fatal error: 'stdio.h' file not found
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 <ericjkort at gmail.com> wrote:
Thank you Herv?. 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 Herv? Pag?s <hpages at 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
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-- Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319