I want to avoid that "fix" because it is not guaranteed to work in the future. Can someone who did NOT instal the system-level headers below please report the actual issue? The whole point of using the SDK was to make sure it's not necessary.
Thanks, Simon > On Jul 24, 2019, at 10:54 AM, Bryan Hanson <han...@depauw.edu> wrote: > > If it helps troubleshoot, I updated more or less on the same timeline as Roy > did and had the same problems Roy had, and Roy’s most recent response below > gives the same response on my Mac. Roy’s fix * fixed things for me. Bryan > > * open > /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > >> On Jul 24, 2019, at 10:46 AM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac >> <r-sig-mac@r-project.org> wrote: >> >> Hi Simon: >> >>> ls /Library/Developer/CommandLineTools/SDKs >>> MacOSX.sdk MacOSX10.14.sdk >> >> Also when have done: >> >>> sudo xcode-select --install >> >> I often get a message to install through App store (the command line tools). >> I am not certain exactly what macOS_SDK_headers_for_macOS_10.14.pkg >> installs nor where, but I as I said I went from being able to install >> packages from source to not being able to because headers couldn't be found >> to be able to. And I have a feeling others will run into the same problem. >> >> Thanks! >> >> -Roy >> >> >>> On Jul 23, 2019, at 9:33 PM, Simon Urbanek <simon.urba...@r-project.org> >>> wrote: >>> >>> 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 >>> >> >> ********************** >> "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
