From h@@@n@bu|ut @end|ng |rom omu@edu@tr Sun Apr 2 08:15:02 2023 From: h@@@n@bu|ut @end|ng |rom omu@edu@tr (HASAN BULUT) Date: Sun, 2 Apr 2023 09:15:02 +0300 (TRT) Subject: [R-SIG-Mac] Install error for gmm package Message-ID: <1485444289.7495505.1680416102858.JavaMail.zimbra@omu.edu.tr> Hi everyone, I have Macbook air M2 and I need the "gmm" package. But I cannot install conventionally this package. When I install and call this package, I see below error message: Loading required package: sandwich Error: package or namespace load failed for ?gmm? in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gmm/libs/gmm.so': dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gmm/libs/gmm.so, 0x0006): Library not loaded: /opt/R/arm64/gfortran/lib/libgomp.1.dylib Referenced from: <47242657-5A5D-3982-936B-398527D642B4> /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gmm/libs/gmm.so Reason: tried: '/opt/R/arm64/gfortran/lib/libgomp.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/R/arm64/gfortran/lib/libgomp.1.dylib' (no such file), '/opt/R/arm64/gfortran/lib/libgomp.1.dylib' (no such file), '/usr/local/lib/libgomp.1.dylib' (no such file), '/usr/lib/libgomp.1.dylib' (no such file, not in dyld cache) Could you help me? Best wishes. Hasan Bulut -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: indir.png Type: image/png Size: 6052 bytes Desc: not available URL: From @|mon@urb@nek @end|ng |rom R-project@org Sun Apr 2 10:20:30 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Sun, 2 Apr 2023 20:20:30 +1200 Subject: [R-SIG-Mac] Install error for gmm package In-Reply-To: <1485444289.7495505.1680416102858.JavaMail.zimbra@omu.edu.tr> References: <1485444289.7495505.1680416102858.JavaMail.zimbra@omu.edu.tr> Message-ID: <72A85615-63B6-4FCD-85DE-984BCA7A63B0@R-project.org> 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 Terminal (under Application->Utilities) and type cd /tmp curl -O https://mac.r-project.org/tools/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz sudo tar fxz gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C / Cheers, Simon > On Apr 2, 2023, at 6:15 PM, HASAN BULUT wrote: > > Hi everyone, > > I have Macbook air M2 and I need the "gmm" package. But I cannot install conventionally this package. > When I install and call this package, I see below error message: > > Loading required package: sandwich > Error: package or namespace load failed for ?gmm? in dyn.load(file, DLLpath = DLLpath, ...): > unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gmm/libs/gmm.so': > dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gmm/libs/gmm.so, 0x0006): Library not loaded: /opt/R/arm64/gfortran/lib/libgomp.1.dylib > Referenced from: <47242657-5A5D-3982-936B-398527D642B4> /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gmm/libs/gmm.so > Reason: tried: '/opt/R/arm64/gfortran/lib/libgomp.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/R/arm64/gfortran/lib/libgomp.1.dylib' (no such file), '/opt/R/arm64/gfortran/lib/libgomp.1.dylib' (no such file), '/usr/local/lib/libgomp.1.dylib' (no such file), '/usr/lib/libgomp.1.dylib' (no such file, not in dyld cache) > > Could you help me? > > Best wishes. > > Hasan Bulut > > > > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From Jenn||er@Wok@ty @end|ng |rom @ph@cuny@edu Tue Apr 4 18:26:43 2023 From: Jenn||er@Wok@ty @end|ng |rom @ph@cuny@edu (Jennifer Wokaty) Date: Tue, 4 Apr 2023 16:26:43 +0000 Subject: [R-SIG-Mac] Symbol not found: _timespec_get Message-ID: 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-branch-x86_64.pkg -target / installer: Package name is R 4.3.0 for macOS (X86_64) installer: Upgrading at base path / installer: The upgrade was successful. $ R dyld: lazy symbol binding failed: Symbol not found: _timespec_get Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: _timespec_get Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) Expected in: /usr/lib/libSystem.B.dylib Abort trap: 6 Is this a problem with the .pkg file? Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team [[alternative HTML version deleted]] From tom@@@k@||ber@ @end|ng |rom gm@||@com Tue Apr 4 19:45:53 2023 From: tom@@@k@||ber@ @end|ng |rom gm@||@com (Tomas Kalibera) Date: Tue, 4 Apr 2023 19:45:53 +0200 Subject: [R-SIG-Mac] Symbol not found: _timespec_get In-Reply-To: References: Message-ID: 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-branch-x86_64.pkg -target / > installer: Package name is R 4.3.0 for macOS (X86_64) > installer: Upgrading at base path / > installer: The upgrade was successful. > $ R > dyld: lazy symbol binding failed: Symbol not found: _timespec_get > Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: _timespec_get > Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) > Expected in: /usr/lib/libSystem.B.dylib > > Abort trap: 6 > > Is this a problem with the .pkg file? Hi Jen, could you please report your macOS version, e.g. via sessionInfo()? Is it at least 11? Tomas > > Jennifer Wokaty (they/them) > > Waldron Lab at CUNY SPH > Bioconductor Core Team > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From Jenn||er@Wok@ty @end|ng |rom @ph@cuny@edu Tue Apr 4 20:04:59 2023 From: Jenn||er@Wok@ty @end|ng |rom @ph@cuny@edu (Jennifer Wokaty) Date: Tue, 4 Apr 2023 18:04:59 +0000 Subject: [R-SIG-Mac] Symbol not found: _timespec_get In-Reply-To: References: Message-ID: Sorry, thank you for kindly reminding me! R aborts so I can't provide sessionInfo(), but that's likely the problem as we're running macOS 10.14.6 Mojave x86_64-apple-darwin18.7.0. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team ________________________________ From: Tomas Kalibera Sent: Tuesday, April 4, 2023 1:45 PM To: Jennifer Wokaty ; R list Subject: Re: [R-SIG-Mac] Symbol not found: _timespec_get ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** On 4/4/23 18:26, Jennifer Wokaty wrote: > Hi, > > I tried installing the x86_64 alpha available today at https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.r-2Dproject.org_big-2Dsur-2Dx86-5F64_R-2D4.3-2Dbranch_R-2D4.3-2Dbranch-2Dx86-5F64.pkg&d=DwICaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=DmuhCksnwNg84omqA0JKgHs0D19_LtdOtLYF5PHjwhrrAGJd-oipKLVnv0P5zaCs&s=LxWPN-ZaCdXshO1N0P-FIM2vDwLCBud23G9_f9cQwQU&e= ; however, I'm getting the following error: > > $ sudo installer -pkg R-4.3-branch-x86_64.pkg -target / > installer: Package name is R 4.3.0 for macOS (X86_64) > installer: Upgrading at base path / > installer: The upgrade was successful. > $ R > dyld: lazy symbol binding failed: Symbol not found: _timespec_get > Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: _timespec_get > Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) > Expected in: /usr/lib/libSystem.B.dylib > > Abort trap: 6 > > Is this a problem with the .pkg file? Hi Jen, could you please report your macOS version, e.g. via sessionInfo()? Is it at least 11? Tomas > > Jennifer Wokaty (they/them) > > Waldron Lab at CUNY SPH > Bioconductor Core Team > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwICaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=DmuhCksnwNg84omqA0JKgHs0D19_LtdOtLYF5PHjwhrrAGJd-oipKLVnv0P5zaCs&s=nz6Y3C8Ar-2cbE9KbTe2YIlyYm7i3AdQqFFmd3VhVSo&e= [[alternative HTML version deleted]] From r|p|ey @end|ng |rom @t@t@@ox@@c@uk Tue Apr 4 20:14:55 2023 From: r|p|ey @end|ng |rom @t@t@@ox@@c@uk (Prof Brian Ripley) Date: Tue, 4 Apr 2023 19:14:55 +0100 Subject: [R-SIG-Mac] Symbol not found: _timespec_get In-Reply-To: References: Message-ID: 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-branch-x86_64.pkg -target / >> installer: Package name is R 4.3.0 for macOS (X86_64) >> installer: Upgrading at base path / >> installer: The upgrade was successful. >> $ R >> dyld: lazy symbol binding failed: Symbol not found: _timespec_get >> ?? Referenced from: >> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) >> ?? Expected in: /usr/lib/libSystem.B.dylib >> >> dyld: Symbol not found: _timespec_get >> ?? Referenced from: >> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) >> ?? Expected in: /usr/lib/libSystem.B.dylib >> >> Abort trap: 6 >> >> Is this a problem with the .pkg file? > > Hi Jen, > > could you please report your macOS version, e.g. via sessionInfo()? Is > it at least 11? 'they' probably cannot run R to run sessionInfo(). Use 'About this Mac' from the Apple menu to find the version without R. The header has __API_AVAILABLE(macosx(10.15), ios(13.0), tvos(13.0), watchos(6.0)) int timespec_get(struct timespec *ts, int base); which says timespec_get is available from macOS 10.15 (Catalina) We have had trouble with this before: configure.ac says ## timespec_get is C11. ## macOS added timespec_get in 10.15 but used 10.15's SDK for 10.14 (Darwin 18) and it skips detection for Darwin <= 18. > > Tomas > >> >> Jennifer Wokaty (they/them) >> >> Waldron Lab at CUNY SPH >> Bioconductor Core Team-- Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford From @|mon@urb@nek @end|ng |rom R-project@org Tue Apr 4 22:54:41 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Wed, 5 Apr 2023 08:54:41 +1200 Subject: [R-SIG-Mac] Symbol not found: _timespec_get In-Reply-To: References: Message-ID: 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 wrote: > > Sorry, thank you for kindly reminding me! > > R aborts so I can't provide sessionInfo(), but that's likely the problem as we're running macOS 10.14.6 Mojave x86_64-apple-darwin18.7.0. > > Jennifer Wokaty (they/them) > > Waldron Lab at CUNY SPH > Bioconductor Core Team > ________________________________ > From: Tomas Kalibera > Sent: Tuesday, April 4, 2023 1:45 PM > To: Jennifer Wokaty ; R list > Subject: Re: [R-SIG-Mac] Symbol not found: _timespec_get > > ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** > > > On 4/4/23 18:26, Jennifer Wokaty wrote: >> Hi, >> >> I tried installing the x86_64 alpha available today at https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.r-2Dproject.org_big-2Dsur-2Dx86-5F64_R-2D4.3-2Dbranch_R-2D4.3-2Dbranch-2Dx86-5F64.pkg&d=DwICaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=DmuhCksnwNg84omqA0JKgHs0D19_LtdOtLYF5PHjwhrrAGJd-oipKLVnv0P5zaCs&s=LxWPN-ZaCdXshO1N0P-FIM2vDwLCBud23G9_f9cQwQU&e= ; however, I'm getting the following error: >> >> $ sudo installer -pkg R-4.3-branch-x86_64.pkg -target / >> installer: Package name is R 4.3.0 for macOS (X86_64) >> installer: Upgrading at base path / >> installer: The upgrade was successful. >> $ R >> dyld: lazy symbol binding failed: Symbol not found: _timespec_get >> Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) >> Expected in: /usr/lib/libSystem.B.dylib >> >> dyld: Symbol not found: _timespec_get >> Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (which was built for Mac OS X 11.0) >> Expected in: /usr/lib/libSystem.B.dylib >> >> Abort trap: 6 >> >> Is this a problem with the .pkg file? > > Hi Jen, > > could you please report your macOS version, e.g. via sessionInfo()? Is > it at least 11? > > Tomas > >> >> Jennifer Wokaty (they/them) >> >> Waldron Lab at CUNY SPH >> Bioconductor Core Team >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwICaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=DmuhCksnwNg84omqA0JKgHs0D19_LtdOtLYF5PHjwhrrAGJd-oipKLVnv0P5zaCs&s=nz6Y3C8Ar-2cbE9KbTe2YIlyYm7i3AdQqFFmd3VhVSo&e= > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From j@g@nmn2 @end|ng |rom gm@||@com Fri Apr 14 21:48:00 2023 From: j@g@nmn2 @end|ng |rom gm@||@com (Mikael