Re: [R-SIG-Mac] Link to headers lost? Headers not where they should be?
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 > 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 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 >>^~ >> 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
Re: [R-SIG-Mac] Link to headers lost? Headers not where they should be?
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 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 > ^~ > 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
[R-SIG-Mac] Link to headers lost? Headers not where they should be?
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 ^~ 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
