Kevin, which clang gives /usr/bin/clang, and xcode-select -p and xcrun --show-sdk-path give same output as yours.
I am sure it is something I messed up along the way, and/or is related to having homebrew also installed. Someday soon I will upgrade to Catalina and see if that resolves the issue (or makes it worse). Best regards, Eric On Wed, Apr 29, 2020 at 1:31 PM Kevin Ushey <kevinus...@gmail.com> wrote: > Normally, you shouldn't need to set -isysroot or SDKROOT when using > Apple Clang -- it will automatically find and use system headers for > you. > > Per Hervé's original point, I wonder if you have a different compiler > on the PATH? What is the output of: > > which clang > > My suspicion is that you might have an alternate compiler on the PATH > that is being used instead of the default Apple Clang. > > You might also check e.g. > > xcode-select -p > xcrun --show-sdk-path > > just to make sure those are pointing in the right place -- e.g. I have: > > kevinushey@Kevins-MBP:~ > $ xcode-select -p > /Library/Developer/CommandLineTools > kevinushey@Kevins-MBP:~ > $ xcrun --show-sdk-path > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > > You could also set CC=/usr/bin/clang just to force the use of the > system compiler (and avoid looking up whatever is first on the PATH). > > Best, > Kevin > > On Wed, Apr 29, 2020 at 10:24 AM Eric K <ericjk...@gmail.com> wrote: > > > > One more update. I had to add the -isysroot flag to avoid collisions > > between incompatible headers when building some packages. Thinking about > it > > more I remembered that I have also used Homebrew in the past for some > > installations of unrelated software (so my installation is not as > "Vanilla" > > as I previously asserted). I wonder then if the source of my woes here is > > collisions between homebrew and Xcode? Regardless, this ~/.R/Makevars is > > working for me to allow building source packages with the official R 4.0 > > binary on macOs 10.14.6 with XCode 11.3.1 : > > > > CFLAGS = > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include > > -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot > > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > > CXXFLAGS = > > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include > > -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot > > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > > CPPFLAGS = > > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include > > -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot > > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > > > > Thanks again! > > -Eric > > > > > > On Wed, Apr 29, 2020 at 1:01 PM Eric K <ericjk...@gmail.com> wrote: > > > > > Thank you Hervé. > > > > > > So yes, with this ~/.R/Makevars everything works fine again (with a > couple > > > extra flags to keep things quiet): > > > > > > CFLAGS = > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include > > > -Wno-nullability-completeness -Wno-expansion-to-defined > > > CXXFLAGS = > > > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include > > > -Wno-nullability-completeness -Wno-expansion-to-defined > > > CPPFLAGS = > > > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include > > > -Wno-nullability-completeness -Wno-expansion-to-defined > > > > > > I am curious why I need this Makevars with what I believe to be a > vanilla > > > MacOS / XCode / R installation? But since things are working, my > > > curiosity will not keep me up at night. > > > > > > Thanks again for pointing me in the right direction. > > > > > > -Eric > > > > > > > > > On Wed, Apr 29, 2020 at 12:42 PM Hervé Pagès <hpa...@fredhutch.org> > wrote: > > > > > >> Hi Eric, > > >> > > >> FWIW, here is what I see on my system (Mojave): > > >> > > >> machv2:~ biocbuild$ which clang > > >> /usr/bin/clang > > >> > > >> machv2:~ biocbuild$ clang -v > > >> Apple LLVM version 10.0.1 (clang-1001.0.46.4) > > >> Target: x86_64-apple-darwin18.7.0 > > >> Thread model: posix > > >> InstalledDir: /Library/Developer/CommandLineTools/usr/bin > > >> > > >> machv2:~ biocbuild$ ls -l > > >> > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h > > >> -r--r--r-- 1 root wheel 16319 Feb 22 2019 > > >> > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h > > >> > > >> I'm not a Mac expert but I believe these locations for Apple clang and > > >> associated standard C header files have not changed for years. > > >> > > >> Hope this helps, > > >> H. > > >> > > >> > > >> On 4/29/20 07:05, Eric K wrote: > > >> > Running R 3.6 has been working fine. I just upgraded to R 4.0 and I > > >> cannot > > >> > build packages from source. I have tried the following: > > >> > > > >> > 1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation > went > > >> > fine, but when I try to build packages from source I get errors like > > >> this: > > >> > > > >> > * installing *source* package ‘MASS’ ... > > >> > ** package ‘MASS’ successfully unpacked and MD5 sums checked > > >> > ** using staged installation > > >> > ** libs > > >> > clang -mmacosx-version-min=10.13 > > >> > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > > >> > -I/usr/local/include -fPIC -Wall -g -O2 -c MASS.c -o MASS.o > > >> > MASS.c:18:10: fatal error: 'stdlib.h' file not found > > >> > #include <stdlib.h> > > >> > > > >> > Indeed, stdlib.h is not in /usr/local/include. > > >> > > > >> > 2. So I installed Command_Line_Tools_for_Xcode_11.3.1.dmg, but that > did > > >> not > > >> > fix the problem > > >> > > > >> > 3. So I installed Xcode 11.3.1 itself. That did not fix the problem. > > >> > > > >> > 4. For good measure, I re-ran xcode-select --install > > >> > > > >> > 5. Googling suggested installing > /Library/Developer/CommandLineTools/ > > >> > Packages/macOS_SDK_headers_for_macOS_10.14.pkg, but that package is > not > > >> on > > >> > my computer. > > >> > > > >> > 6. I tried building R 4.0 from source with this config.site: > > >> > > > >> > CC=clang > > >> > OBJC=$CC > > >> > FC=/usr/local/gfortran/bin/gfortran > > >> > CXX=clang++ > > >> > > > >> > configure went ok, but then the build failed with: > > >> > > > >> > trying to compile and link a JNI program > > >> > detected JNI cpp flags : -I$(JAVA_HOME)/include > > >> > -I$(JAVA_HOME)/include/darwin > > >> > detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm > > >> > clang -I"/Users/Eric.Kort/build/R-4.0.0/include" -DNDEBUG > > >> > > -I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include > > >> > > > >> > -I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/darwin > > >> > -I/usr/local/include -fPIC -g -O2 -c conftest.c -o conftest.o > > >> > In file included from conftest.c:1: > > >> > > > >> > /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/jni.h:39:10: > > >> > fatal error: 'stdio.h' file not found > > >> > #include <stdio.h> > > >> > > > >> > Can anyone spot what I am doing wrong? Thank you! > > >> > > > >> > -Eric > > >> > > > >> > [[alternative HTML version deleted]] > > >> > > > >> > _______________________________________________ > > >> > R-SIG-Mac mailing list > > >> > R-SIG-Mac@r-project.org > > >> > > > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=MF1GsseSwZpmjo7qspeJtAlyY9nDQ_XZnJGweoVjCfE&s=oFtPJDZ3gSkizBSLFUqqZ2SGa402cZZHDFxpHmk5rNM&e= > > >> > > > >> > > >> -- > > >> Hervé Pagès > > >> > > >> Program in Computational Biology > > >> Division of Public Health Sciences > > >> Fred Hutchinson Cancer Research Center > > >> 1100 Fairview Ave. N, M1-B514 > > >> P.O. Box 19024 > > >> Seattle, WA 98109-1024 > > >> > > >> E-mail: hpa...@fredhutch.org > > >> Phone: (206) 667-5791 > > >> Fax: (206) 667-1319 > > >> > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
