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

[Eric K]

Kevin,

which clang gives /usr/bin/clang, and xcode-select -p and xcrun
--show-sdk-path give same output as yours.

I am sure it is something I messed up along the way, and/or is related to
having homebrew also installed.

Someday soon I will upgrade to Catalina and see if that resolves the issue
(or makes it worse).

Best regards,
Eric


On Wed, Apr 29, 2020 at 1:31 PM Kevin Ushey <kevinushey using gmail.com> wrote:

> 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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