[R-SIG-Mac] catalina humbug

Koenker, Roger W rkoenker @end|ng |rom ||||no|@@edu
Wed Oct 14 15:27:20 CEST 2020 

Exactly!!!  Thanks very much to all for your patience,  and especially for Berend’s suggestion.
All now seems well without .R/Makevars



> On Oct 14, 2020, at 2:18 PM, Berend Hasselman <bhh using xs4all.nl> wrote:
> 
> Do you by any chance have ~/.R/Makevars ?
> If yes does it define CC and CXX and LDFLAGS  with clang7?
> Try removing them.
> 
> Berend
> 
>> On 14 Oct 2020, at 14:14, Koenker, Roger W <rkoenker using illinois.edu> wrote:
>> 
>> Humm…  so I have now removed clang7 from /usr/local  and I now see:
>> 
>> /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
>> /bin/sh: /usr/local/clang7/bin/clang: No such file or directory
>> 
>> But unfortunately I still don’t see where R CMD build is asking for clang7.  I tried reinstalling R
>> after removing clang7 but this didn’t change the result above.  Nothing in my environment or
>> in .Rprofile refers to clang
>> 
>> My ChangeLog reveals that I had a similar problem a couple of years ago, but unhelpfully it doesn’t reveal
>> how it was fixed, only that the one C source file of the package was removed for a while, and then reinstated
>> after resolving a problem with header files for clang6.
>> 
>> Roger
>> 
>> 
>> 
>> 
>>> On Oct 14, 2020, at 12:36 PM, Ken Beath <ken using kjbeath.com.au> wrote:
>>> 
>>> clang7 seems to be unnecessary for current R. It isn’t in my system and from memory was one of the things I removed to get everything working. This involved removing the clang and fortran that had been previously installed. I may have needed some other things but my systems will build your package.
>>> 
>>> Ken
>>> 
>>>> On 14 Oct 2020, at 10:01 pm, Koenker, Roger W <rkoenker using illinois.edu> wrote:
>>>> 
>>>> Simon,
>>>> 
>>>> Thanks,  I still have the same error:
>>>> 
>>>> 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>
>>>> 
>>>> I didn’t do anything beyond upgrading R and installing fortran 8.2.0, and the CLT 12.2.
>>>> but I didn’t remove anything, should I have?  I now see:
>>>> 
>>>> yzzy: which clang
>>>> /usr/bin/clang
>>>> yzzy: clang --version
>>>> Apple clang version 12.0.0 (clang-1200.0.32.2)
>>>> Target: x86_64-apple-darwin19.6.0
>>>> Thread model: posix
>>>> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>>> 
>>>> 
>>>> The last time I faced this sort of thing James suggested this: 
>>>> https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY
>>>> 
>>>> but the names and locations are somewhat different now, so I’m reluctant to experiment.
>>>> 
>>>> Roger
>>>> 
>>>> 
>>>> 
>>>>> On Oct 14, 2020, at 11:48 AM, Simon Urbanek <simon.urbanek using R-project.org> wrote:
>>>>> 
>>>>> Roger,
>>>>> 
>>>>> the error points to an old local clang - did you remove (or move aside) that one? Check your /usr/local - you seem to have some old stuff there that is breaking. That would solve the original issue. You seem to have done a lot after that error, but didn't tell us what happened then… you can't have the same error if you removed it ;) 
>>>>> 
>>>>> Cheers,
>>>>> Simon
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Oct 14, 2020, at 10:28 PM, Koenker, Roger W <rkoenker using illinois.edu> wrote:
>>>>>> 
>>>>>> I’ve recently “upgraded” to catalina, and compilation of my quantreg package failed with:
>>>>>> 
>>>>>> 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>
>>>>>> 
>>>>>> So I’ve tried the following:
>>>>>> 
>>>>>> 	1.  Upgraded R to 4.0.3
>>>>>> 	2.  Upgraded the fortran compiler to 8.2.0 as suggested.
>>>>>> 	3.  Attempted to reinstall command line tools with Xcode-select —install.  This fails with
>>>>>> 		a popup that says:
>>>>>> 
>>>>>> 		Can’t install the software because it is not currently available from the Software Update server.
>>>>>> 	4.  Tried again to reinstall Command line tools 12.2 beta 3 from https://developer.apple.com/download/more/
>>>>>> 		which successfully installed, but my stdio.h error persisted.
>>>>>> 	5.  Following thread: http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html
>>>>>> 		I  looked at:
>>>>>> 
>>>>>> 		yzzy: which clang /usr/bin/clang 
>>>>>> 		yzzy: xcode-select -p /Applications/Xcode.app/Contents/Developer 
>>>>>> 		yzzy: xcrun --show-sdk-path /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
>>>>>> 
>>>>>> 		but that didn’t speak to me so further googling led me to:
>>>>>> 		https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files
>>>>>> 		so lurking in: /Library/Developer/CommandLineTools/usr/include/c++/v1
>>>>>> 		is stdio.h, but I’m feeling a bit queasy  at this point and would appreciate some  expert advice.
>>>>>> 
>>>>>> Roger
>>>>>> 
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>>>>> 
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