fatal error: 'stdio.h' file not found

Normally, you shouldn't need to set -isysroot or SDKROOT when using
Apple Clang -- it will automatically find and use system headers for
you.

Per Herv?'s original point, I wonder if you have a different compiler
on the PATH? What is the output of:

    which clang

My suspicion is that you might have an alternate compiler on the PATH
that is being used instead of the default Apple Clang.

You might also check e.g.

    xcode-select -p
    xcrun --show-sdk-path

just to make sure those are pointing in the right place -- e.g. I have:

    kevinushey at Kevins-MBP:~
    $ xcode-select -p
    /Library/Developer/CommandLineTools
    kevinushey at Kevins-MBP:~
    $ xcrun --show-sdk-path
    /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

You could also set CC=/usr/bin/clang just to force the use of the
system compiler (and avoid looking up whatever is first on the PATH).

Best,
Kevin

On Wed, Apr 29, 2020 at 10:24 AM Eric K <ericjkort at gmail.com> wrote:

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

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