Message-ID: <D1C53079-ED68-4DE6-BFBC-162F359098F6@xs4all.nl>
Date: 2020-10-14T13:18:19Z
From: Berend Hasselman
Subject: catalina humbug
In-Reply-To: <94C5670B-AEA9-4A25-AAF4-8A017457B6C2@illinois.edu>
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 at 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 at 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 at 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 at 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 at 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
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>
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