Jagan) Date: Fri, 14 Apr 2023 15:48:00 -0400 Subject: [R-SIG-Mac] typo in mac.r-project.org index? Message-ID: <0f0fe8c1-3f17-6b84-31ae-1d04881eb217@gmail.com> Hi Simon, Maybe I'm off the mark, but: > R 4.3.0 CRAN builds are using Xcode 14.2, macOS 11.3 SDK and targetting macOS 11 (Big Sur) AFAICT, Xcode 14.x includes an SDK for macOS 12.3 but not one for macOS 11.3. https://developer.apple.com/documentation/xcode-release-notes/xcode-14-release-notes Mikael From @|mon@urb@nek @end|ng |rom R-project@org Sat Apr 15 03:36:37 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Sat, 15 Apr 2023 13:36:37 +1200 Subject: [R-SIG-Mac] typo in mac.r-project.org index? In-Reply-To: <0f0fe8c1-3f17-6b84-31ae-1d04881eb217@gmail.com> References: <0f0fe8c1-3f17-6b84-31ae-1d04881eb217@gmail.com> Message-ID: <306A5663-8266-43EE-BF1D-57B67DC6F186@R-project.org> 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 SDK version. Cheers, Simon > On Apr 15, 2023, at 7:48 AM, Mikael Jagan wrote: > > Hi Simon, > > Maybe I'm off the mark, but: > > > R 4.3.0 CRAN builds are using Xcode 14.2, macOS 11.3 SDK and targetting macOS 11 (Big Sur) > > AFAICT, Xcode 14.x includes an SDK for macOS 12.3 but not one for macOS 11.3. > > https://developer.apple.com/documentation/xcode-release-notes/xcode-14-release-notes > > Mikael > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From @|mon@urb@nek @end|ng |rom R-project@org Tue Apr 18 05:18:03 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Tue, 18 Apr 2023 15:18:03 +1200 Subject: [R-SIG-Mac] Please test R 4.3.0 RC, more information below Message-ID: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1@R-project.org> 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 leverage new compilers (important for modern C++ support) and libraries. As usual, there are two releases: one for the older Intel Macs (x86_64) and one for the new M1/M2 Macs (arm64) - please install the matching version. R users can stop reading here, just test, please! 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 GNU Fortran compiler that works both on Intel and arm64 Macs - you can download an Apple Installer from https://mac.r-project.org/tools/ There are two major changes for the Intel build relevant to advanced users: a) .Platfrom$pkgType is "mac.binary.big-sur-x86_64" since we are targeting a new macOS version (this is to match arm64 which uses "mac.binary.big-sur-arm64"). It means that binaries for contributed packages in repositories live in bin/macosx/big-sur-x86_64/contrib/4.3. b) the Intel build now matches the arm64 build such that dependent libraries are expected in /opt/R/x86_64 (to match arm64's /opt/R/arm64) to avoid conflicts with other tools. You can still add -I/usr/local/include to CPPFLAGS or -L/usr/local/lib to LDFLAGS if you want to use 3rd party libraries from /usr/local (refer to R and package documentation for details). Finally, R will no longer sets the macos-version-min flag by default, which means R will build for the currently installed macOS version. This allows users to build packages that use the latest SDK and capabilities of the latest macOS without any changes. However, if you are distributing package binaries for use others, we strongly recommend that you set export MACOSX_DEPLOYMENT_TARGET=11.0 when compiling binaries which will make sure that they will run on macOS 11 and higher, otherwise your binary may not be compatible. CRAN also uses the macOS11 SDK via export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk However, depending on your Xcode version you may not have such SDK, so it is optional. Cheers, Simon From gb @end|ng |rom eh@r@@e Tue Apr 18 12:01:15 2023 From: gb @end|ng |rom eh@r@@e (=?UTF-8?Q?G=c3=b6ran_Brostr=c3=b6m?=) Date: Tue, 18 Apr 2023 12:01:15 +0200 Subject: [R-SIG-Mac] Please test R 4.3.0 RC, more information below In-Reply-To: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1@R-project.org> References: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1@R-project.org> Message-ID: <4e29ff48-b3ad-5020-e63f-a9aa57db1d86@ehar.se> 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 GNU Fortran compiler that works both on Intel > and arm64 Macs - you can download an Apple Installer from > https://mac.r-project.org/tools/ I have GNU Fortran (GCC) 12.0.1 20220312 (experimental) in /opt/R/arm64/gfortran/bin/gfortran Should it be uninstalled/removed in some way before installing gfortran-12.2-universal.pkg, and if so, how? Thanks, G?ran > Cheers, Simon > > _______________________________________________ R-SIG-Mac mailing > list R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From r|p|ey @end|ng |rom @t@t@@ox@@c@uk Tue Apr 18 12:13:10 2023 From: r|p|ey @end|ng |rom @t@t@@ox@@c@uk (Prof Brian Ripley) Date: Tue, 18 Apr 2023 11:13:10 +0100 Subject: [R-SIG-Mac] Please test R 4.3.0 RC, more information below In-Reply-To: <4e29ff48-b3ad-5020-e63f-a9aa57db1d86@ehar.se> References: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1@R-project.org> <4e29ff48-b3ad-5020-e63f-a9aa57db1d86@ehar.se> Message-ID: <5a94d359-771f-a6a8-7f24-2682bc8edc81@stats.ox.ac.uk> On 18/04/2023 11:01, G?ran Brostr?m 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 GNU Fortran compiler that works both on Intel >> and arm64 Macs - you can download an Apple Installer from >> https://mac.r-project.org/tools/ > > I have GNU Fortran (GCC) 12.0.1 20220312 (experimental) > > in /opt/R/arm64/gfortran/bin/gfortran > > Should it be uninstalled/removed in some way before installing > gfortran-12.2-universal.pkg, and if so, how? Not necessary, as the newer compiler installs into /opt/gfortran. You may need to change FC and FLIBS in a ~/.R/Makevars if you use one, and you may need to adjust your path if you use Fortran other than for R packages. To remove the older version, delete /opt/R/arm64/gfortran/ . -- Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford From j@g@nmn2 @end|ng |rom gm@||@com Tue Apr 18 15:43:01 2023 From: j@g@nmn2 @end|ng |rom gm@||@com (Mikael Jagan) Date: Tue, 18 Apr 2023 09:43:01 -0400 Subject: [R-SIG-Mac] R-SIG-Mac Digest, Vol 241, Issue 5 In-Reply-To: References: Message-ID: <3c52eebc-f656-604d-f1f6-68411475788f@gmail.com> The OpenMP binaries provided here https://mac.r-project.org/openmp/ still have the usr/local/ prefix. Is that intentional? If that prefix were simply deleted, then users could unpack with (for example) tar -xvf openmp-14.0.6-darwin20-Release.tar.gz -C /opt/R/$(uname -m) And then 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-SIG-Mac] Please test R 4.3.0 RC, more information below > Message-ID: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1 at R-project.org> > Content-Type: text/plain; charset="us-ascii" > > 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 leverage new compilers (important for modern C++ support) and libraries. As usual, there are two releases: one for the older Intel Macs (x86_64) and one for the new M1/M2 Macs (arm64) - please install the matching version. > > R users can stop reading here, just test, please! > > 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 GNU Fortran compiler that works both on Intel and arm64 Macs - you can download an Apple Installer from > https://mac.r-project.org/tools/ > > There are two major changes for the Intel build relevant to advanced users: > > a) .Platfrom$pkgType is "mac.binary.big-sur-x86_64" since we are targeting a new macOS version (this is to match arm64 which uses "mac.binary.big-sur-arm64"). It means that binaries for contributed packages in repositories live in bin/macosx/big-sur-x86_64/contrib/4.3. > > b) the Intel build now matches the arm64 build such that dependent libraries are expected in /opt/R/x86_64 (to match arm64's /opt/R/arm64) to avoid conflicts with other tools. You can still add -I/usr/local/include to CPPFLAGS or -L/usr/local/lib to LDFLAGS if you want to use 3rd party libraries from /usr/local (refer to R and package documentation for details). > > Finally, R will no longer sets the macos-version-min flag by default, which means R will build for the currently installed macOS version. This allows users to build packages that use the latest SDK and capabilities of the latest macOS without any changes. However, if you are distributing package binaries for use others, we strongly recommend that you set > > export MACOSX_DEPLOYMENT_TARGET=11.0 > > when compiling binaries which will make sure that they will run on macOS 11 and higher, otherwise your binary may not be compatible. > > CRAN also uses the macOS11 SDK via > > export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk > > However, depending on your Xcode version you may not have such SDK, so it is optional. > > Cheers, > Simon From murdoch@dunc@n @end|ng |rom gm@||@com Tue Apr 18 18:58:05 2023 From: murdoch@dunc@n @end|ng |rom gm@||@com (Duncan Murdoch) Date: Tue, 18 Apr 2023 12:58:05 -0400 Subject: [R-SIG-Mac] Please test R 4.3.0 RC, more information below In-Reply-To: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1@R-project.org> References: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1@R-project.org> Message-ID: <7e9f556c-8a6b-70ba-fc3b-60b41aafab49@gmail.com> Hi Simon. I'm seeing crashes when I try to compile rgl and run it in the new R on my Intel notebook. I only installed R, I didn't update all the libs/tools/etc. The crash report is copied below. One oddity I notice on the 4th line of the report: it says it is running "R 4.2.3 GUI 1.79 Big Sur Intel build (8220)". When I run R.app and `version`, I see > version _ platform x86_64-apple-darwin20 arch x86_64 os darwin20 system x86_64, darwin20 status RC major 4 minor 3.0 year 2023 month 04 day 13 svn rev 84266 language R version.string R version 4.3.0 RC (2023-04-13 r84266) nickname Already Tomorrow but when I choose "About R" in the GUI, I see 4.2.3 reported. Maybe I've got both installed, and that's the cause of the crash? Duncan Murdoch ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: R [73019] Path: /Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: R 4.2.3 GUI 1.79 Big Sur Intel build (8220) Code Type: X86-64 (Native) Parent Process: launchd [1] User ID: 501 Date/Time: 2023-04-18 12:52:03.3210 -0400 OS Version: macOS 12.6.5 (21G531) Report Version: 12 Anonymous UUID: 2FE3AC85-3E2D-5190-5592-56ECA0EE7FA1 Sleep/Wake UUID: 26969829-5168-4FF8-8E98-CBCCF23BAFDB Time Awake Since Boot: 230000 seconds Time Since Wake: 2451 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x000000000004c9f0 Exception Codes: 0x0000000000000001, 0x000000000004c9f0 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [73019] VM Region Info: 0x4c9f0 is not in any region. Bytes before following region: 4414989840 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 1072c3000-10734f000 [ 560K] r-x/r-x SM=COW ...tents/MacOS/R Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libR.dylib 0x124689ab9 Rf_install + 73 1 rgl.so 0x11ff0f504 rgl::X11GUIFactory::createWindowImpl(rgl::Window*) + 52 (x11gui.cpp:655) 2 rgl.so 0x11ff00806 rgl::Window::Window(rgl::View*, rgl::GUIFactory*) + 118 (gui.cpp:162) 3 rgl.so 0x11fedf294 rgl::Device::Device(int, bool) + 148 (device.cpp:16) 4 rgl.so 0x11fedfec5 rgl::DeviceManager::createTestWindow() + 37 (devicemanager.cpp:167) 5 rgl.so 0x11ff00f39 rgl_init + 313 (init.cpp:97) 6 libR.dylib 0x10799dfde R_doDotCall + 862 (dotcode.c:877) 7 libR.dylib 0x1079ee818 bcEval + 105112 (eval.c:8002) 8 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 