Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
Thanks, I have finally traced it down. It is a combination of the removal of headers from system location *and* our custom toolchain. Apple's macOS 10.14 clang builds automatically insert the path to the SDK: "/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.14.0 [...] -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk [...] #include <...> search starts here: /usr/local/include /Library/Developer/CommandLineTools/usr/lib/clang/10.0.0/include /Library/Developer/CommandLineTools/usr/include /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks (framework directory) Whereas out clang6 build uses the system location: #include <...> search starts here: /usr/local/include /usr/local/clang6/lib/clang/6.0.0/include /System/Library/Frameworks (framework directory) /Library/Frameworks (framework directory) So, similar to the R-admin suggestions all that's needed is -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk and hope that Apple will maintain the non-versioned symlink to the SDK. I'll see if I can release a new build of clang that will use it automatically. From my tests so far that location is valid all the way down to 10.11 so should work for us. Probably the fastest fix for now if you just need to install a package is to set PKG_CPPFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' It will work as long as you use the command line tools (recommended) - if you use Xcode directly you may need to check its location with xcrun --show-sdk-path Cheers, Simon > On Apr 4, 2019, at 4:19 PM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac > 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 >> 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 >>> 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 >> >
Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
On 04/04/2019 22:37, Kevin Ushey wrote: 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 :-) This is documented in the manual, including that updating CLT wiped out the headers in /usr/include: https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#macOS . On my Mojave system the OS update to 10.14.4 updated the CLT without asking separately. Note too that the fix to reinstate the headers is hinted by Apple to be for 10.14 only, so the alternative (to set CPPFLAGS) may be preferable. On Thu, Apr 4, 2019 at 2:09 PM Roy Mendelssohn - NOAA Federal via R-SIG-Mac 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 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 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 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 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.noa
Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
FWIW, I had the same experience - updated to 10.14.4 and got a Command Line Tools update and then found /usr/include wiped clean. From my installation log, it looks like these two items macOS 10.14.4 Update Command Line Tools (macOS Mojave version 10.14) for Xcode have the same timestamp followed by another macOS 10.14.4 Update about 20 minutes later (which I think is usual looking at earlier updates). I've not updated Xcode per se for a very long time. The files in the Xcode.app directory are all time-stamped from 2016. In fact, I cannot even start the Xcode.app - it may need to be reinstalled. --- I fixed things just as others have reported, viz by running the "sudo installer -pkg " idiom from the install and admin manual appendix C.3, "As from macOS 10.14 (‘Mojave’) an additional step is needed ..." HTH, Chuck > On Apr 4, 2019, at 1:58 PM, Simon Urbanek 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 > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
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 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 > > 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 > >> 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 > >>> 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 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 > >> NO
Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
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 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 >> 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 >>> 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 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/N
Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
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 > 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 >> 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 >>> 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. > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
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 > 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 >> 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. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
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 > 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
Many thanks Roy - it helped me, at least! Simon: This command ought perhaps to be included on https://cran.r-project.org/bin/macosx/tools/ as part of the "important note" It is obscure, with no good duckduckgo or stackoverflow results if the user types in their error message. Best, tim > On 30 Mar 2019, at 6:21 pm, Roy Mendelssohn - NOAA Federal via R-SIG-Mac > wrote: > > I recently updated to Mojave and started getting header not found errors when > trying to compile packages. > 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 University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)
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
