[R-SIG-Mac] catalina humbug
Koenker, Roger W
rkoenker @end|ng |rom ||||no|@@edu
Wed Oct 14 14:14:41 CEST 2020
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.
> 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.
>> On 14 Oct 2020, at 10:01 pm, Koenker, Roger W <rkoenker using illinois.edu> wrote:
>> 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
>> yzzy: clang --version
>> Apple clang version 12.0.0 (clang-1188.8.131.52)
>> 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:
>> but the names and locations are somewhat different now, so I’m reluctant to experiment.
>>> On Oct 14, 2020, at 11:48 AM, Simon Urbanek <simon.urbanek using R-project.org> wrote:
>>> 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 ;)
>>>> 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:
>>>> 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.
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