9 libR.dylib 0x1079f47ac R_execClosure + 2284 10 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 11 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 12 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 13 libR.dylib 0x1079f47ac R_execClosure + 2284 14 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 15 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 16 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 17 libR.dylib 0x1079f2bac forcePromise + 172 (eval.c:833) 18 libR.dylib 0x107a00434 FORCE_PROMISE + 8 (eval.c:5467) [inlined] 19 libR.dylib 0x107a00434 getvar + 372 (eval.c:5508) 20 libR.dylib 0x1079d8b5f bcEval + 15839 (eval.c:7198) 21 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 22 libR.dylib 0x1079f2bac forcePromise + 172 (eval.c:833) 23 libR.dylib 0x107a00434 FORCE_PROMISE + 8 (eval.c:5467) [inlined] 24 libR.dylib 0x107a00434 getvar + 372 (eval.c:5508) 25 libR.dylib 0x1079d8b5f bcEval + 15839 (eval.c:7198) 26 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 27 libR.dylib 0x1079f2bac forcePromise + 172 (eval.c:833) 28 libR.dylib 0x107a00434 FORCE_PROMISE + 8 (eval.c:5467) [inlined] 29 libR.dylib 0x107a00434 getvar + 372 (eval.c:5508) 30 libR.dylib 0x1079d8b5f bcEval + 15839 (eval.c:7198) 31 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 32 libR.dylib 0x1079f2bac forcePromise + 172 (eval.c:833) 33 libR.dylib 0x107a00434 FORCE_PROMISE + 8 (eval.c:5467) [inlined] 34 libR.dylib 0x107a00434 getvar + 372 (eval.c:5508) 35 libR.dylib 0x1079d8b5f bcEval + 15839 (eval.c:7198) 36 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 37 libR.dylib 0x1079f47ac R_execClosure + 2284 38 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 39 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 40 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 41 libR.dylib 0x1079f47ac R_execClosure + 2284 42 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 43 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 44 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 45 libR.dylib 0x1079f47ac R_execClosure + 2284 46 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 47 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 48 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 49 libR.dylib 0x1079f47ac R_execClosure + 2284 50 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 51 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 52 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 53 libR.dylib 0x1079f47ac R_execClosure + 2284 54 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 55 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 56 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 57 libR.dylib 0x1079f47ac R_execClosure + 2284 58 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 59 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 60 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 61 libR.dylib 0x1079f2bac forcePromise + 172 (eval.c:833) 62 libR.dylib 0x107a00434 FORCE_PROMISE + 8 (eval.c:5467) [inlined] 63 libR.dylib 0x107a00434 getvar + 372 (eval.c:5508) 64 libR.dylib 0x1079d8b5f bcEval + 15839 (eval.c:7198) 65 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 66 libR.dylib 0x1079f2bac forcePromise + 172 (eval.c:833) 67 libR.dylib 0x107a00434 FORCE_PROMISE + 8 (eval.c:5467) [inlined] 68 libR.dylib 0x107a00434 getvar + 372 (eval.c:5508) 69 libR.dylib 0x1079d8b5f bcEval + 15839 (eval.c:7198) 70 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 71 libR.dylib 0x1079f2bac forcePromise + 172 (eval.c:833) 72 libR.dylib 0x107a00434 FORCE_PROMISE + 8 (eval.c:5467) [inlined] 73 libR.dylib 0x107a00434 getvar + 372 (eval.c:5508) 74 libR.dylib 0x1079d8b5f bcEval + 15839 (eval.c:7198) 75 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 76 libR.dylib 0x1079f2bac forcePromise + 172 (eval.c:833) 77 libR.dylib 0x107a00434 FORCE_PROMISE + 8 (eval.c:5467) [inlined] 78 libR.dylib 0x107a00434 getvar + 372 (eval.c:5508) 79 libR.dylib 0x1079d8b5f bcEval + 15839 (eval.c:7198) 80 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 81 libR.dylib 0x1079f47ac R_execClosure + 2284 82 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 83 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 84 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 85 libR.dylib 0x1079f47ac R_execClosure + 2284 86 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 87 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 88 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 89 libR.dylib 0x1079f47ac R_execClosure + 2284 90 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 91 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 92 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 93 libR.dylib 0x1079f47ac R_execClosure + 2284 94 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 95 libR.dylib 0x1079dba87 bcEval + 27911 (eval.c:7414) 96 libR.dylib 0x1079d4713 Rf_eval + 531 (eval.c:1013) 97 libR.dylib 0x1079f47ac R_execClosure + 2284 98 libR.dylib 0x1079f34e3 Rf_applyClosure + 483 (eval.c:2113) 99 libR.dylib 0x1079d49e4 Rf_eval + 1252 (eval.c:1140) 100 libR.dylib 0x107a31181 R_ReplDLLdo1 + 449 (main.c:396) 101 R 0x1072dfc47 run_REngineRmainloop + 263 102 R 0x1072d4d5f -[REngine runREPL] + 143 103 R 0x1072c4718 main + 792 104 dyld 0x10ef5d52e start + 462 Thread 1: 0 libsystem_kernel.dylib 0x7ff803411d4a __select + 10 1 R 0x1072c7191 -[RController readThread:] + 641 2 Foundation 0x7ff804361994 __NSThread__start__ + 1009 3 libsystem_pthread.dylib 0x7ff8034464e1 _pthread_start + 125 4 libsystem_pthread.dylib 0x7ff803441f6b thread_start + 15 Thread 2:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x7ff80340996a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x7ff803409cd8 mach_msg + 56 2 CoreFoundation 0x7ff80350d34d __CFRunLoopServiceMachPort + 319 3 CoreFoundation 0x7ff80350b9d8 __CFRunLoopRun + 1276 4 CoreFoundation 0x7ff80350ae1c CFRunLoopRunSpecific + 562 5 AppKit 0x7ff8060b298e _NSEventThread + 132 6 libsystem_pthread.dylib 0x7ff8034464e1 _pthread_start + 125 7 libsystem_pthread.dylib 0x7ff803441f6b thread_start + 15 Thread 3: 0 libsystem_pthread.dylib 0x7ff803441f48 start_wqthread + 0 Thread 4: 0 libsystem_pthread.dylib 0x7ff803441f48 start_wqthread + 0 Thread 5: 0 libsystem_pthread.dylib 0x7ff803441f48 start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x7ff803441f48 start_wqthread + 0 Thread 7: 0 libsystem_kernel.dylib 0x7ff80340c2ae __semwait_signal + 10 1 libsystem_c.dylib 0x7ff803320863 nanosleep + 196 2 cli.so 0x11fdea44a clic_thread_func + 74 (thread.c:37) 3 libsystem_pthread.dylib 0x7ff8034464e1 _pthread_start + 125 4 libsystem_pthread.dylib 0x7ff803441f6b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000060000167b360 rcx: 0x000000000000993e rdx: 0x0000000020000000 rdi: 0x000000011ff18f1e rsi: 0x0000000000000020 rbp: 0x00007ff7b8c24bb0 rsp: 0x00007ff7b8c24b80 r8: 0x00008282c84db360 r9: 0x0000000000000000 r10: 0x00000000fffffff0 r11: 0xffffffffffff1a90 r12: 0x00006000011ec1e0 r13: 0x0000000000000012 r14: 0x000000011ff18f10 r15: 0x00000000022967a3 rip: 0x0000000124689ab9 rfl: 0x0000000000010212 cr2: 0x000000000004c9f0 Logical CPU: 2 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Thread 0 instruction stream: 16 00 e8 e0 5c ff ff 48-8d 3d 19 62 17 00 e8 a4 ....\..H.=.b.... d8 0e 00 0f 1f 40 00 55-48 89 e5 41 57 41 56 41 ..... at .UH..AWAVA 55 41 54 53 50 49 89 fe-e8 9a ed f7 ff 4c 63 f8 UATSPI.......Lc. 49 69 c7 81 1c 53 55 48-89 c1 48 c1 e9 3f 48 c1 Ii...SUH..H..?H. f8 2e 01 c8 69 c0 05 c0-00 00 44 89 f9 29 c1 48 ....i.....D..).H 8d 05 c1 b1 34 00 48 8b-00 48 63 c9 48 89 4d d0 ....4.H..Hc.H.M. [4c]8b 24 c8 48 8d 05 e4-b0 34 00 4c 8b 28 4d 39 L.$.H....4.L.(M9 <== ec 74 38 0f 1f 40 00 66-41 83 7c 24 06 00 0f 85 .t8.. at .fA.|$.... b1 00 00 00 49 8b 5c 24-20 48 8b 73 20 48 83 c6 ....I.\$ H.s H.. 30 4c 89 f7 e8 b2 5a 16-00 85 c0 0f 84 82 00 00 0L....Z......... 00 4d 8b 64 24 28 4d 39-ec 75 cc 41 80 3e 00 0f .M.d$(M9.u.A.>.. 84 8e 00 00 00 4c 89 f7-e8 b8 5a 16 00 48 3d 11 .....L....Z..H=. 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Device: BRCM20702 Hub USB Device: Bluetooth USB Host Controller USB Device: composite_device USB Device: composite_device Thunderbolt Bus: MacBook Air, Apple Inc., 27.2 From murdoch@dunc@n @end|ng |rom gm@||@com Tue Apr 18 19:06:42 2023 From: murdoch@dunc@n @end|ng |rom gm@||@com (Duncan Murdoch) Date: Tue, 18 Apr 2023 13:06:42 -0400 Subject: [R-SIG-Mac] Please test R 4.3.0 RC, more information below In-Reply-To: <7e9f556c-8a6b-70ba-fc3b-60b41aafab49@gmail.com> References: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1@R-project.org> <7e9f556c-8a6b-70ba-fc3b-60b41aafab49@gmail.com> Message-ID: On 18/04/2023 12:58 p.m., Duncan Murdoch wrote: > Hi Simon. > > I'm seeing crashes when I try to compile rgl and run it in the new R on > my Intel notebook. I only installed R, I didn't update all the > libs/tools/etc. > > The crash report is copied below. One oddity I notice on the 4th line > of the report: it says it is running "R 4.2.3 GUI 1.79 Big Sur Intel > build (8220)". When I run R.app and `version`, I see > > > version > _ > platform x86_64-apple-darwin20 > arch x86_64 > os darwin20 > system x86_64, darwin20 > status RC > major 4 > minor 3.0 > year 2023 > month 04 > day 13 > svn rev 84266 > language R > version.string R version 4.3.0 RC (2023-04-13 r84266) > nickname Already Tomorrow > > but when I choose "About R" in the GUI, I see 4.2.3 reported. Maybe > I've got both installed, and that's the cause of the crash? > > Duncan Murdoch Sorry, I think that was (mostly) a false alarm. I may have had some old object files which weren't recompiled after the install; at least after a new clean build I'm not seeing the crash any more. The bad version report in R.app is still there. Duncan Murdoch From @|mon@urb@nek @end|ng |rom R-project@org Tue Apr 18 22:46:43 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Wed, 19 Apr 2023 08:46:43 +1200 Subject: [R-SIG-Mac] R-SIG-Mac Digest, Vol 241, Issue 5 In-Reply-To: <3c52eebc-f656-604d-f1f6-68411475788f@gmail.com> References: <3c52eebc-f656-604d-f1f6-68411475788f@gmail.com> Message-ID: <0598CF22-B3EF-4768-A9A1-8290C4098839@R-project.org> Mikael, the OpenMP binaries are entirely unrelated to the R release. Also you cannot put libiomp anywhere else without modification, because it contains the path and is signed. Given that you need additional flags for OpenMP anyway, this is not really an issue, since you have to know what you are doing in the first place so you need several flags to make this work. If you are interested in OpenMP for your package then I'd suggest trying a static iomp build. Cheers, Simon > On Apr 19, 2023, at 1:43 AM, Mikael Jagan wrote: > > The OpenMP binaries provided here > > https://mac.r-project.org/openmp/ > > still have the usr/local/ prefix. Is that intentional? If that prefix were > simply deleted, then users could unpack with (for example) > > tar -xvf openmp-14.0.6-darwin20-Release.tar.gz -C /opt/R/$(uname -m) > > And then not need > > CPPFLAGS += -I/usr/local/include > LDFLAGS += -L/usr/local/lib > > just to include the header or link the shared library. > > Mikael > >> Date: Tue, 18 Apr 2023 15:18:03 +1200 >> From: Simon Urbanek >> To: R list >> Subject: [R-SIG-Mac] Please test R 4.3.0 RC, more information below >> Message-ID: <19B7BFE5-2BB9-491D-99A2-BF572A5B41D1 at R-project.org> >> Content-Type: text/plain; charset="us-ascii" >> Dear