Exactly!!! Thanks very much to all for your patience, and especially for Berend’s suggestion. All now seems well without .R/Makevars
> On Oct 14, 2020, at 2:18 PM, Berend Hasselman <b...@xs4all.nl> wrote: > > 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 <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 > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
