Thank you Simon, that was spot-on! There was a stale Makevars file from about a year ago when a particular package needed a kluge to compile with openMP. Much appreciated! Bryan
> On Oct 22, 2021, at 3:54 PM, Simon Urbanek <simon.urba...@r-project.org> > wrote: > > Bryan, > > you seen to be using non-standard compiler in /usr/local/clang4. Remove it > and check you overrides - do you have some forgotten invalid ~/.R/Makeconf > file? Remove those if you do - and check ~/.R for any old stuff. (In fact the > latter will probably fix it alone). > > Cheers, > Simon > > > >> On Oct 23, 2021, at 11:29 AM, Bryan Hanson <han...@depauw.edu> wrote: >> >> I don’t know how/when this problem arose, but as of a few days ago, I can’t >> build source packages any longer. I’ve been through quite a lot of >> resources looking for answers and no luck so far, so turning to the mercies >> of this list. >> >> I have this problem with either R 4.1.1 or R 4.2.0 I’ve disabled .Rprofile >> and .cshrc files and the problem persists. Running BigSur 10.16 >> >> When I try for instance to install MASS (as an example, the problem occurs >> with any pkg needing compilation) I see this: >> >> [Abbott-2:~/Desktop] bryanhanson% R CMD INSTALL MASS >> * installing to library >> ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ >> * installing *source* package ‘MASS’ ... >> ** package ‘MASS’ successfully unpacked and MD5 sums checked >> ** using staged installation >> ** libs >> /usr/local/clang4/bin/clang >> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG >> -I/usr/local/include -fPIC -Wall -g -O2 -c MASS.c -o MASS.o >> MASS.c:18:10: fatal error: 'stdlib.h' file not found >> #include <stdlib.h> >> ^~~~~~~~~~ >> 1 error generated. >> make: *** [MASS.o] Error 1 >> ERROR: compilation failed for package ‘MASS’ >> * removing >> ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/MASS’ >> * restoring previous >> ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/MASS’ >> >> I think this feedback says the compiler is present and working. >> >> Most resources about "fatal error: 'stdlib.h' file not found” end up being >> cases of the headers are actually not installed. However I can see the >> “missing” headers in /Library/Developer/CommandLineTools/usr/include/c++/v1 >> but I’m not sure this is place R is looking (information on the web is >> sometimes dated, and Apple seems to have moved things around in recent >> versions). So my best guess is that R is looking elsewhere or doesn’t have >> a link to the correct location. R Installation and Administration doesn’t >> appear to spell the location or I missed it. >> >> I have carefully uninstalled Xcode (13) and re-installed it, and run >> Xcode-select —install (it thinks the CLTs are already installed). This does >> not make any difference, the problem persists. Restarting the machine after >> updates does not make a difference either. >> >> Thanks for any suggestions, as I’m really stuck... >> >> Bryan >> >> >>> sessionInfo() >> R version 4.1.1 Patched (2021-10-18 r81073) >> Platform: x86_64-apple-darwin17.0 (64-bit) >> Running under: macOS Big Sur 10.16 >> >> Matrix products: default >> BLAS: >> /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib >> LAPACK: >> /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib >> >> Random number generation: >> RNG: Mersenne-Twister >> Normal: Inversion >> Sample: Rounding >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] compiler_4.1.1 >> >> _______________________________________________ >> 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