Mac users, >> the next major R release R 4.3.0 is coming very soon so I would like to ask you to, please, test the pre-releases from >> https://mac.R-project.org >> such that any possible new issues are detected *before* the release. The upcoming release will be for macOS 11 and higher only to leverage new compilers (important for modern C++ support) and libraries. As usual, there are two releases: one for the older Intel Macs (x86_64) and one for the new M1/M2 Macs (arm64) - please install the matching version. >> R users can stop reading here, just test, please! >> Package developers, please check the CRAN result pages for your package to make sure it passes checks. Also please note that we are now using a universal GNU Fortran compiler that works both on Intel and arm64 Macs - you can download an Apple Installer from >> https://mac.r-project.org/tools/ >> There are two major changes for the Intel build relevant to advanced users: >> a) .Platfrom$pkgType is "mac.binary.big-sur-x86_64" since we are targeting a new macOS version (this is to match arm64 which uses "mac.binary.big-sur-arm64"). It means that binaries for contributed packages in repositories live in bin/macosx/big-sur-x86_64/contrib/4.3. >> b) the Intel build now matches the arm64 build such that dependent libraries are expected in /opt/R/x86_64 (to match arm64's /opt/R/arm64) to avoid conflicts with other tools. You can still add -I/usr/local/include to CPPFLAGS or -L/usr/local/lib to LDFLAGS if you want to use 3rd party libraries from /usr/local (refer to R and package documentation for details). >> Finally, R will no longer sets the macos-version-min flag by default, which means R will build for the currently installed macOS version. This allows users to build packages that use the latest SDK and capabilities of the latest macOS without any changes. However, if you are distributing package binaries for use others, we strongly recommend that you set >> export MACOSX_DEPLOYMENT_TARGET=11.0 >> when compiling binaries which will make sure that they will run on macOS 11 and higher, otherwise your binary may not be compatible. >> CRAN also uses the macOS11 SDK via >> export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk >> However, depending on your Xcode version you may not have such SDK, so it is optional. >> Cheers, >> Simon > From b@rryz2013 @end|ng |rom gm@||@com Fri Apr 21 13:54:15 2023 From: b@rryz2013 @end|ng |rom gm@||@com (Barry Zeeberg) Date: Fri, 21 Apr 2023 07:54:15 -0400 Subject: [R-SIG-Mac] question about using edit() function on mac Message-ID: I have a question about using the edit() function inside an R program that I am running in the standard R console, and on a mac mini with the most recent OS. (1) I was wondering if there is a way to programmatically control the screen location where the edit window appears, and the size of the edit window. (2) I also notice that the edit window for an array with say 4 columns shows up with a fifth column that is empty and that stretches all the way across to the right edge of the screen. Can I suppress this extra empty column from showing up? (3) Finally, and less importantly to me, is there any way to select the font style and the font size that is used in the edit window? Write to R [[alternative HTML version deleted]] From murdoch@dunc@n @end|ng |rom gm@||@com Fri Apr 21 20:35:55 2023 From: murdoch@dunc@n @end|ng |rom gm@||@com (Duncan Murdoch) Date: Fri, 21 Apr 2023 14:35:55 -0400 Subject: [R-SIG-Mac] question about using edit() function on mac In-Reply-To: References: Message-ID: <6b3d0831-993d-8e9c-7735-0fdc10ff049e@gmail.com> On 21/04/2023 7:54 a.m., Barry Zeeberg wrote: > I have a question about using the edit() function inside an R program that > I am running in the standard R console, and on a mac mini with the most > recent OS. I believe you mean R.app. > > (1) I was wondering if there is a way to programmatically control the > screen location where the edit window appears, and the size of the edit > window. I don't think there's anything in R, but it does remember the size from invocation to invocation (even across sessions), so it must be saving it somewhere. Maybe if you found that spot you could change the value before opening it. > > (2) I also notice that the edit window for an array with say 4 columns > shows up with a fifth column that is empty and that stretches all the way > across to the right edge of the screen. Can I suppress this extra empty > column from showing up? Again, I don't think so: that wouldn't really be compatible with maintaining the size. > > (3) Finally, and less importantly to me, is there any way to select the > font style and the font size that is used in the edit window? As far as I can see, no. Duncan Murdoch From murdoch@dunc@n @end|ng |rom gm@||@com Sun Apr 23 20:27:54 2023 From: murdoch@dunc@n @end|ng |rom gm@||@com (Duncan Murdoch) Date: Sun, 23 Apr 2023 14:27:54 -0400 Subject: [R-SIG-Mac] [R-pkg-devel] 'Default' macos (x86) download URL now gone? In-Reply-To: <25669.19936.694972.114117@rob.eddelbuettel.com> References: <25669.19936.694972.114117@rob.eddelbuettel.com> Message-ID: On 23/04/2023 11:25 a.m., Dirk Eddelbuettel wrote: > > The URL ${CRAN}/bin/macosx/R-latest.pkg is in fairlt widespread use. A quick > Google query [1] reveals about 1.1k hits. And it happens to be used too in a > CI job a colleague noticed failing yesterday. > > The bin/macosx/ page now prominently displays both leading flavours > R-4.3.0-arm64.pkg > R-4.3.0-x86_64.pkg > which makes sense give the architecture choices. We can of course update the > CI script, and likely will. > > But given that this was apparently a somewhat widely-used URL to fetch R on > macOS, may I suggest that the convenience link be reestablished as a courtesy? [Moved from R-pkg-devel] Would that make sense? You suggest pointing to R-4.3.0-x86_64.pkg, but I think fewer and fewer MacOS users would want that, so maybe it's not a good idea. On the other hand, maybe R-latest-arm64.pkg and R-latest-x86_64.pkg should be created. Duncan Murdoch From v@r|n@@ch@ @end|ng |rom y@hoo@|r Sun Apr 23 23:05:35 2023 From: v@r|n@@ch@ @end|ng |rom y@hoo@|r (varin sacha) Date: Sun, 23 Apr 2023 23:05:35 +0200 Subject: [R-SIG-Mac] Problem installing RUcausal library on MAC References: <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D.ref@yahoo.fr> Message-ID: <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D@yahoo.fr> R-experts, What is going wrong? At the end of this page there is the installation command : https://gitlab.science.ru.nl/gbucur/RUcausal/-/blob/master/README.Rmd Working with a MAC, I have tried to install the RUcausal library (copy and paste the installation command). It is written that the package has been built on Linux using the GNU Compiler Collection. To install the package, open an R instance and run: install.packages('devtools') # required package devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal') I get this error message : ERROR: package installation failed Error: Failed to install 'RUcausal' from Git: ! System command 'R' failed 0d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? install.packages('devtools') # required package --- Please select a CRAN mirror for use in this session --- trying URL 'https://stat.ethz.ch/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz' Content type 'application/x-gzip' length 421790 bytes (411 KB) ================================================== downloaded 411 KB The downloaded binary packages are in /var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T//Rtmp7SUtUd/downloaded_packages > devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal') Downloading git repo https://gitlab.science.ru.nl/gbucur/RUcausal '/usr/bin/git' clone --depth 1 --no-hardlinks https://gitlab.science.ru.nl/gbucur/RUcausal /var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T//Rtmp7SUtUd/file61a2a8e336a ?? R CMD build ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ? installing the package to process help pages -----------------------------------ges ? installing *source* package ?RUcausal? ... ** using staged installation ** libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c compute_DAG_probabilities_BGe_fast.cpp -o compute_DAG_probabilities_BGe_fast.o clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RUcausal.so RcppExports.o compute_DAG_probabilities_BGe_fast.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [RUcausal.so] Error 1 ERROR: compilation failed for package ?RUcausal? ? removing ?/private/var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? ----------------------------------- ERROR: package installation failed Error: Failed to install 'RUcausal' from Git: ! System command 'R' failed 0d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? Envoy? de mon iPhone From ken @end|ng |rom kjbe@th@com@@u Mon Apr 24 06:32:21 2023 From: ken @end|ng |rom kjbe@th@com@@u (kjbeath) Date: Mon, 24 Apr 2023 14:32:21 +1000 Subject: [R-SIG-Mac] Problem installing RUcausal library on MAC In-Reply-To: <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D@yahoo.fr> References: <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D.ref@yahoo.fr> <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D@yahoo.fr> Message-ID: It looks like you don?t have fortran. An installer can be obtained from https://mac.r-project.org/tools/ Ken > On 24 Apr 2023, at 7:05 am, varin sacha via R-SIG-Mac wrote: > > R-experts, > > What is going wrong? > > At the end of this page there is the installation command : > https://gitlab.science.ru.nl/gbucur/RUcausal/-/blob/master/README.Rmd > > Working with a MAC, I have tried to install the RUcausal library (copy and paste the installation command). > > It is written that the package has been built on Linux using the GNU Compiler Collection. To install the package, open an R instance and run: > install.packages('devtools') # required package > devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal') > > I get this error message : > > ERROR: package installation failed > Error: Failed to install 'RUcausal' from Git: > ! System command 'R' failed > 0d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? > > > > install.packages('devtools') # required package > --- Please select a CRAN mirror for use in this session --- > trying URL 'https://stat.ethz.ch/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz' > Content type 'application/x-gzip' length 421790 bytes (411 KB) > ================================================== > downloaded 411 KB > > > The downloaded binary packages are in > /var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T//Rtmp7SUtUd/downloaded_packages >> devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal') > Downloading git repo https://gitlab.science.ru.nl/gbucur/RUcausal > '/usr/bin/git' clone --depth 1 --no-hardlinks https://gitlab.science.ru.nl/gbucur/RUcausal /var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T//Rtmp7SUtUd/file61a2a8e336a > ?? R CMD build ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? > ? installing the package to process help pages > -----------------------------------ges > ? installing *source* package ?RUcausal? ... > ** using staged installation > ** libs > clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o > clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c compute_DAG_probabilities_BGe_fast.cpp -o compute_DAG_probabilities_BGe_fast.o > clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RUcausal.so RcppExports.o compute_DAG_probabilities_BGe_fast.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation > ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' > ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' > ld: library not found for -lgfortran > clang: error: linker command failed with exit code 1 (use -v to see invocation) > make: *** [RUcausal.so] Error 1 > ERROR: compilation failed for package ?RUcausal? > ? removing ?/private/var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? > ----------------------------------- > ERROR: package installation failed > Error: Failed to install 'RUcausal' from Git: > ! System command 'R' failed > 0d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? > > > Envoy? de mon iPhone > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] From @|mon@urb@nek @end|ng |rom R-project@org Mon Apr 24 08:17:05 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Mon, 24 Apr 2023 18:17:05 +1200 Subject: [R-SIG-Mac] Problem installing RUcausal library on MAC In-Reply-To: <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D@yahoo.fr> References: <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D.ref@yahoo.fr> <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D@yahoo.fr> Message-ID: 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/gcc-darwin-arm64/releases/tag/R-4.2.0-release Cheers, Simon > On Apr 24, 2023, at 9:05 AM, varin sacha via R-SIG-Mac wrote: > > R-experts, > > What is going wrong? > > At the end of this page there is the installation command : > https://gitlab.science.ru.nl/gbucur/RUcausal/-/blob/master/README.Rmd > > Working with a MAC, I have tried to install the RUcausal library (copy and paste the installation command). > > It is written that the package has been built on Linux using the GNU Compiler Collection. To install the package, open an R instance and run: > install.packages('devtools') # required package > devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal') > > I get this error message : > > ERROR: package installation failed > Error: Failed to install 'RUcausal' from Git: > ! System command 'R' failed > 0d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? > > > > install.packages('devtools') # required package > --- Please select a CRAN mirror for use in this session --- > trying URL 'https://stat.ethz.ch/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz' > Content type 'application/x-gzip' length 421790 bytes (411 KB) > ================================================== > downloaded 411 KB > > > The downloaded binary packages are in > /var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T//Rtmp7SUtUd/downloaded_packages >> devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal') > Downloading git repo https://gitlab.science.ru.nl/gbucur/RUcausal > '/usr/bin/git' clone --depth 1 --no-hardlinks https://gitlab.science.ru.nl/gbucur/RUcausal /var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T//Rtmp7SUtUd/file61a2a8e336a > ?? R CMD build ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? > ? installing the package to process help pages > -----------------------------------ges > ? installing *source* package ?RUcausal? ... > ** using staged installation > ** libs > clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o > clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c compute_DAG_probabilities_BGe_fast.cpp -o compute_DAG_probabilities_BGe_fast.o > clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RUcausal.so RcppExports.o compute_DAG_probabilities_BGe_fast.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation > ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' > ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' > ld: library not found for -lgfortran > clang: error: linker command failed with exit code 1 (use -v to see invocation) > make: *** [RUcausal.so] Error 1 > ERROR: compilation failed for package ?RUcausal? > ? removing ?/private/var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? > ----------------------------------- > ERROR: package installation failed > Error: Failed to install 'RUcausal' from Git: > ! System command 'R' failed > 0d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? > > > Envoy? de mon iPhone > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From @|mon@urb@nek @end|ng |rom R-project@org Mon Apr 24 08:28:21 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Mon, 24 Apr 2023 18:28:21 +1200 Subject: [R-SIG-Mac] 'Default' macos (x86) download URL now gone? In-Reply-To: <25669.19936.694972.114117@rob.eddelbuettel.com> References: <25669.19936.694972.114117@rob.eddelbuettel.com> Message-ID: <5F0CF217-5A2E-466F-9738-B49A43688CAA@R-project.org> 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 the link works for a particular system - that's why I have originally removed it with the R 4.3.0 release. I have restored it now, making it point to the R 4.3.0 arm64 release since that is arguably the closest to a single "latest R". R releases have not been stored in /bin/macosx since 2015, so anyone using a link there is asking for trouble. For any CI I would strongly recommend using the "last-success" links: https://mac.r-project.org/big-sur/last-success/ in particular the .xz versions are they are specifically designed to be used by CI (small download, fast and localized install). Cheers, Simon > On 24/04/2023, at 3:25 AM, Dirk Eddelbuettel wrote: > > > The URL ${CRAN}/bin/macosx/R-latest.pkg is in fairlt widespread use. A quick > Google query [1] reveals about 1.1k hits. And it happens to be used too in a > CI job a colleague noticed failing yesterday. > > The bin/macosx/ page now prominently displays both leading flavours > R-4.3.0-arm64.pkg > R-4.3.0-x86_64.pkg > which makes sense give the architecture choices. We can of course update the > CI script, and likely will. > > But given that this was apparently a somewhat widely-used URL to fetch R on > macOS, may I suggest that the convenience link be reestablished as a courtesy? > > Best, Dirk > > https://github.com/search?q=macosx%2FR-latest.pkg&type=code > > -- > dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org > From r|p|ey @end|ng |rom @t@t@@ox@@c@uk Mon Apr 24 09:00:47 2023 From: r|p|ey @end|ng |rom @t@t@@ox@@c@uk (Prof Brian Ripley) Date: Mon, 24 Apr 2023 08:00:47 +0100 Subject: [R-SIG-Mac] Problem installing RUcausal library on MAC In-Reply-To: References: <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D.ref@yahoo.fr> <4342BFA2-F398-4B16-AE73-7F67B7C7BC5D@yahoo.fr> Message-ID: <6f5f5e54-5e1d-5290-bcd6-07a6c47cefea@stats.ox.ac.uk> 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 Fortran from here: https://github.com/R-macos/gcc-darwin-arm64/releases/tag/R-4.2.0-release Or if you do have a gfortran installation which does not match that used for a binary installation of R you can use a ~/.R/Makevars file, as in https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Customizing-package-compilation . > > Cheers, > Simon > > > >> On Apr 24, 2023, at 9:05 AM, varin sacha via R-SIG-Mac wrote: >> >> R-experts, >> >> What is going wrong? >> >> At the end of this page there is the installation command : >> https://gitlab.science.ru.nl/gbucur/RUcausal/-/blob/master/README.Rmd >> >> Working with a MAC, I have tried to install the RUcausal library (copy and paste the installation command). >> >> It is written that the package has been built on Linux using the GNU Compiler Collection. To install the package, open an R instance and run: >> install.packages('devtools') # required package >> devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal') >> >> I get this error message : >> >> ERROR: package installation failed >> Error: Failed to install 'RUcausal' from Git: >> ! System command 'R' failed >> 0d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? >> >> >> >> install.packages('devtools') # required package >> --- Please select a CRAN mirror for use in this session --- >> trying URL 'https://stat.ethz.ch/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz' >> Content type 'application/x-gzip' length 421790 bytes (411 KB) >> ================================================== >> downloaded 411 KB >> >> >> The downloaded binary packages are in >> /var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T//Rtmp7SUtUd/downloaded_packages >>> devtools::install_git('https://gitlab.science.ru.nl/gbucur/RUcausal') >> Downloading git repo https://gitlab.science.ru.nl/gbucur/RUcausal >> '/usr/bin/git' clone --depth 1 --no-hardlinks https://gitlab.science.ru.nl/gbucur/RUcausal /var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T//Rtmp7SUtUd/file61a2a8e336a >> ?? R CMD build ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? >> ? installing the package to process help pages >> -----------------------------------ges >> ? installing *source* package ?RUcausal? ... >> ** using staged installation >> ** libs >> clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o >> clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -c compute_DAG_probabilities_BGe_fast.cpp -o compute_DAG_probabilities_BGe_fast.o >> clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RUcausal.so RcppExports.o compute_DAG_probabilities_BGe_fast.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation >> ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' >> ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' >> ld: library not found for -lgfortran >> clang: error: linker command failed with exit code 1 (use -v to see invocation) >> make: *** [RUcausal.so] Error 1 >> ERROR: compilation failed for package ?RUcausal? >> ? removing ?/private/var/folders/t_/myv0vvms11g40d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? >> ----------------------------------- >> ERROR: package installation failed >> Error: Failed to install 'RUcausal' from Git: >> ! System command 'R' failed >> 0d0bz2p4xg640000gn/T/RtmpMs1teQ/Rinst6453ee77bb8/RUcausal? >> >> >> Envoy? de mon iPhone >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford From ken@knob|@uch @end|ng |rom |n@erm@|r Mon Apr 24 14:41:43 2023 From: ken@knob|@uch @end|ng |rom |n@erm@|r (Kenneth Knoblauch) Date: Mon, 24 Apr 2023 12:41:43 +0000 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 Message-ID: Hi, I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links big-sur-x86_64 and big-sur-arm64 lead to a page with header: Index of /bin/macosx/big-sur-arm64 Is this just a heading error or is there a misdirect in the link? The formalities: sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.6.5 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Europe/Paris tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.3.0 > capabilities() jpeg png tiff tcltk X11 aqua http/ftp TRUE TRUE TRUE TRUE TRUE TRUE TRUE sockets libxml fifo cledit iconv NLS Rprof TRUE FALSE TRUE TRUE TRUE TRUE TRUE profmem cairo ICU long.double libcurl TRUE TRUE TRUE TRUE TRUE Thank you. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen L?pine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ From ||gge@ @end|ng |rom @t@t|@t|k@tu-dortmund@de Mon Apr 24 14:51:01 2023 From: ||gge@ @end|ng |rom @t@t|@t|k@tu-dortmund@de (Uwe Ligges) Date: Mon, 24 Apr 2023 14:51:01 +0200 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 In-Reply-To: References: Message-ID: <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de> On 24.04.2023 14:41, Kenneth Knoblauch wrote: > Hi, > > I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links > > big-sur-x86_64 and big-sur-arm64 lead to a page with header: > > Index of /bin/macosx/big-sur-arm64 > > Is this just a heading error or is there a misdirect in the link? Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. Best, Uwe Ligges > > The formalities: > > sessionInfo() > R version 4.3.0 (2023-04-21) > Platform: x86_64-apple-darwin20 (64-bit) > Running under: macOS Monterey 12.6.5 > > Matrix products: default > BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib > LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > time zone: Europe/Paris > tzcode source: internal > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] compiler_4.3.0 >> capabilities() > jpeg png tiff tcltk X11 aqua http/ftp > TRUE TRUE TRUE TRUE TRUE TRUE TRUE > sockets libxml fifo cledit iconv NLS Rprof > TRUE FALSE TRUE TRUE TRUE TRUE TRUE > profmem cairo ICU long.double libcurl > TRUE TRUE TRUE TRUE TRUE > > Thank you. > > best, > > Ken > > > ___ > Kenneth Knoblauch > Inserm U1208 > Stem-cell and Brain Research Institute > 18 avenue du Doyen L?pine > 69500 Bron > France > tel: +33 (0)4 72 91 34 77 > fax: +33 (0)4 72 91 34 61 > portable: +33 (0)6 84 10 64 10 > https://sbri.fr/public-profile/63/single-member/ > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From ken@knob|@uch @end|ng |rom |n@erm@|r Mon Apr 24 15:12:26 2023 From: ken@knob|@uch @end|ng |rom |n@erm@|r (Kenneth Knoblauch) Date: Mon, 24 Apr 2023 13:12:26 +0000 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 In-Reply-To: <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de> References: , <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de> Message-ID: Thank you Uwe for the rapid response, I tried: install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/", type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3/PACKAGES' and install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3", type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3/PACKAGES' and install.packages(p42, .libPaths()[1], repos = "https://cran.r-project.org", type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/contrib/4.3: cannot open URL 'https://cran.r-project.org/bin/macosx/contrib/4.3/PACKAGES' where p42 was a character vector of the package names that I had installed under 4.2 Any guidance would be greatly appreciated. Thank you, in advance. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen L?pine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ De : Uwe Ligges Envoy? : lundi 24 avril 2023 14:51 ? : Kenneth Knoblauch; r-sig-mac at r-project.org Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64 ? On 24.04.2023 14:41, Kenneth Knoblauch wrote: > Hi, > > I am upgrading to R 4.3.? and trying to upgrade the packages.? I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions.? I was looking at the Mac binaries at the R for mac OS page and it looks like both links > > big-sur-x86_64 and big-sur-arm64 lead to a page with header: > > Index of /bin/macosx/big-sur-arm64 > > Is this just a heading error or is there a misdirect in the link? Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. Best, Uwe Ligges > > The formalities: > > sessionInfo() > R version 4.3.0 (2023-04-21) > Platform: x86_64-apple-darwin20 (64-bit) > Running under: macOS Monterey 12.6.5 > > Matrix products: default > BLAS:?? /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib > LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;? LAPACK version 3.11.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > time zone: Europe/Paris > tzcode source: internal > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base > > loaded via a namespace (and not attached): > [1] compiler_4.3.0 >> capabilities() >???????? jpeg???????? png??????? tiff?????? tcltk???????? X11??????? aqua??? http/ftp >???????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE >????? sockets????? libxml??????? fifo????? cledit?????? iconv???????? NLS?????? Rprof >???????? TRUE?????? FALSE??????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE >????? profmem?????? cairo???????? ICU long.double???? libcurl >???????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE > >?? Thank you. > > best, > > Ken >??? >?? >??? ___ >??? Kenneth Knoblauch >?? Inserm U1208 >?? Stem-cell and Brain Research Institute >?? 18 avenue du Doyen L?pine >?? 69500 Bron >?? France >?? tel: +33 (0)4 72 91 34 77 >?? fax: +33 (0)4 72 91 34 61 >?? portable: +33 (0)6 84 10 64 10 >?? https://sbri.fr/public-profile/63/single-member/ >????? > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From ken@knob|@uch @end|ng |rom |n@erm@|r Mon Apr 24 16:18:27 2023 From: ken@knob|@uch @end|ng |rom |n@erm@|r (Kenneth Knoblauch) Date: Mon, 24 Apr 2023 14:18:27 +0000 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 In-Reply-To: References: , <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de>, Message-ID: <127cf26e8ca846d890f3e42c455a92a0@inserm.fr> Actually, I was able to update everything from source. I initially didn't think that would work because of the need to update Xcode and gfortran, but it all worked and none of that was necessary. Thanks. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen L?pine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ De : Kenneth Knoblauch Envoy? : lundi 24 avril 2023 15:12 ? : Uwe Ligges; r-sig-mac at r-project.org Objet : RE: [R-SIG-Mac] binaries for R 4.3 x86_64 ? Thank you Uwe for the rapid response, I tried: install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/", type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3: ? cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3/PACKAGES' and install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3", type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3: ? cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3/PACKAGES' and install.packages(p42, .libPaths()[1], repos = "https://cran.r-project.org", type = "mac.binary") Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/contrib/4.3: ? cannot open URL 'https://cran.r-project.org/bin/macosx/contrib/4.3/PACKAGES' where p42 was a character vector of the package names that I had installed under 4.2 Any guidance would be greatly appreciated. Thank you, in advance. best, Ken ? ___ ? Kenneth Knoblauch ?Inserm U1208 ?Stem-cell and Brain Research Institute ?18 avenue du Doyen L?pine ?69500 Bron ?France ?tel: +33 (0)4 72 91 34 77 ?fax: +33 (0)4 72 91 34 61 ?portable: +33 (0)6 84 10 64 10 ?https://sbri.fr/public-profile/63/single-member/ ??? De : Uwe Ligges Envoy? : lundi 24 avril 2023 14:51 ? : Kenneth Knoblauch; r-sig-mac at r-project.org Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64 ??? On 24.04.2023 14:41, Kenneth Knoblauch wrote: > Hi, > > I am upgrading to R 4.3.? and trying to upgrade the packages.? I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions.? I was looking at the Mac binaries at the R for mac OS page and? it looks like both links > > big-sur-x86_64 and big-sur-arm64 lead to a page with header: > > Index of /bin/macosx/big-sur-arm64 > > Is this just a heading error or is there a misdirect in the link? Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. Best, Uwe Ligges > > The formalities: > > sessionInfo() > R version 4.3.0 (2023-04-21) > Platform: x86_64-apple-darwin20 (64-bit) > Running under: macOS Monterey 12.6.5 > > Matrix products: default > BLAS:?? /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib > LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;? LAPACK version 3.11.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > time zone: Europe/Paris > tzcode source: internal > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base > > loaded via a namespace (and not attached): > [1] compiler_4.3.0 >> capabilities() >???????? jpeg???????? png??????? tiff?????? tcltk???????? X11??????? aqua??? http/ftp >???????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE >????? sockets????? libxml??????? fifo????? cledit?????? iconv???????? NLS?????? Rprof >???????? TRUE?????? FALSE??????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE >????? profmem?????? cairo???????? ICU long.double???? libcurl >???????? TRUE??????? TRUE??????? TRUE??????? TRUE??????? TRUE > >?? Thank you. > > best, > > Ken >??? >?? >??? ___ >??? Kenneth Knoblauch >?? Inserm U1208 >?? Stem-cell and Brain Research Institute >?? 18 avenue du Doyen L?pine >?? 69500 Bron >?? France >?? tel: +33 (0)4 72 91 34 77 >?? fax: +33 (0)4 72 91 34 61 >?? portable: +33 (0)6 84 10 64 10 >?? https://sbri.fr/public-profile/63/single-member/ >????? > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ??? From @|mon@urb@nek @end|ng |rom R-project@org Mon Apr 24 23:19:36 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Tue, 25 Apr 2023 09:19:36 +1200 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 In-Reply-To: <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de> References: <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de> Message-ID: 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 wrote: >> Hi, >> I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links >> big-sur-x86_64 and big-sur-arm64 lead to a page with header: >> Index of /bin/macosx/big-sur-arm64 >> Is this just a heading error or is there a misdirect in the link? > > Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. > > Best, > Uwe Ligges > >> The formalities: >> sessionInfo() >> R version 4.3.0 (2023-04-21) >> Platform: x86_64-apple-darwin20 (64-bit) >> Running under: macOS Monterey 12.6.5 >> Matrix products: default >> BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib >> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> time zone: Europe/Paris >> tzcode source: internal >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> loaded via a namespace (and not attached): >> [1] compiler_4.3.0 >>> capabilities() >> jpeg png tiff tcltk X11 aqua http/ftp >> TRUE TRUE TRUE TRUE TRUE TRUE TRUE >> sockets libxml fifo cledit iconv NLS Rprof >> TRUE FALSE TRUE TRUE TRUE TRUE TRUE >> profmem cairo ICU long.double libcurl >> TRUE TRUE TRUE TRUE TRUE >> Thank you. >> best, >> Ken >> ___ >> Kenneth Knoblauch >> Inserm U1208 >> Stem-cell and Brain Research Institute >> 18 avenue du Doyen L?pine >> 69500 Bron >> France >> tel: +33 (0)4 72 91 34 77 >> fax: +33 (0)4 72 91 34 61 >> portable: +33 (0)6 84 10 64 10 >> https://sbri.fr/public-profile/63/single-member/ >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From @|mon@urb@nek @end|ng |rom R-project@org Mon Apr 24 23:23:00 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Tue, 25 Apr 2023 09:23:00 +1200 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 In-Reply-To: References: <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de> Message-ID: <1F9488EA-0ED8-4DD2-AAE4-6FBF6DEFA791@R-project.org> 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 Knoblauch wrote: > > Thank you Uwe for the rapid response, > > I tried: > > install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/", type = "mac.binary") > > Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3: > cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/bin/macosx/contrib/4.3/PACKAGES' > > and > > install.packages(p42[3], .libPaths()[1], repos = "https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3", type = "mac.binary") > > Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3: > cannot open URL 'https://cran.