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