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

[Simon Urbanek]

I'm not saying you should upgrade, just that I hope this is now fixed in the latest R release.


> On Apr 28, 2019, at 18:22, Roy Mendelssohn - NOAA Federal <roy.mendelssohn using noaa.gov> wrote:
> 
> I just saw that the Mac version was now available.  given the numbering this would mean reinstalling packages correct?

Yes, correct.


>  If i use in mechanism in the R GUI to do so,  does it preserve location - that is the packages in the Framework directory are update  to that system location,  and the packages in my own library stay in my own library?
> 

The GUI allows you to replicate the package install, but the each library is separate (so it doesn't break). It works for the system location, I don't think it knows or handles any custom user libraries - that you' dhave to do with a script.

Cheers,
Simon



> If not,  I should be able to write a script to do so, but if the GUI will already do it,  i would prefer to use that.  May wait a few days for packages to keep up.
> 
> thanks for all your work,
> 
> -roy
> 
> 
>> On Apr 28, 2019, at 3:13 PM, Simon Urbanek <simon.urbanek using R-project.org> wrote:
>> 
>> Yes, I did, if you used R 3.6.0 there would be no issue (as long as you have command line tools installed).
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> On Apr 24, 2019, at 12:06, Roy Mendelssohn - NOAA Federal via R-SIG-Mac <r-sig-mac using r-project.org> wrote:
>>> 
>>> Yes that is where I found the command.  I would add though that I had done that for Xcode 10.2.0, and appears that when you install the new versions that the installer actually deletes the headers at that location.  At least that is what happened to me when I updated to Xcode 10.2.1.  So people should be aware of this.  Each update may delete the headers.
>>> 
>>> In the previous thread,  Simon was looking into possibly changing where the R tools look for the headers, but that sort of thing is beyond my pay grade.  
>>> 
>>> -Roy
>>> 
>>>> On Apr 24, 2019, at 9:01 AM, Tierney, Luke <luke-tierney using uiowa.edu> wrote:
>>>> 
>>>> 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
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>> 
>>>>>> **********************
>>>>>> "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]]
>>>>> 
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac using r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>> 
>>>> 
>>>> -- 
>>>> 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
>>> 
>>> **********************
>>> "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.
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac using r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>