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

2022-04-25 Thread Prof Brian Ripley
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

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

2022-01-14 Thread Prof Brian Ripley
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

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

2021-12-21 Thread Prof Brian Ripley
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

2021-12-14 Thread Prof Brian Ripley
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

2021-12-09 Thread Prof Brian Ripley
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.

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

2021-11-17 Thread Prof Brian Ripley
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

2021-11-17 Thread Prof Brian Ripley
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

2021-11-16 Thread Prof Brian Ripley
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

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

2021-11-03 Thread Prof Brian Ripley
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

2021-09-24 Thread Prof Brian Ripley
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

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

2021-09-18 Thread Prof Brian Ripley
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

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

2021-09-09 Thread Prof Brian Ripley
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

2021-09-09 Thread Prof Brian Ripley
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 Apple

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

2021-09-09 Thread Prof Brian Ripley
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

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

2021-09-06 Thread Prof Brian Ripley
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

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

2021-08-27 Thread Prof Brian Ripley
-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

2021-08-27 Thread Prof Brian Ripley
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

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

2021-08-19 Thread Prof Brian Ripley
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

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

2021-08-19 Thread Prof Brian Ripley
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

2021-08-14 Thread Prof Brian Ripley
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

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

2021-08-06 Thread Prof Brian Ripley
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

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"

2021-07-18 Thread Prof Brian Ripley
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

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

2021-03-08 Thread Prof Brian Ripley
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)

2021-02-09 Thread Prof Brian Ripley
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

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

2021-02-09 Thread Prof Brian Ripley
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

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

2021-02-06 Thread Prof Brian Ripley
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

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

2021-01-17 Thread Prof Brian Ripley
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

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

2021-01-14 Thread Prof Brian Ripley
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 advised to use

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

2021-01-13 Thread Prof Brian Ripley
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

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

2020-12-12 Thread Prof Brian Ripley
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,

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

2020-11-26 Thread Prof Brian Ripley
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 an old and buggy LAPACK

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

2020-11-26 Thread Prof Brian Ripley
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

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

2020-11-23 Thread Prof Brian Ripley
(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("tests.pdf") #

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

2020-11-22 Thread Prof Brian Ripley
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

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

2020-11-19 Thread Prof Brian Ripley
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

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

2020-11-17 Thread Prof Brian Ripley
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")

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

2020-09-29 Thread Prof Brian Ripley
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

Re: [R-SIG-Mac] svn location

2020-09-04 Thread Prof Brian Ripley
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

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

2020-08-31 Thread Prof Brian Ripley
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

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

2020-08-05 Thread Prof Brian Ripley
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

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

2020-07-15 Thread Prof Brian Ripley
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

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

2020-07-14 Thread Prof Brian Ripley
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

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

2020-07-13 Thread Prof Brian Ripley
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

2020-07-13 Thread Prof Brian Ripley
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

[R-SIG-Mac] Timezone databases on macOS

2020-06-21 Thread Prof Brian Ripley
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

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

2020-06-12 Thread Prof Brian Ripley
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

2020-04-20 Thread Prof Brian Ripley
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

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

2020-04-04 Thread Prof Brian Ripley
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

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

2020-04-02 Thread Prof Brian Ripley
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

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

2020-04-01 Thread Prof Brian Ripley
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

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

2020-04-01 Thread Prof Brian Ripley
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

[R-SIG-Mac] Xcode/CLT 11

2019-09-11 Thread Prof Brian Ripley
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

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

2019-08-29 Thread Prof Brian Ripley
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

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

2019-07-21 Thread Prof Brian Ripley
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

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

2019-06-07 Thread Prof Brian Ripley
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

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

2019-06-06 Thread Prof Brian Ripley
have are from Adobe, e.g. old uninstallers. -pd (*) ="dogs dinner" On 4 Jun 2019, at 17:10 , Prof Brian Ripley wrote: My Mojave machine today prompted me to update to version 11 of Command Line Tools (apparently 'beta 1', but I am not a Beta tester). In short: don't do tha

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

2019-06-04 Thread Prof Brian Ripley
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

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

2018-11-16 Thread Prof Brian Ripley
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

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

2018-09-25 Thread Prof Brian Ripley
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

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

2018-09-09 Thread Prof Brian Ripley
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

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

2018-03-28 Thread Prof Brian Ripley
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

Re: [R-SIG-Mac] package building

2018-03-13 Thread Prof Brian Ripley
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

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

2018-02-14 Thread Prof Brian Ripley
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

