fatal error: 'stdio.h' file not found

Eric K

Wed, Apr 29, 2020 10:01 AM

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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fatal error: 'stdio.h' file not found

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