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/bin/macosx/contrib/4.3/PACKAGES' > > and > > install.packages(p42, .libPaths()[1], repos = "https://cran.r-project.org", type = "mac.binary") > > Warning: unable to access index for repository https://cran.r-project.org/bin/macosx/contrib/4.3: > cannot open URL 'https://cran.r-project.org/bin/macosx/contrib/4.3/PACKAGES' > > where p42 was a character vector of the package names that I had installed under 4.2 > > Any guidance would be greatly appreciated. > > Thank you, in advance. > > best, > > Ken > > ___ > Kenneth Knoblauch > Inserm U1208 > Stem-cell and Brain Research Institute > 18 avenue du Doyen L?pine > 69500 Bron > France > tel: +33 (0)4 72 91 34 77 > fax: +33 (0)4 72 91 34 61 > portable: +33 (0)6 84 10 64 10 > https://sbri.fr/public-profile/63/single-member/ > > > > > > De : Uwe Ligges > Envoy? : lundi 24 avril 2023 14:51 > ? : Kenneth Knoblauch; r-sig-mac at r-project.org > Objet : Re: [R-SIG-Mac] binaries for R 4.3 x86_64 > > > > On 24.04.2023 14:41, Kenneth Knoblauch wrote: >> Hi, >> >> I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links >> >> big-sur-x86_64 and big-sur-arm64 lead to a page with header: >> >> Index of /bin/macosx/big-sur-arm64 >> >> Is this just a heading error or is there a misdirect in the link? > > Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure > Simon will fix it soon, too. > > Best, > Uwe Ligges > >> >> The formalities: >> >> sessionInfo() >> R version 4.3.0 (2023-04-21) >> Platform: x86_64-apple-darwin20 (64-bit) >> Running under: macOS Monterey 12.6.5 >> >> Matrix products: default >> BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib >> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> time zone: Europe/Paris >> tzcode source: internal >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] compiler_4.3.0 >>> capabilities() >> jpeg png tiff tcltk X11 aqua http/ftp >> TRUE TRUE TRUE TRUE TRUE TRUE TRUE >> sockets libxml fifo cledit iconv NLS Rprof >> TRUE FALSE TRUE TRUE TRUE TRUE TRUE >> profmem cairo ICU long.double libcurl >> TRUE TRUE TRUE TRUE TRUE >> >> Thank you. >> >> best, >> >> Ken >> >> >> ___ >> Kenneth Knoblauch >> Inserm U1208 >> Stem-cell and Brain Research Institute >> 18 avenue du Doyen L?pine >> 69500 Bron >> France >> tel: +33 (0)4 72 91 34 77 >> fax: +33 (0)4 72 91 34 61 >> portable: +33 (0)6 84 10 64 10 >> https://sbri.fr/public-profile/63/single-member/ >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > From ken@knob|@uch @end|ng |rom |n@erm@|r Tue Apr 25 00:14:04 2023 From: ken@knob|@uch @end|ng |rom |n@erm@|r (Kenneth Knoblauch) Date: Mon, 24 Apr 2023 22:14:04 +0000 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 In-Reply-To: References: <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de>, Message-ID: <504C3743-2430-420C-BC1E-1B27B4E071F4@inserm.fr> Simon, Thank you. Ken Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen L?pine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ On 24 Apr 2023, at 23:27, Simon Urbanek wrote: ?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 wrote: Hi, I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links big-sur-x86_64 and big-sur-arm64 lead to a page with header: Index of /bin/macosx/big-sur-arm64 Is this just a heading error or is there a misdirect in the link? Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. Best, Uwe Ligges The formalities: sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.6.5 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Europe/Paris tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.3.0 capabilities() jpeg png tiff tcltk X11 aqua http/ftp TRUE TRUE TRUE TRUE TRUE TRUE TRUE sockets libxml fifo cledit iconv NLS Rprof TRUE FALSE TRUE TRUE TRUE TRUE TRUE profmem cairo ICU long.double libcurl TRUE TRUE TRUE TRUE TRUE Thank you. best, Ken ___ Kenneth Knoblauch Inserm U1208 Stem-cell and Brain Research Institute 18 avenue du Doyen L?pine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 https://sbri.fr/public-profile/63/single-member/ _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] From ||gge@ @end|ng |rom @t@t|@t|k@tu-dortmund@de Tue Apr 25 10:01:24 2023 From: ||gge@ @end|ng |rom @t@t|@t|k@tu-dortmund@de (Uwe Ligges) Date: Tue, 25 Apr 2023 10:01:24 +0200 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 In-Reply-To: References: <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de> Message-ID: No, you have fixed the direct link to the binary, but further down the page there is a link "big-sur-x86_64" that 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 > > 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 wrote: >>> Hi, >>> I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links >>> big-sur-x86_64 and big-sur-arm64 lead to a page with header: >>> Index of /bin/macosx/big-sur-arm64 >>> Is this just a heading error or is there a misdirect in the link? >> >> Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. >> >> Best, >> Uwe Ligges >> >>> The formalities: >>> sessionInfo() >>> R version 4.3.0 (2023-04-21) >>> Platform: x86_64-apple-darwin20 (64-bit) >>> Running under: macOS Monterey 12.6.5 >>> Matrix products: default >>> BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib >>> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> time zone: Europe/Paris >>> tzcode source: internal >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> loaded via a namespace (and not attached): >>> [1] compiler_4.3.0 >>>> capabilities() >>> jpeg png tiff tcltk X11 aqua http/ftp >>> TRUE TRUE TRUE TRUE TRUE TRUE TRUE >>> sockets libxml fifo cledit iconv NLS Rprof >>> TRUE FALSE TRUE TRUE TRUE TRUE TRUE >>> profmem cairo ICU long.double libcurl >>> TRUE TRUE TRUE TRUE TRUE >>> Thank you. >>> best, >>> Ken >>> ___ >>> Kenneth Knoblauch >>> Inserm U1208 >>> Stem-cell and Brain Research Institute >>> 18 avenue du Doyen L?pine >>> 69500 Bron >>> France >>> tel: +33 (0)4 72 91 34 77 >>> fax: +33 (0)4 72 91 34 61 >>> portable: +33 (0)6 84 10 64 10 >>> https://sbri.fr/public-profile/63/single-member/ >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> R-SIG-Mac at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > From @|mon@urb@nek @end|ng |rom R-project@org Tue Apr 25 10:21:50 2023 From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek) Date: Tue, 25 Apr 2023 20:21:50 +1200 Subject: [R-SIG-Mac] binaries for R 4.3 x86_64 In-Reply-To: References: <0051a4c2-c300-8ec7-bec8-0f6ed77eeead@statistik.tu-dortmund.de> Message-ID: Ah, ok, thanks, It wasn't clear to me from the description, now also fixed. Cheers, Simon > On Apr 25, 2023, at 8:01 PM, Uwe Ligges wrote: > > No, you have fixed the direct link to the binary, but further down the page there is a link "big-sur-x86_64" that 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 >> 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 wrote: >>>> Hi, >>>> I am upgrading to R 4.3. and trying to upgrade the packages. I had to upgrade to macOS 12 first because I was at 10 and my 2017 Intel Mac Air doesn't seem to be able to run later versions. I was looking at the Mac binaries at the R for mac OS page and it looks like both links >>>> big-sur-x86_64 and big-sur-arm64 lead to a page with header: >>>> Index of /bin/macosx/big-sur-arm64 >>>> Is this just a heading error or is there a misdirect in the link? >>> >>> Misdirect, simply replace arm64 by x86_64 in the link for now. I am sure Simon will fix it soon, too. >>> >>> Best, >>> Uwe Ligges >>> >>>> The formalities: >>>> sessionInfo() >>>> R version 4.3.0 (2023-04-21) >>>> Platform: x86_64-apple-darwin20 (64-bit) >>>> Running under: macOS Monterey 12.6.5 >>>> Matrix products: default >>>> BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib >>>> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> time zone: Europe/Paris >>>> tzcode source: internal >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> loaded via a namespace (and not attached): >>>> [1] compiler_4.3.0 >>>>> capabilities() >>>> jpeg png tiff tcltk X11 aqua http/ftp >>>> TRUE TRUE TRUE TRUE TRUE TRUE TRUE >>>> sockets libxml fifo cledit iconv NLS Rprof >>>> TRUE FALSE TRUE TRUE TRUE TRUE TRUE >>>> profmem cairo ICU long.double libcurl >>>> TRUE TRUE TRUE TRUE TRUE >>>> Thank you. >>>> best, >>>> Ken >>>> ___ >>>> Kenneth Knoblauch >>>> Inserm U1208 >>>> Stem-cell and Brain Research Institute >>>> 18 avenue du Doyen L?pine >>>> 69500 Bron >>>> France >>>> tel: +33 (0)4 72 91 34 77 >>>> fax: +33 (0)4 72 91 34 61 >>>> portable: +33 (0)6 84 10 64 10 >>>> https://sbri.fr/public-profile/63/single-member/ >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> R-SIG-Mac at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> > From iist_em@ii m@iii@g oii icioud@com Wed Apr 26 12:50:10 2023 From: iist_em@ii m@iii@g oii icioud@com (iist_em@ii m@iii@g oii icioud@com) Date: Wed, 26 Apr 2023 03:50:10 -0700 Subject: [R-SIG-Mac] Using Microsoft Access from a Macintosh using R Message-ID: How can I make a Mac get data from a Microsoft Access database using R? I?m sorry if this has been asked a million times before but the list archives don?t seem to be searchable and the Mac FAQ doesn?t mention this. Also, I?m asking for a colleague who doesn?t like messing around with a lot of technical computer stuff and I do not have R on my own system. So please be patient. It seems that there is a package called RODBC which needs to be installed. Is that done using R?s package manager? And it seems that there is a driver from Actual Technologies with a Mac installer package. Assuming that these two steps are taken, is there anything else that needs to be done? Can R then access the Access database directly or is there an intermediate step such as an Excel file? Is there a very short MWE that demonstrates accessing a public Microsoft Access database using this method? My colleague is thinking of buying a Windows system just to solve this problem! Many thanks, Jerry From m@rc_@chw@rtz @end|ng |rom me@com Wed Apr 26 14:02:46 2023 From: m@rc_@chw@rtz @end|ng |rom me@com (Marc Schwartz) Date: Wed, 26 Apr 2023 08:02:46 -0400 Subject: [R-SIG-Mac] Using Microsoft Access from a Macintosh using R In-Reply-To: References: Message-ID: Hi, You have identified the key components that you will need, which are the RODBC package: ??https://cran.r-project.org/web/packages/RODBC/index.html and the Actual Technologies ODBC driver pack for MS Access: ??https://www.actualtech.com/product_access.php The latter has some basic installation instructions for that product on the above page, and Actual offers a limited function evaluation option, if you want to try before you buy. Actual also has their own tech support available. The key is using their tools to set up the correct DSN specification for the database that you want to retrieve data from within R. I used to use the Actual ODBC driver pack for Oracle on my Mac, and it worked quite well, albeit, it has now been a few years since I needed that functionality. For the RODBC package, it can be installed from within an R session using: ? install.packages("RODBC") Note that Prof. Ripley has spent a significant amount of time over the years creating a vignette for the RODBC package: ??https://cran.r-project.org/web/packages/RODBC/vignettes/RODBC.pdf in addition to the package manual, and I would urge you to review the vignette for helpful information. That