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

2017-11-21 Thread Prof Brian Ripley
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.,

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

2017-10-05 Thread Prof Brian Ripley
[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

Re: [R-SIG-Mac] Xcode 9

2017-09-27 Thread Prof Brian Ripley
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:

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

2017-04-23 Thread Prof Brian Ripley
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(,

Re: [R-SIG-Mac] pcre on OS X

2017-03-10 Thread Prof Brian Ripley
On 10/03/2017 20:38, de Leeuw, Jan wrote: Not sure of this has already been discussed. There is now a libpcre sitting in /usr/lib (OS X 10.12.4) and R-devel does not like OS X / macOS has had pcre 8.02 for years, and R has required at least 8.12 for years. (opensource.apple.com is currently

Re: [R-SIG-Mac] Fwd: Mac binaries for R devel

2017-02-27 Thread Prof Brian Ripley
On 27/02/2017 19:41, Obenchain, Valerie wrote: Re-sending ... this went out before I joined the r-sig-mac list so the original is being held for moderation. In the absence of a quick response from Simon (and you wrote to a list, not a person): Note that 3.4.0 does not have a release date

Re: [R-SIG-Mac] Feature request: install R in ~/Library/Frameworks

2017-02-07 Thread Prof Brian Ripley
On 07/02/2017 15:26, Gábor Csárdi wrote: On Tue, Feb 7, 2017 at 10:54 AM, Gábor Csárdi <csardi.ga...@gmail.com <mailto:csardi.ga...@gmail.com>> wrote: On Tue, Feb 7, 2017 at 10:22 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk <mailto:rip...@stats.ox.ac.uk>> wrote:

Re: [R-SIG-Mac] Feature request: install R in ~/Library/Frameworks

2017-02-07 Thread Prof Brian Ripley
On 07/02/2017 09:02, 美彦 馬場 wrote: Hi, On Feb 7, 2017, at 17:46, Gábor Csárdi wrote: Hi all, I realize that this is not the typical use case on macOS, but for my work, it would be great to be able to install R into ~/Library/Frameworks. This would allow having

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

2016-12-28 Thread Prof Brian Ripley
On 27/12/2016 19:19, Watson, David W. (MSFC-ES62) wrote: I have been trying to download the “patched” version of 3.3.2 for Mac from CRAN, What makes you think there is a patched version on CRAN? Did you follow the link on https://cran.r-project.org/bin/macosx/ to

Re: [R-SIG-Mac] Does R CMD check create invisible files?

2016-12-16 Thread Prof Brian Ripley
On 16/12/2016 11:44, cstrato wrote: Dear all, On my Mac running Yosemite I zip my package: $ tar czf xps_1.35.1.tar.gz xps The directoy 'xps' does not contain any hidden files! However, when I run: $ R CMD check xps_1.35.1.tar.gz I get: ... * checking for hidden files and directories

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

2016-09-30 Thread Prof Brian Ripley
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 the posting guide asks for 'at a minimum' the output

Re: [R-SIG-Mac] Experiences with macOS Sierra

2016-09-23 Thread Prof Brian Ripley
Capitan: copy /usr/bin/xml2-config to somewhere earlier on your path (~/bin in my case) and edit line 3 from prefix=$(xcrun -show-sdk-path)/usr to prefix=/usr Best, Kasper On Thu, Sep 22, 2016 at 2:39 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk <mailto:rip...@stats.ox.ac.uk>> wr

[R-SIG-Mac] Experiences with macOS Sierra

2016-09-22 Thread Prof Brian Ripley
So far I have encountered few problems. R.app runs but I do not normally use it so my tests were minimal. My observations are about installing packages from source. - It seems Apple has been tidying up, and I had ca 20GB more free space after upgrading (which is worthwhile on my MBA with a

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

2016-09-01 Thread Prof Brian Ripley
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 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

Re: [R-SIG-Mac] Problems with lzma headers file compiling R 3.3.1 under mac os x 10.7.5

2016-08-29 Thread Prof Brian Ripley
Better advice is in the manual, at https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X (although there is no guarantee that all of the binary packages will work with 10.7, many of them will). And for PCRE, at

Re: [R-SIG-Mac] RODBC

2016-08-25 Thread Prof Brian Ripley
On 25/08/2016 17:24, Emilio wrote: Hi, I'm having trouble reading into R an access table (.accdb) with a Mac OS X 10.11.6 I've created a DSN connection to my data base so when I use the odbcConnect function it returns: RODBC Connection 1 Details: case=nochange DSN=mydsn

