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 <k...@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 <rkoen...@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.urba...@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 <rkoen...@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@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
