[R-SIG-Mac] catalina humbug

[Simon Urbanek]

Roger,

check your ~/.R - it looks like you may have custom ~/.R/Makevars which overrides the CRAN R settings.

Cheers,
Simon


> On Oct 15, 2020, at 1:14 AM, 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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>