Re: [R-SIG-Mac] Experience with upgrade to 3.3.0 beta

2016-04-14 Thread Prof Brian Ripley
On 14/04/2016 03:31, David Winsemius wrote: I upgraded to 3.3.0 beta from: R-3.3-branch-mavericks-signed.pkg (70Mb, installer incl. GUI) at the suggestion of Gabor Grothendieck who wanted to know whether Ryacas would install from github in R 3.3.0. So I installed the binary that includes

Re: [R-SIG-Mac] install RNetCDF_1.8-1.tar.gz failed

2016-02-16 Thread Prof Brian Ripley
On 16/02/2016 19:50, Marc Girondot wrote: Dear experts... I try to install the lastest version of RNetCDF (1.8-1.tar.gz) on MacosX (El Capitan) but without success. I send you the precise procedure I have used and some tests: 1/ I have installed MacPort as described here:

Re: [R-SIG-Mac] Issues with rJava on OS X El Capitan

2016-02-14 Thread Prof Brian Ripley
Your Java is seriously old. Start by updating it (1.8.0_74 is current, AFAIK). I can reproduce this with the CRAN binary packages, but installing the packages from source works for me on El Capitan (using the CRAN binary R). So I suspect a problem with the CRAN binary package of rJava,

Re: [R-SIG-Mac] Issues with rJava on OS X El Capitan

2016-02-14 Thread Prof Brian Ripley
On 14/02/2016 11:24, Berend Hasselman wrote: On 14 Feb 2016, at 11:48, Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote: Your Java is seriously old. Start by updating it (1.8.0_74 is current, AFAIK). I can reproduce this with the CRAN binary packages, but installing the packages from

[R-SIG-Mac] detecting cores

2016-02-05 Thread Prof Brian Ripley
sysctl on 10.11 has options which would enable us to differentiate between logical and physical codes on parallel::detectCores --- however these are not documented in Apple's online man pages, which are for 10.9. Could someone running 10.9 and someone for 10.10 report if /usr/sbin/sysctl -n

Re: [R-SIG-Mac] Removing (completely) TCl/Tk

2015-12-09 Thread Prof Brian Ripley
On 09/12/2015 16:12, Federico Calboli wrote: Hi All, I have TCL/Tk installed from the latest DMG image for R 3.2.2 I will upgrade to R 3.2.3 as soon as the DMG is available). I’d like to *completely remove* Tcl/Tk as installed by the DMG image. I can get a list of files from: pkgutil

Re: [R-SIG-Mac] svg() fails (cairo.so unable to load)

2015-10-19 Thread Prof Brian Ripley
On 18/10/2015 19:29, Marius Hofert wrote: Hi, I get ... svg(filename=(file <- "foo.svg")) Warning messages: 1: In svg(filename = (file <- "foo.svg")) : unable to load shared object '/usr/local/R/R-3.2.2_build/library/grDevices/libs//cairo.so':

Re: [R-SIG-Mac] svn update > "xcrun: error: invalid active developer path" after uipgrade to 10.11 El Capitan

2015-10-16 Thread Prof Brian Ripley
On 16/10/2015 09:06, Spencer Graves wrote: Hello: I'm having a problem with "svn update" (with R-Forge) that may be due to a recent upgrade to OS X 10.11 El Capitan. I'm getting the following: $ svn update xcrun: error: invalid active developer path

Re: [R-SIG-Mac] function data.entry() doesn't work and generate error

2015-10-14 Thread Prof Brian Ripley
Well, it appears that your build (which is not one of those supported here) did not include X11, and that must have been purposely excluded. So the error is correct and the warning adds information To use data.entry() you need to be using R.app, Windows or have R compiled to use X11 and

Re: [R-SIG-Mac] function data.entry() doesn't work and generate error

2015-10-14 Thread Prof Brian Ripley
On 14/10/2015 12:45, peter dalgaard wrote: On 14 Oct 2015, at 11:37 , Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote: Well, it appears that your build (which is not one of those supported here) did not include X11, and that must have been purposely excluded. So the error is c

Re: [R-SIG-Mac] XCode / gcc / R compatibility issues on Yosemite with XCode 7 and on El Capitan

2015-10-08 Thread Prof Brian Ripley
On 08/10/2015 02:37, Simon Urbanek wrote: Jenny, I suspect you may not have the correct information. The CRAN Mavericks binary of R is not built with gcc, it's actually build using Apple clang and we're neither using nor requiring homebrew, so most of what you are describing doesn't make

