Thanks Bryan. Given my age, I always have to wonder if I am hallucinating or did something careless. I want to emphasize that I don't think it is an R issue, it really does look like when installing the new Xcode, the headers got wiped out. Since both a new Xcode and a new Command Line Tools were installed, I don't know which did the damage.
-Roy > On Jul 24, 2019, at 7:54 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 > ********************** "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
