirements for the Eclipse int

[R-SIG-Mac] Installing R on 10.14 (Mojave)

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 Prof

Re: [R-SIG-Mac] disabling threads when using Accelerate BLAS

On 08/09/2018 22:01, Kasper Daniel Hansen wrote: For timing purposes, is it possible to control the number of threads / cores when I have compiled R to use the BLAS in the Accelerate framework (by building R using ./configure --with-blas="-framework Accelerate" --with-lapack ) ? (The alternat

Re: [R-SIG-Mac] R and Java 10 ➜ rJava not able to build

On 27/03/2018 20:25, Luis Puerto wrote: ... rJava is not yet compatible with Java 10 Is the correct answer. How to work around this is in the current manual, specifically R-admin for R 3.5.0 alpha or R-devel. Java 10 has been out for 8 days, and the rJava maintainer was made aware of the i

Re: [R-SIG-Mac] package building

On 12/03/2018 23:01, Julia Silge wrote: Hello there! I maintain the tidytext package: https://cran.r-project.org/web/checks/check_results_tidytext.html Recently I have been working to get tidytext to build on R-oldrel, and I believe that v0.1.7 should do so. The check page above shows that v0.1.

Re: [R-SIG-Mac] Update of RcppParallel failed

On 14/02/2018 14:01, Keith O'Hara wrote: This looks like an issue to bring up with the Rcpp guys, not R… but can you provide a full printout of the error? I’m guessing this failed when compiling a C file, not C++. RcppParalllel is not part of Rcpp, and orphaned. It seems to be a mac-specifi

Re: [R-SIG-Mac] trying to compile packages from source, but lacking /opt/local/bin/gcc-mp-5

On 21/11/2017 04:03, Vincent Carey wrote: %vjcair> R CMD config CC /opt/local/bin/gcc-mp-5 I don't seem to be able to override this using environment variable CC. And When all else fails, read the manual (but, see the posting guide, before posting here)! This is covered in, e.g., https:

[R-SIG-Mac] R 3.4.2 on High Sierra (10.13)

[Repeating for convenient reference a comment in an earlier thread.] R 3.4.2 was in code freeze when High Sierra as released, and so there was no opportunity to make and test workarounds for undocumented changes to the latter. R will be unable to find the system timezone on High Sierra (confi

Re: [R-SIG-Mac] Xcode 9

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

Re: [R-SIG-Mac] Rcmdr¡

On 20/06/2017 08:49, Agustin Diez Castillo wrote: I guess what German is referring to is that only applications for identified developers [1, 2], but it is only a guess. Hmm, the R package is signed by an identifiable developer: those links should not be relevant and if you find otherwise you

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

Note that at the moment there are many missing binary packages for 3.4.0, and BioC will update all their versions when BioC 3.5 is released this coming week. So I would wait a few days before updating, especially if you prefer to use binary packages. > nrow(available.packages(, type="source")

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