Re: [R-SIG-Mac] Experiences with El Capitan

2015-10-05 Thread Prof Brian Ripley
On 05/10/2015 09:03, Mikko Korpela wrote: On 04.10.2015 19:53, Prof Brian Ripley wrote: The machine which provides the 'r-devel-osx-x86_64-clang' checks on the CRAN check farm has been upgraded from Yosemite to El Capitan and a complete round of checks has been run. Thank you, this is great

Re: [R-SIG-Mac] Problems to install a package

2015-08-04 Thread Prof Brian Ripley
On 04/08/2015 08:57, peter dalgaard wrote: On 03 Aug 2015, at 23:48 , Simon Urbanek simon.urba...@r-project.org wrote: Sorry, I thought it was obvious so I didn't elaborate in more detail - our Mavericks compiler binary (gfortran-4.8) itself is using more advanced instruction set so it

Re: [R-SIG-Mac] latex errors, Rd problems

2015-03-21 Thread Prof Brian Ripley
On 21/03/2015 12:38, Adrian Dușa wrote: On Sat, Mar 21, 2015 at 12:57 PM, Prof Brian Ripley rip...@stats.ox.ac.uk mailto:rip...@stats.ox.ac.uk wrote: [...] I also tried R CMD Rd2pdf (in the command line), and I get this at the end: Error in texi2dvi(file = file

Re: [R-SIG-Mac] latex errors, Rd problems

2015-03-21 Thread Prof Brian Ripley
errors are more MacTex related than R-related at this point. On Sat, Mar 21, 2015 at 3:02 PM, Adrian Dușa dusa.adr...@unibuc.ro mailto:dusa.adr...@unibuc.ro wrote: On Sat, Mar 21, 2015 at 3:09 PM, Prof Brian Ripley rip...@stats.ox.ac.uk mailto:rip...@stats.ox.ac.uk wrote: On 21/03

Re: [R-SIG-Mac] checking for pdflatex

2015-03-17 Thread Prof Brian Ripley
- From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk] Sent: March-16-15 3:56 PM To: j...@mcmaster.ca; 'Berend Hasselman' Cc: r-sig-mac@r-project.org Subject: Re: [R-SIG-Mac] checking for pdflatex Note that it not just MacTex which uses /usr/texbin. /usr/texbin is a link to /Library/TeX

Re: [R-SIG-Mac] checking for pdflatex

2015-03-16 Thread Prof Brian Ripley
Note that it not just MacTex which uses /usr/texbin. /usr/texbin is a link to /Library/TeX/Distributions/Programs/texbin which is an /etc/alternatives scheme to manage multiple TeX distributions which used (prior to Yosemite, at least) to be controlled by a Systems Preferences widget. See

Re: [R-SIG-Mac] Fixing configure scripts for rgeos and rgdal for OS X

2015-03-10 Thread Prof Brian Ripley
On 10/03/2015 00:18, Bill Behrman wrote: CRAN does not currently offer binaries for rgeos or rgdal for OS X Maverick+, and the configure scripts do not work for compiling these packages from source. Not true: see the 'mavericks' lines in the CRAN check summaries for those packages, and

Re: [R-SIG-Mac] linker warnings

2015-01-30 Thread Prof Brian Ripley
On 30/01/2015 18:28, Jan de Leeuw wrote: In my current compiles of R-devel from source (using clang from Yosemite and gfortran from homebrew) I added -Wl,-no_compact_unwind to my LDFLAGS to get around the annoying warning create compact unwind for foo: stack subq instruction is too different

Re: [R-SIG-Mac] tcltk

2014-12-26 Thread Prof Brian Ripley
On 26/12/2014 20:28, Simon Urbanek wrote: On Dec 26, 2014, at 3:25 AM, Ivan Calandra ivan.calan...@univ-reims.fr wrote: Thank you Simon for your answer. But I cannot find Xcode for MacOS 10.6... Go to https://developer.apple.com/downloads and search for Xcode 4.2 or use

Re: [R-SIG-Mac] Is Yosemite now safe for most of us?

2014-12-24 Thread Prof Brian Ripley
On 25/12/2014 02:16, Hadley Wickham wrote: Yes, the bugs have been well and truly worked out. Worked around, more precisely. There are still bugs in Yosemite's handling of environment variables, and R = 3.1.2 has workarounds that resolve some of those. But they can still bite when building

  1   2   3   >