[R-SIG-Mac] fatal error: 'stdio.h' file not found

[Hervé Pagès]

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 using 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: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319