Thanks Simon, some comments to selected aspects > 1) Despite what you said, what you are showing below is output from CRAN R
That's what Homebrew installs (now? perhaps it was different in the past?), I didn't install R by hand and certainly got this R from Homebrew, and reading the ruby script it runs, it is grabbing the latest binary from CRAN. I think in the short term I'll try this route of renaming /opt/homebrew out of the way temporarily just to get working again with mgcv. > 3) If the mgcv package on CRAN does not come with OpenMP support then I'd > contact the maintainers and ask them why they don't enable it. Packages that > benefit significantly from OpenMP typically enable it for their CRAN binaries > (good example is data.table), so if it is not enabled it may mean that the > authors don't recommend it or there is no significant benefit. The CRAN binary certainly doesn't work with omp out of the box on Mac (Note, this is using the package shipped with R, not the one I was trying to compile, and I just nuked mgcv on my system and reinstalled from the CRAN binary to the same effect): > mgcv:::mgcv.omp() [1] FALSE OpenMP is the way Simon enables parallel computation of GAMs in `gam()` and `bam()` - which is kind of the point of at least `bam()`. ./src/Makevars does have PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CFLAGS) PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) which includes openMP-related things, but this seemingly(?) isn't sufficient to get it to work on MacOS X as with the CRAN binary of mgcv's test for working omp returns FALSE, and mgcv never uses more than a single thread - which is why I was trying to compile the package myself in the first place. FWIW, glmmTMB::omp_check() is also `FALSE` on my machine, so something seems to be off broadly. I'll email Simon after investigating how data.table does things so I have something concrete to suggest to him - that said enabling openmp seems very convoluted if the configure script in data.table is anything to go by, which I presume is important because even though *I* don't need to do very much on my computer to enable compilation using openmp, getting it to work on other systems seems decidedly non-trivial in general. I was perhaps operating under the false assumption that openMP wasn't supported *at all* on Mac because of the issue with Apple's clang - which is why I went down this route in the first place. Going entirely with CRAN's R for Mac seems to resign a user to having to manage the rest of their software on their machine by hand. If I understand correctly then, I'm likely to run into problems using CRAN's R binary alongside a package I compile manually using libraries I have installed via homebrew (i.e. gettext, which I note in homebrew is a couple of versions ahead of the one in your recipes, even if it is the same gnu gettext)? This is not meant as a complaint; I am very grateful that the binaries exist - it has been quite the revelation from my decades on Linux where I endured hours of update time at each new R release recompiling all the R packages I had been using. I am however revealing my naivety regarding the Mac platform and trying to understand what is best for me longer-term - I really don't want to have to manually install and maintain all the other software I need besides R. From what you are saying, it seems I'll need to go back to my Linux-like days and install R and R packages from sources, and use a package manager to manage installing the needed libraries and tools. Anyway, thanks for the comments and suggestions. When I get chance, I'll see if the same opm issues persist if I remove all the homebrew stuff and retry with CRAN's mac binary directly and then follow back up here and also with the respective package maintainers. All the best and "God Påske" as they say in my parts (Happy Easter) Gavin On Sat, 19 Apr 2025 at 23:40, Simon Urbanek <simon.urba...@r-project.org> wrote: > > Gavin, > > there are few issues here with different possible solutions. > > In general, you cannot mix R from Homebrew and CRAN - they use different > toolchains and libraries so you have to pick one. > > > 1) Despite what you said, what you are showing below is output from CRAN R, > so one option (which I'd recommend) is to go the CRAN way. First, simply > remove (or rename) /opt/homebrew so it doesn't break things (may or may not > be necessary). Then the error you see is because mgcv seems to require > gettext so install it from https://mac.r-project.org/bin/ - either follow the > instructions there (which will work even from more complex cases) or in your > case you can simply use > > curl > https://mac.r-project.org/bin/darwin20/arm64/gettext-0.22.5-darwin.20-arm64.tar.xz > | tar xz -C / > > (if you don't have write permissions in /opt/R either run "sudo chown -R > $USER /opt/R" or put "sudo" before the tar above). > > Once you got whatever you needed compiled you can rename /opt/homebrew back > since we only need to remove it for compilation. The above works, because R > itself already has the necessary static library built-in (as it uses it > itself) so all you need are the gettext headers to appease mgcv. > > > 2) If you want to go fully the Homebrew way then you have to make sure you > are picking up R from Homebrew and not CRAN. Then you cannot use CRAN > binaries, you are entirely on your own since we don't support that setup, so > I do NOT recommend it, but it's possible. Typically, that requires you to > install the full compiler toolchain from Homebrew as well as well compiling > all R packages from sources. In that scenario you don't use anything from > mac.R-project.org but instead rely fully on Homebrew. This includes OpenMP, > because the compilers in Homebrew are not from Apple so they use their own > OpenMP. > > > 3) If the mgcv package on CRAN does not come with OpenMP support then I'd > contact the maintainers and ask them why they don't enable it. Packages that > benefit significantly from OpenMP typically enable it for their CRAN binaries > (good example is data.table), so if it is not enabled it may mean that the > authors don't recommend it or there is no significant benefit. > > > Cheers, > Simon > > > > > On Apr 20, 2025, at 12:45 AM, Gavin Simpson <ucfa...