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

[Kevin Ushey]

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 Hervé'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 using Kevins-MBP:~
    $ xcode-select -p
    /Library/Developer/CommandLineTools
    kevinushey using 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 using 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 using gmail.com> wrote:
>
> > 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]]
> >> >
> >> > _______________________________________________
> >> > 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
> >>
> >
>
>         [[alternative HTML version deleted]]
>
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