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

[Eric K]

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 <hpages using 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]]
> >
> > _______________________________________________
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> > 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
>

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