R devel - Aug 2019 - #include_next <stdio.h> not found

Dear All,

Just when I thought I had the plague of gfortran-9 under control, I made the
tactical error
of allowing my mac mini to ?upgrade? to macOS 10.14.6 which apparently also
upgraded
Xcode to 10.3.  In consequence I?m having difficulty building my packages.  The
current
symptom is:

/usr/local/clang7/bin/clang
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  
-I/usr/local/clang7/include/c++/v1  -fPIC  -Wall -g -O2  -c mcmb.c -o mcmb.o
In file included from mcmb.c:11:
/usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h'
file not found
#include_next <stdio.h>
              ^~~~~~~~~

My first thought was I should install Simon?s clang-7.0.0 and gfortran-6.1
packages
which I dutifully did.  The next thought was to update my ~/.R/Makevars file to:

CC=/usr/local/clang7/bin/clang
CXX=/usr/local/clang7/bin/clang++
LDFLAGS=-L/usr/local/clang7/lib
CPPFLAGS=-I/usr/local/clang7/include/c++/v1
FC=/usr/local/gfortran/bin/gfortran
FLIBS=-L/usr/local/gfortran/lib -lgfortran

Further googling has left me unenlightened?  oh, and I?m running
R version 3.6.1 (2019-07-05) -- "Action of the Toes"

Roger Koenker
r.koenker at ucl.ac.uk
Department of Economics, UCL
London  WC1H 0AX.

Hi Roger:

This came up in the r-sig-mac list.  Try removing the CPPFLAGS.   Updates to
Xcode appear to erase the headers where you are pointing to.  The CRAN flags
that Simon uses  point elsewhere. Look at the r-sig-mac under topic "Xcode
10.3 and header flles".

HTH,

-Roy

> On Aug 7, 2019, at 8:46 AM, Koenker, Roger W <rkoenker at
illinois.edu> wrote:
> 
> Dear All,
> 
> Just when I thought I had the plague of gfortran-9 under control, I made
the tactical error
> of allowing my mac mini to ?upgrade? to macOS 10.14.6 which apparently also
upgraded
> Xcode to 10.3.  In consequence I?m having difficulty building my packages. 
The current
> symptom is:
> 
> /usr/local/clang7/bin/clang
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  
-I/usr/local/clang7/include/c++/v1  -fPIC  -Wall -g -O2  -c mcmb.c -o mcmb.o
> In file included from mcmb.c:11:
> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error:
'stdio.h' file not found
> #include_next <stdio.h>
>              ^~~~~~~~~
> 
> My first thought was I should install Simon?s clang-7.0.0 and gfortran-6.1
packages
> which I dutifully did.  The next thought was to update my ~/.R/Makevars
file to:
> 
> CC=/usr/local/clang7/bin/clang
> CXX=/usr/local/clang7/bin/clang++
> LDFLAGS=-L/usr/local/clang7/lib
> CPPFLAGS=-I/usr/local/clang7/include/c++/v1
> FC=/usr/local/gfortran/bin/gfortran
> FLIBS=-L/usr/local/gfortran/lib -lgfortran
> 
> Further googling has left me unenlightened?  oh, and I?m running
> R version 3.6.1 (2019-07-05) -- "Action of the Toes"
> 
> Roger Koenker
> r.koenker at ucl.ac.uk
> Department of Economics, UCL
> London  WC1H 0AX.
> 
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
**********************
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Government or NOAA."
**********************
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NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
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"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice"
-MLK Jr.