[R-SIG-Mac] [External] Re: Xcode 10.2.1

[Tierney, Luke]

Also documented in the 'R Installation and Administration' manual --
always a good place to look.

Best,

luke

On Wed, 24 Apr 2019, Kasper Daniel Hansen wrote:

> Doh! Sorry to have missed that email thread.
>
> This advice solved the issue for me.
>
> On Wed, Apr 24, 2019 at 11:41 AM Roy Mendelssohn - NOAA Federal <
> roy.mendelssohn using noaa.gov> wrote:
>
>> Hi Kaspar:
>>
>> There is an issue of where Xcode puts headers.  I have posted on this
>> previously.  I did the same update as you,  and not only doesn't Xcode put
>> the headers where R expects,  it appears to delete the existing headers.
>>
>> Anyhow,  try running the following and see if your problems go away:
>>
>>> sudo installer -pkg \
>>>
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>> \
>>> -target /
>>
>> -Roy
>>
>>> On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen <
>> kasperdanielhansen using gmail.com> wrote:
>>>
>>> I am on Mojave. I recently updated to Xcode 10.2.1 and I did the
>> associated
>>> update of the command line tools. Following this, I reinstalled clang6
>> and
>>> gfortran 6 from CRAN.
>>>
>>> When I use the clang6 compiler from CRAN, it is unable to find stdio.h.
>>>
>>> When I compare the include path from clang6 to the Apple suppled clang
>> with
>>> `$CC -E - -v` I get
>>>
>>> with Apple clang
>>> #include <...> search starts here:
>>> /usr/local/include
>>>
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.1/include
>>>
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
>>>
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include
>>>
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks
>>> (framework directory)
>>> End of search list.
>>>
>>> with clang6 from CRAN
>>> #include <...> search starts here:
>>> /usr/local/include
>>> /usr/local/clang6/lib/clang/6.0.0/include
>>> /System/Library/Frameworks (framework directory)
>>> /Library/Frameworks (framework directory)
>>> End of search list.
>>>
>>> Did Apple move the headers around? Or have I somehow hosed my system?
>>>
>>> Best,
>>> Kasper
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac using r-project.org
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>>
>> **********************
>> "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 using 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.
>>
>>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney using uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu