[R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)

Fri Apr 5 08:12:52 CEST 2019

On 04/04/2019 22:37, Kevin Ushey wrote:
> I also recall after updating to Xcode 10.2 on my Mojave machine that
> the system headers normally installed at /usr/include had vanished,
> and re-installing the headers with the aforementioned package at
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> fixed things up. So I would echo the sentiment that it would be
> helpful to have a note :-)

This is documented in the manual, including that updating CLT wiped out 
the headers in /usr/include: 
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#macOS .

On my Mojave system the OS update to 10.14.4 updated the CLT without 
asking separately.

Note too that the fix to reinstate the headers is hinted by Apple to be 
for 10.14 only, so the alternative (to set CPPFLAGS) may be preferable.

> On Thu, Apr 4, 2019 at 2:09 PM Roy Mendelssohn - NOAA Federal via
> R-SIG-Mac <r-sig-mac using r-project.org> wrote:
>>
>> Yes I had a feeling that the Xcode update did it,  which is why I included that fact.  The upgrade must have also zapped someone else,  because that note was in the R Admin and Install Doc.  I am not even quite certain all that command does,  just know the problem magically went away.
>>
>> -Roy
>>
>>
>>> On Apr 4, 2019, at 1:58 PM, Simon Urbanek <simon.urbanek using R-project.org> wrote:
>>>
>>> Roy,
>>>
>>> great, thanks, I'll try to replicate that. I'm really surprised that an upgrade would delete headers - that's very unfriendly to say the least ;). I did upgrade Mojave but I did not upgrade Xcode (newer version tend to break more and more things) so that's maybe why I didn't see it.
>>>
>>> Thanks,
>>> Simon
>>>
>>>
>>>
>>>> On Apr 4, 2019, at 4:19 PM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn using noaa.gov> wrote:
>>>>
>>>> Hi Simon:
>>>>
>>>> here goes.  I was running 10.13.xx,  xx being whatever was the most recent version.  I was compiling packages from source no problem.  Also,  the Upgrade Section of App Store was telling me there was an incompatible version of software available,  which was a new version of Xcode.
>>>>
>>>> I upgraded to 10.14.4,  by the usual means,  did nothing special.
>>>>
>>>> Upgrades in App Store said there was a new version of Xcode (among other things).  So installed that.
>>>>
>>>> Ran Xcode,  so that it would install "Other Components" which it often does with a new version.
>>>>
>>>> To be certain I had the Command lIne Tools,  in a terminal I ran:   sudo xcode-select --install
>>>>
>>>> Next time I ran RStudio,  two package upgrades were from source  (I apologize I don't remember which packages).  Compilation failed with errors of couldn't find the appropriate header files.
>>>>
>>>> Ran the command in my note.
>>>>
>>>> Restarted RStudio,  asked it to check for package updates,  same packages appeared,  compilation went fine.
>>>>
>>>> I am running Xcode 10.2
>>>>
>>>> HTH,
>>>>
>>>> -Roy
>>>>
>>>>
>>>>> On Apr 4, 2019, at 12:26 PM, Simon Urbanek <simon.urbanek using R-project.org> wrote:
>>>>>
>>>>> Roy,
>>>>>
>>>>> thanks, but can you give some details? I'm on a Mojave system and don't see any issues - this will likely depend on your Xcode installation. Does it mean some Xcode version is lacking headers? Which version, how did you install it?
>>>>>
>>>>> Thanks,
>>>>> Simon
>>>>>
>>>>>
>>>>>> On Mar 30, 2019, at 2:21 PM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac <r-sig-mac using r-project.org> wrote:
>>>>>>
>>>>>> I recently updated to Mojave and all of a sudden I was getting header not found errors when trying to compile packages.  I was pretty certain my Makevars files was correct,  as I had been compiling before the upgrade successfully,  and the compilers hadn't changed.
>>>>>>
>>>>>> The following is in some of the docs,  but just in case it helps,  cause it took me awhile to find it,  after installing the Command Line Tools for Xcode,  you should run:
>>>>>>
>>>>>> sudo installer -pkg \
>>>>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \
>>>>>> -target /
>>>>>>
>>>>>> and voila packages that had failed to compile just a few minutes ago compiled successfully.
>>>>>>
>>>>>> Hope this helps someone.
>>>>>>
>>>>>> -Roy
>>>>>>
>>>>>>
>>>>>> **********************
>>>>>> "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
>>>>>
>>>>
>>>> **********************
>>>> "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.
>>>>
>>>
>>
>> **********************
>> "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
> 
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-- 
Brian D. Ripley,                  ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford