Doh! Sorry to have missed that email thread. This advice solved the issue for me.
On Wed, Apr 24, 2019 at 11:41 AM Roy Mendelssohn - NOAA Federal < roy.mendelss...@noaa.gov> wrote: > Hi Kaspar: > > There is an issue of where Xcode puts headers. I have posted on this > previously. I did the same update as you, and not only doesn't Xcode put > the headers where R expects, it appears to delete the existing headers. > > Anyhow, try running the following and see if your problems go away: > > > sudo installer -pkg \ > > > /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > \ > > -target / > > -Roy > > > On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > > > > I am on Mojave. I recently updated to Xcode 10.2.1 and I did the > associated > > update of the command line tools. Following this, I reinstalled clang6 > and > > gfortran 6 from CRAN. > > > > When I use the clang6 compiler from CRAN, it is unable to find stdio.h. > > > > When I compare the include path from clang6 to the Apple suppled clang > with > > `$CC -E - -v` I get > > > > with Apple clang > > #include <...> search starts here: > > /usr/local/include > > > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.1/include > > > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include > > > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include > > > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks > > (framework directory) > > End of search list. > > > > with clang6 from CRAN > > #include <...> search starts here: > > /usr/local/include > > /usr/local/clang6/lib/clang/6.0.0/include > > /System/Library/Frameworks (framework directory) > > /Library/Frameworks (framework directory) > > End of search list. > > > > Did Apple move the headers around? Or have I somehow hosed my system? > > > > Best, > > Kasper > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ********************** > "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > ********************** > Roy Mendelssohn > Supervisory Operations Research Analyst > NOAA/NMFS > Environmental Research Division > Southwest Fisheries Science Center > ***Note new street address*** > 110 McAllister Way > Santa Cruz, CA 95060 > Phone: (831)-420-3666 > Fax: (831) 420-3980 > e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/ > > "Old age and treachery will overcome youth and skill." > "From those who have been given much, much will be expected" > "the arc of the moral universe is long, but it bends toward justice" -MLK > Jr. > > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac