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