@gmail.com> wrote: > > > > Dear list > > > > I seem to be running into a new issue after upgrading to R 4.5.0 that > > seems related to this > > > > * configure is now able to find an external libintl on macOS (the code > > from an older GNU gettext distribution failed to try linking with the > > macOS Core Foundation framework). > > > > I'm pretty new to MacOS and I have installed R from homebrew, and > > typically use the MacOS X binaries kindly provided by CRAN. However, > > for a couple of packages I make extensive use of, I want to make use > > of openMP, and so I have been following the excellent instructions on > > the mac.r-project.org pages to install the relevant fortran compiler > > and libomp. > > > > Specifically, I am trying to in compile the latest mgcv sources with > > openMP support. I have been doing this successfully for some time for > > the 4.3 and 4.4 releases of R. But after upgrading to R 4.5.0, > > compiling mgcv now throws an compilation error > > > > In file included from magic.c:27: > > ./general.h:4:10: fatal error: 'libintl.h' file not found > > 4 | #include <libintl.h> > > | ^~~~~~~~~~~ > > > > (The full compile log is included below if neccessary.) > > > > I do have gettext installed and I do have libintl.h on my system > > > > % find /opt -name "libintl.*" -print > > /opt/homebrew/include/libintl.h > > /opt/homebrew/lib/libintl.dylib > > /opt/homebrew/lib/libintl.8.dylib > > /opt/homebrew/lib/libintl.a > > /opt/homebrew/Cellar/gettext/0.24/include/libintl.h > > /opt/homebrew/Cellar/gettext/0.24/lib/libintl.dylib > > /opt/homebrew/Cellar/gettext/0.24/lib/libintl.8.dylib > > /opt/homebrew/Cellar/gettext/0.24/lib/libintl.a > > > > My $PATH is > > > > % print $PATH > > /opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/usr/local/laps:/usr/local/munki:/usr/local/munkireport:/Applications/quarto/bin:/Users/au690221/.local/bin:/Users/au690221/.local/bin > > > > I have edited ./src/Makevars in mgcv's sources such that it reads > > > > % cat ./repo/src/Makevars > > PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CFLAGS) > > PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) > > > > PKG_LIBS += -lomp > > PKG_CPPFLAGS = -Xclang -fopenmp > > ## *Both* the above must be *uncommented* for release > > > > #PKG_CFLAGS = -g -O0 -Wall -pedantic $(SHLIB_OPENMP_CFLAGS) > > ## Actually it now seems that you need to reset optimization flag in > > ## cd /usr/local/lib/R/etc/ > > ## sudo pico Makeconf > > ## This file can add flags but not modify what's in the above! > > ## `#' out previous line for release (but not without uncommenting openMP) > > > > But I have tried it with the final pair of PKG_LIBS definitions that > > add omp support commented out also. > > > > My system details are > > > >> sessionInfo() > > R version 4.5.0 (2025-04-11) > > Platform: aarch64-apple-darwin20 > > Running under: macOS Sequoia 15.4.1 > > > > Matrix products: default > > BLAS: > > /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib > > LAPACK: > > /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; > > LAPACK version 3.12.1 > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > time zone: Europe/Copenhagen > > tzcode source: internal > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > loaded via a namespace (and not attached): > > [1] compiler_4.5.0 > > > > and > > > > % clang -v > > Apple clang version 17.0.0 (clang-1700.0.13.3) > > Target: arm64-apple-darwin24.4.0 > > Thread model: posix > > InstalledDir: /Library/Developer/CommandLineTools/usr/bin > > > > (So I have installed LLVM 18.1.8 from https://mac.r-project.org/openmp/ ) > > > > I suspect I will need to solve this by adding the homebrew lib > > location to my LD_PATH or similar, but I'm not very familiar with this > > process in general and especially so on MacOS X. > > > > I'd appreciate any help with resolving this issue. > > > > TIA > > > > Gavin > > > > % R CMD INSTALL mgcv_1.9-3.tar.gz > > * installing to library ‘/Users/au690221/Library/R/arm64/4.5/library’ > > * installing *source* package ‘mgcv’ ... > > ** this is package ‘mgcv’ version ‘1.9-3’ > > ** using staged installation > > ** libs > > using C compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’ > > using SDK: ‘MacOSX15.4.sdk’ > > clang -arch arm64 > > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > > coxph.c -o coxph.o > > clang -arch arm64 > > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > > davies.c -o davies.o > > clang -arch arm64 > > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > > discrete.c -o discrete.o > > clang -arch arm64 > > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > > gdi.c -o gdi.o > > clang -arch arm64 > > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > > init.c -o init.o > > clang -arch arm64 > > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > > magic.c -o magic.o > > In file included from magic.c:27: > > ./general.h:4:10: fatal error: 'libintl.h' file not found > > 4 | #include <libintl.h> > > | ^~~~~~~~~~~ > > 1 error generated. > > make: *** [magic.o] Error 1 > > ERROR: compilation failed for package ‘mgcv’ > > * removing ‘/Users/au690221/Library/R/arm64/4.5/library/mgcv’ > > * restoring previous ‘/Users/au690221/Library/R/arm64/4.5/library/mgcv’ > > -- > > Gavin Simpson, PhD [he/him/his] > > [tw] @ucfagls [OrciD] 0000-0002-9084-8413 > > [web] fromthebottomoftheheap.net > > • Assistant Professor > > • Department of Animal & Veterinary Sciences, Aarhus University > > • Adjunct Professor, Department of Biology, University of Regina. > > > > _______________________________________________ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > -- Gavin Simpson, PhD [he/him/his] [tw] @ucfagls [OrciD] 0000-0002-9084-8413 [web] fromthebottomoftheheap.net • Assistant Professor • Department of Animal & Veterinary Sciences, Aarhus University • Adjunct Professor, Department of Biology, University of Regina. _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
