From roy@mende|@@ohn @end|ng |rom no@@@gov  Wed Aug  7 18:04:46 2019
From: roy@mende|@@ohn @end|ng |rom no@@@gov (Roy Mendelssohn - NOAA Federal)
Date: Wed, 7 Aug 2019 09:04:46 -0700
Subject: [Rd] #include_next <stdio.h>  not found
In-Reply-To: <390DEEEC-339B-4330-A0A1-E00ECA988719@illinois.edu>
References: <390DEEEC-339B-4330-A0A1-E00ECA988719@illinois.edu>
Message-ID: <5F17AFFE-C89D-4249-873C-206A15CB02EC@noaa.gov>

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

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"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.



[Rd] #include_next <stdio.h> not found
Roy Mendelssohn - NOAA Federal