should get you started. Note also that there is a specific e-mail list for R and databases: ??https://stat.ethz.ch/mailman/listinfo/r-sig-db however the traffic on that list has been essentially non-existent for some time, and since this is a Mac specific issue, feel free to continue this thread, or post subsequent questions, here. Regards, Marc Schwartz On April 26, 2023 at 6:50:10 AM, list_email--- via R-SIG-Mac (r-sig-mac at r-project.org (mailto:r-sig-mac at r-project.org)) wrote: > How can I make a Mac get data from a Microsoft Access database using R? > > I?m sorry if this has been asked a million times before but the list archives don?t seem to be searchable and the Mac FAQ doesn?t mention this. > > Also, I?m asking for a colleague who doesn?t like messing around with a lot of technical computer stuff and I do not have R on my own system. So please be patient. > > It seems that there is a package called RODBC which needs to be installed. Is that done using R?s package manager? > > And it seems that there is a driver from Actual Technologies with a Mac installer package. > > Assuming that these two steps are taken, is there anything else that needs to be done? Can R then access the Access database directly or is there an intermediate step such as an Excel file? Is there a very short MWE > that demonstrates accessing a public Microsoft Access database using this method? > > My colleague is thinking of buying a Windows system just to solve this problem! > > Many thanks, > > Jerry > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac From edd @end|ng |rom deb|@n@org Wed Apr 26 16:02:33 2023 From: edd @end|ng |rom deb|@n@org (Dirk Eddelbuettel) Date: Wed, 26 Apr 2023 09:02:33 -0500 Subject: [R-SIG-Mac] 'Default' macos (x86) download URL now gone? In-Reply-To: <5F0CF217-5A2E-466F-9738-B49A43688CAA@R-project.org> References: <25669.19936.694972.114117@rob.eddelbuettel.com> <5F0CF217-5A2E-466F-9738-B49A43688CAA@R-project.org> Message-ID: <25673.12025.938360.399881@rob.eddelbuettel.com> Simon, On 24 April 2023 at 18:28, Simon Urbanek wrote: | 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 the link works for a particular system - that's why I have originally removed it with the R 4.3.0 release. I have restored it now, making it point to the R 4.3.0 arm64 release since that is arguably the closest to a single "latest R". R releases have not been stored in /bin/macosx since 2015, so anyone using a link there is asking for trouble. Restoring it _but switching the architecture under it_ is another subtle way to still break things where the expectation based on a decade+ of prior practice was that this works: installer: Error - R 4.3.0 for macOS (ARM64) can?t be installed on this computer. Error: Process completed with exit code 1. I long have repaired my (main) script in r-ci but this will likely surprise others. | For any CI I would strongly recommend using the "last-success" links: https://mac.r-project.org/big-sur/last-success/ in particular the .xz versions are they are specifically designed to be used by CI (small download, fast and localized install). That is a fine idea but no replacement as it leads to a need for a different deployment and how / where to untar etc. Maybe you are someone wants to wrap that into a suitable script or 'action snippet' and document that? I can't, I don't even have a mac. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org From r@p@r@p@ @end|ng |rom mcw@edu Sat Apr 29 23:17:44 2023 From: r@p@r@p@ @end|ng |rom mcw@edu (Sparapani, Rodney) Date: Sat, 29 Apr 2023 21:17:44 +0000 Subject: [R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical' Message-ID: Hi Gang: After hours of debugging, I?m stuck and hoping that someone has an idea of what the issue is here. Any hints/tips/etc. are greatly appreciated! I?m getting this error from my CRAN package, nftbart. Right now, I?m preparing for a new release: v1.6. However, I?m stumped by this error message that I get when installing with OpenMP. Without OpenMP, everything is fine; however, the package benefits greatly from OpenMP. I am getting the same results for R 4.2.3 and 4.3.0 RC. The source code is on github at https://github.com/rsparapa/bnptools.git So, to demonstrate, you just need to do something like this? $ git clone https://github.com/rsparapa/bnptools.git DIR $ cd DIR $ R CMD build nftbart $ R CMD INSTALL nftbart_1.6.tar.gz * installing to library ?/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library? * installing *source* package ?nftbart? ... ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes checking for clang++ -arch x86_64 -std=gnu++17 option to support OpenMP... -lomp -Xclang -fopenmp configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ?Apple clang version 14.0.3 (clang-1403.0.22.14.1)? using C++ compiler: ?Apple clang version 14.0.3 (clang-1403.0.22.14.1)? using SDK: ?? clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -lomp -Xclang -fopenmp -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -lomp -Xclang -fopenmp -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nftbart.cpp -o nftbart.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o nftbart.so init.o nftbart.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs ** R ** data ** demo ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ?nftbart? in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so': dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so, 0x0006): symbol not found in flat namespace '___kmpc_critical' Error: loading failed Execution halted ERROR: loading failed * removing ?/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart? * restoring 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 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: America/Chicago tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.3.0 > OpenMP Build: LLVM 14.0.6 $ codesign -d -vv /usr/local/lib/libomp.dylib Executable=/usr/local/lib/libomp.dylib Identifier=libomp Format=Mach-O universal (x86_64 arm64) CodeDirectory v=20400 size=6506 flags=0x0(none) hashes=198+2 location=embedded Signature size=8977 Authority=Developer ID Application: Simon Urbanek (VZLD955F6P) Authority=Developer ID Certification Authority Authority=Apple Root CA Timestamp=Feb 5, 2023 at 4:26:54 PM Info.plist=not bound TeamIdentifier=VZLD955F6P Sealed Resources=none Internal requirements count=1 size=168 -- Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His Director, Wisconsin Chapter of the American Statistical Association Institute for Health and Equity, Division of Biostatistics Medical College of Wisconsin, Milwaukee Campus [[alternative HTML version deleted]] From r@p@r@p@ @end|ng |rom mcw@edu Sun Apr 30 00:31:43 2023 From: r@p@r@p@ @end|ng |rom mcw@edu (Sparapani, Rodney) Date: Sat, 29 Apr 2023 22:31:43 +0000 Subject: [R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical' In-Reply-To: References: Message-ID: Oh, that was totally self-inflicted. I had commented out PKG_LIBS in Makevars.in That does work on Linux with OpenMP somehow. However, it does NOT with macOS. Thanks -- Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His Director, Wisconsin Chapter of the American Statistical Association Institute for Health and Equity, Division of Biostatistics Medical College of Wisconsin, Milwaukee Campus From: R-SIG-Mac on behalf of Sparapani, Rodney via R-SIG-Mac Date: Saturday, April 29, 2023 at 4:18 PM To: r-sig-mac at r-project.org Subject: [R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical' ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hi Gang: After hours of debugging, I?m stuck and hoping that someone has an idea of what the issue is here. Any hints/tips/etc. are greatly appreciated! I?m getting this error from my CRAN package, nftbart. Right now, I?m preparing for a new release: v1.6. However, I?m stumped by this error message that I get when installing with OpenMP. Without OpenMP, everything is fine; however, the package benefits greatly from OpenMP. I am getting the same results for R 4.2.3 and 4.3.0 RC. The source code is on github at https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$ So, to demonstrate, you just need to do something like this? $ git clone https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$ DIR $ cd DIR $ R CMD build nftbart $ R CMD INSTALL nftbart_1.6.tar.gz * installing to library ?/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library? * installing *source* package ?nftbart? ... ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes checking for clang++ -arch x86_64 -std=gnu++17 option to support OpenMP... -lomp -Xclang -fopenmp configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ?Apple clang version 14.0.3 (clang-1403.0.22.14.1)? using C++ compiler: ?Apple clang version 14.0.3 (clang-1403.0.22.14.1)? using SDK: ?? clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -lomp -Xclang -fopenmp -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -lomp -Xclang -fopenmp -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nftbart.cpp -o nftbart.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o nftbart.so init.o nftbart.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs ** R ** data ** demo ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ?nftbart? in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so': dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so, 0x0006): symbol not found in flat namespace '___kmpc_critical' Error: loading failed Execution halted ERROR: loading failed * removing ?/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart? * restoring 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 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: America/Chicago tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.3.0 > OpenMP Build: LLVM 14.0.6 $ codesign -d -vv /usr/local/lib/libomp.dylib Executable=/usr/local/lib/libomp.dylib Identifier=libomp Format=Mach-O universal (x86_64 arm64) CodeDirectory v=20400 size=6506 flags=0x0(none) hashes=198+2 location=embedded Signature size=8977 Authority=Developer ID Application: Simon Urbanek (VZLD955F6P) Authority=Developer ID Certification Authority Authority=Apple Root CA Timestamp=Feb 5, 2023 at 4:26:54 PM Info.plist=not bound TeamIdentifier=VZLD955F6P Sealed Resources=none Internal requirements count=1 size=168 -- Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His Director, Wisconsin Chapter of the American Statistical Association Institute for Health and Equity, Division of Biostatistics Medical College of Wisconsin, Milwaukee Campus [[alternative HTML version deleted]] [[alternative HTML version deleted]] From m|k3h@|| @end|ng |rom gm@||@com Sun Apr 30 02:18:12 2023 From: m|k3h@|| @end|ng |rom gm@||@com (Michael Hall) Date: Sat, 29 Apr 2023 19:18:12 -0500 Subject: [R-SIG-Mac] R-SIG-Mac Digest, Vol 241, Issue 15 - symbol not found in flat namespace '___kmpc_critical' In-Reply-To: References: Message-ID: <0A0344F2-C83E-4B04-A5B5-B81107337113@gmail.com> > On Apr 29, 2023, at 5:32 PM, r-sig-mac-request at r-project.org wrote: > > symbol not found in flat namespace ?___kmpc_critical? Seems to suggest a workaround? https://github.com/glmmTMB/glmmTMB/issues/588? Trouble installing with openMP support: Symbol not found: ___kmpc_critical ? Issue #588 ? glmmTMB/glmmTMB github.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 588.png Type: image/png Size: 22094 bytes Desc: not available URL: