Roy, thanks, I just wanted to clarify which headers have been deleted exactly. The system location (/usr/includes) is what Apple doesn't like, which is why we are now using the SDK. Can you check, please, whether you do have /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk I would hope that they don't touch that location. That said, if you have Xcode proper they may think that you no longer need command line tools or something like that -in principle that should be recoverable with sudo xcode-select --install hopefully.
Thanks, Simon > On Jul 23, 2019, at 14:50, Roy Mendelssohn - NOAA Federal via R-SIG-Mac > <r-sig-mac@r-project.org> wrote: > > Hi Simon: > > I am using CRAN release, recommended CRAN compilers. Yesterday morning one > updated package needed to be installed from source, worked. Yesterday > afternoon did the update of Xcode (and OSX). This morning installing a > package update from source failed, couldn't find header files (gee I have > seen this before). Ran the command I put below, everybody was happy. It > does appear that the update literally deleted the headers. > > HTH, > > Roy > > PS - not trying to build R from source, just source updates of some packages > >> On Jul 23, 2019, at 11:17 AM, Simon Urbanek <simon.urba...@r-project.org> >> wrote: >> >> Roy, >> >> that shouldn't be necessary if you use the CRAN release since it >> specifically points to the SDK. If you are compiling your own R you may want >> to add >> CPPFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk >> -I/usr/local/include' >> which is what the CRAN build uses. FWIW you can always check the current >> flags at >> https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build/conf.el-capitan-x86_64 >> >> If the above doesn't address the issue you're seeing, please provide details. >> >> Thanks, >> Simon >> >> >>> On Jul 23, 2019, at 12:47 PM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac >>> <r-sig-mac@r-project.org> wrote: >>> >>> If like me you updated to Xcode 10.3, in Apple's infinite wisdom the >>> install again wipes out the header files. So if you did the update and >>> install from source remember to re-install the headers: >>> >>>> open >>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg >>> >>> -Roy >>> >>> ********************** >>> "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. >>> >>> _______________________________________________ >>> 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. > > _______________________________________________ > 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
