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 <rkoen...@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 <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
