Ah, I think I have an idea - is it possible that you were using an older version of R? That would explain.
Cheers, Simon > On Jul 24, 2019, at 10:46 AM, Roy Mendelssohn - NOAA Federal > <roy.mendelss...@noaa.gov> 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
