I also recall after updating to Xcode 10.2 on my Mojave machine that the system headers normally installed at /usr/include had vanished, and re-installing the headers with the aforementioned package at /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg fixed things up. So I would echo the sentiment that it would be helpful to have a note :-)
On Thu, Apr 4, 2019 at 2:09 PM Roy Mendelssohn - NOAA Federal via R-SIG-Mac <r-sig-mac@r-project.org> wrote: > > Yes I had a feeling that the Xcode update did it, which is why I included > that fact. The upgrade must have also zapped someone else, because that > note was in the R Admin and Install Doc. I am not even quite certain all > that command does, just know the problem magically went away. > > -Roy > > > > On Apr 4, 2019, at 1:58 PM, Simon Urbanek <simon.urba...@r-project.org> > > wrote: > > > > Roy, > > > > great, thanks, I'll try to replicate that. I'm really surprised that an > > upgrade would delete headers - that's very unfriendly to say the least ;). > > I did upgrade Mojave but I did not upgrade Xcode (newer version tend to > > break more and more things) so that's maybe why I didn't see it. > > > > Thanks, > > Simon > > > > > > > >> On Apr 4, 2019, at 4:19 PM, Roy Mendelssohn - NOAA Federal > >> <roy.mendelss...@noaa.gov> wrote: > >> > >> Hi Simon: > >> > >> here goes. I was running 10.13.xx, xx being whatever was the most recent > >> version. I was compiling packages from source no problem. Also, the > >> Upgrade Section of App Store was telling me there was an incompatible > >> version of software available, which was a new version of Xcode. > >> > >> I upgraded to 10.14.4, by the usual means, did nothing special. > >> > >> Upgrades in App Store said there was a new version of Xcode (among other > >> things). So installed that. > >> > >> Ran Xcode, so that it would install "Other Components" which it often > >> does with a new version. > >> > >> To be certain I had the Command lIne Tools, in a terminal I ran: sudo > >> xcode-select --install > >> > >> Next time I ran RStudio, two package upgrades were from source (I > >> apologize I don't remember which packages). Compilation failed with > >> errors of couldn't find the appropriate header files. > >> > >> Ran the command in my note. > >> > >> Restarted RStudio, asked it to check for package updates, same packages > >> appeared, compilation went fine. > >> > >> I am running Xcode 10.2 > >> > >> HTH, > >> > >> -Roy > >> > >> > >>> On Apr 4, 2019, at 12:26 PM, Simon Urbanek <simon.urba...@r-project.org> > >>> wrote: > >>> > >>> Roy, > >>> > >>> thanks, but can you give some details? I'm on a Mojave system and don't > >>> see any issues - this will likely depend on your Xcode installation. Does > >>> it mean some Xcode version is lacking headers? Which version, how did you > >>> install it? > >>> > >>> Thanks, > >>> Simon > >>> > >>> > >>>> On Mar 30, 2019, at 2:21 PM, Roy Mendelssohn - NOAA Federal via > >>>> R-SIG-Mac <r-sig-mac@r-project.org> wrote: > >>>> > >>>> I recently updated to Mojave and all of a sudden I was getting header > >>>> not found errors when trying to compile packages. I was pretty certain > >>>> my Makevars files was correct, as I had been compiling before the > >>>> upgrade successfully, and the compilers hadn't changed. > >>>> > >>>> The following is in some of the docs, but just in case it helps, cause > >>>> it took me awhile to find it, after installing the Command Line Tools > >>>> for Xcode, you should run: > >>>> > >>>> sudo installer -pkg \ > >>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > >>>> \ > >>>> -target / > >>>> > >>>> and voila packages that had failed to compile just a few minutes ago > >>>> compiled successfully. > >>>> > >>>> Hope this helps someone. > >>>> > >>>> -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. > >> > > > > ********************** > "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
