#include_next <stdio.h> not found

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#include_next <stdio.h> not found

Roger Koenker-3
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
[hidden email]
Department of Economics, UCL
London  WC1H 0AX.


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Re: #include_next <stdio.h> not found

R devel mailing list
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 <[hidden email]> 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
> [hidden email]
> Department of Economics, UCL
> London  WC1H 0AX.
>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

**********************
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**********************
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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: [hidden email] 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.

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Re: #include_next <stdio.h> not found

Roger Koenker-3
In reply to this post by Roger Koenker-3
Yes,  this did the trick, thanks very much!  I’m cc’ing r-devel  just for the record.


Roger Koenker
[hidden email]<mailto:[hidden email]>
Department of Economics, UCL
London  WC1H 0AX.


On Aug 7, 2019, at 4:55 PM, Steven Dirkse <[hidden email]<mailto:[hidden email]>> wrote:

Roger,

Updating Xcode has the unfortunate side effect of wiping out the std header files from /usr/include.  The fix - once you know about it - is mercifully easy.  Here's my notes on the subject, recorded only yesterday so I don't waste more time the next time.

Xcode 10.3
Aug 2019: we updated to Xcode 10.3. First, we did the update through the App Store. Next, we opened Xcode in the App Store and said yes to “Install required additional components?” But that's not all! As admin, I did

sudo open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

FYI, I needed an additional step to manually patch /usr/include/sys/ucred.h but it's not likely you'll need that.

-Steve

On Wed, Aug 7, 2019 at 11:46 AM Koenker, Roger W <[hidden email]<mailto:[hidden email]>> 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
[hidden email]<mailto:[hidden email]>
Department of Economics, UCL
London  WC1H 0AX.


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--
Steven Dirkse, Ph.D.
GAMS Development Corp.
office: 202.342.0180



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