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
