Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)
Hi Tim, Be sure that you are running the latest version of Xcode: https://itunes.apple.com/us/app/xcode/id497799835?mt=12 and that you also install/re-install the command line tools afterwards: xcode-select --install With a major macOS version upgrade like this, you should do a fully clean install of R and afterwards, of XQuartz: https://www.xquartz.org Regards, Marc > On Sep 25, 2018, at 11:59 AM, Tim Bates wrote: > > fyi > > home$ sudo installer -pkg \ >> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg >> \ >> -target / > Password: > installer: Error - the package path specified was invalid: > '/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg'. > spearman:OpenMx tim$ > > >> On 25 Sep 2018, at 1:04 pm, Marc Schwartz via R-SIG-Mac >> wrote: >> >> Thanks to both of you for the pointers on this. >> >> I have not used a dark theme since my Fedora days. Still getting used to >> it... :-) >> >> Regards, >> >> Marc Schwartz >> >> >>> On Sep 25, 2018, at 5:55 AM, peter dalgaard wrote: >>> >>> [Oops. Forgot to copy this back to R-sig-mac, it seems...] >>> >>> Thanks, Brian, >>> >>> Yes, we have previously learned the hard way that timing R releases too >>> close to MacOS updates is a bad idea... >>> >>> The manual updates haven't made it to CRAN yet, you need to look in the >>> sources. >>> >>> For those who might be curious, but lazy: >>> >>> >>> As from macOS 10.14 (‘Mojave’) an additional step is needed to install the >>> headers to /usr/include: from a Terminal run >>> >>> sudo installer -pkg \ >>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg >>> \ >>> -target / >>> >>> Alternatively, change the include path via >>> >>> CPPFLAGS="-isystem >>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" >>> >>> >>> >>> Incidentally, probably unrelated, I discovered that the R-patched snapshots >>> had stalled since Sep 13 due to an SVN database error. This should be >>> cleared up now. >>> >>> -pd >>> On 25 Sep 2018, at 08:59 , Prof Brian Ripley wrote: A heads up: The Mojave update removes /usr/include and (re)installing the Command Line Tools does not put the standard system headers there. Workarounds are now described in the R-admin manual for R-devel and R-patched. -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> -- >>> Peter Dalgaard, Professor, >>> Center for Statistics, Copenhagen Business School >>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >>> Phone: (+45)38153501 >>> Office: A 4.23 >>> Email: pd@cbs.dk Priv: pda...@gmail.com ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)
fyi home$ sudo installer -pkg \ > /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > \ > -target / Password: installer: Error - the package path specified was invalid: '/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg'. spearman:OpenMx tim$ > On 25 Sep 2018, at 1:04 pm, Marc Schwartz via R-SIG-Mac > wrote: > > Thanks to both of you for the pointers on this. > > I have not used a dark theme since my Fedora days. Still getting used to > it... :-) > > Regards, > > Marc Schwartz > > >> On Sep 25, 2018, at 5:55 AM, peter dalgaard wrote: >> >> [Oops. Forgot to copy this back to R-sig-mac, it seems...] >> >> Thanks, Brian, >> >> Yes, we have previously learned the hard way that timing R releases too >> close to MacOS updates is a bad idea... >> >> The manual updates haven't made it to CRAN yet, you need to look in the >> sources. >> >> For those who might be curious, but lazy: >> >> >> As from macOS 10.14 (‘Mojave’) an additional step is needed to install the >> headers to /usr/include: from a Terminal run >> >> sudo installer -pkg \ >> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg >> \ >> -target / >> >> Alternatively, change the include path via >> >> CPPFLAGS="-isystem >> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" >> >> >> >> Incidentally, probably unrelated, I discovered that the R-patched snapshots >> had stalled since Sep 13 due to an SVN database error. This should be >> cleared up now. >> >> -pd >> >>> On 25 Sep 2018, at 08:59 , Prof Brian Ripley wrote: >>> >>> A heads up: >>> >>> The Mojave update removes /usr/include and (re)installing the Command Line >>> Tools does not put the standard system headers there. Workarounds are now >>> described in the R-admin manual for R-devel and R-patched. >>> >>> -- >>> Brian D. Ripley, rip...@stats.ox.ac.uk >>> Emeritus Professor of Applied Statistics, University of Oxford >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> -- >> Peter Dalgaard, Professor, >> Center for Statistics, Copenhagen Business School >> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >> Phone: (+45)38153501 >> Office: A 4.23 >> Email: pd@cbs.dk Priv: pda...@gmail.com >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)
Thanks to both of you for the pointers on this. I have not used a dark theme since my Fedora days. Still getting used to it... :-) Regards, Marc Schwartz > On Sep 25, 2018, at 5:55 AM, peter dalgaard wrote: > > [Oops. Forgot to copy this back to R-sig-mac, it seems...] > > Thanks, Brian, > > Yes, we have previously learned the hard way that timing R releases too close > to MacOS updates is a bad idea... > > The manual updates haven't made it to CRAN yet, you need to look in the > sources. > > For those who might be curious, but lazy: > > > As from macOS 10.14 (‘Mojave’) an additional step is needed to install the > headers to /usr/include: from a Terminal run > > sudo installer -pkg \ > /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > \ > -target / > > Alternatively, change the include path via > > CPPFLAGS="-isystem > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" > > > > Incidentally, probably unrelated, I discovered that the R-patched snapshots > had stalled since Sep 13 due to an SVN database error. This should be cleared > up now. > > -pd > >> On 25 Sep 2018, at 08:59 , Prof Brian Ripley wrote: >> >> A heads up: >> >> The Mojave update removes /usr/include and (re)installing the Command Line >> Tools does not put the standard system headers there. Workarounds are now >> described in the R-admin manual for R-devel and R-patched. >> >> -- >> Brian D. Ripley, rip...@stats.ox.ac.uk >> Emeritus Professor of Applied Statistics, University of Oxford >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd@cbs.dk Priv: pda...@gmail.com > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)
[Oops. Forgot to copy this back to R-sig-mac, it seems...] Thanks, Brian, Yes, we have previously learned the hard way that timing R releases too close to MacOS updates is a bad idea... The manual updates haven't made it to CRAN yet, you need to look in the sources. For those who might be curious, but lazy: As from macOS 10.14 (‘Mojave’) an additional step is needed to install the headers to /usr/include: from a Terminal run sudo installer -pkg \ /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \ -target / Alternatively, change the include path via CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" Incidentally, probably unrelated, I discovered that the R-patched snapshots had stalled since Sep 13 due to an SVN database error. This should be cleared up now. -pd > On 25 Sep 2018, at 08:59 , Prof Brian Ripley wrote: > > A heads up: > > The Mojave update removes /usr/include and (re)installing the Command Line > Tools does not put the standard system headers there. Workarounds are now > described in the R-admin manual for R-devel and R-patched. > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Emeritus Professor of Applied Statistics, University of Oxford > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Installing R on 10.14 (Mojave)
A heads up: The Mojave update removes /usr/include and (re)installing the Command Line Tools does not put the standard system headers there. Workarounds are now described in the R-admin manual for R-devel and R-patched. -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac