ICBW, but you seem to be sudo-ing the curl but not the tar? Maybe curl ..... | sudo tar ... ?
- Peter > On 24 Apr 2025, at 08:27 , Duncan Murdoch <murdoch.dun...@gmail.com> wrote: > > I didn't use sudo, but adding it doesn't help. > > Here's the latest failed run: > > https://github.com/dmurdoch/parseLatex/actions/runs/14634872157/job/41063801330 > > It fails to create opt/R/arm64. I also tried x86_64, with similar results. > > Duncan Murdoch > > On 2025-04-23 4:17 p.m., Simon Urbanek wrote: >>> On Apr 24, 2025, at 4:50 AM, Duncan Murdoch <murdoch.dun...@gmail.com> >>> wrote: >>> >>> I am getting the same missing libintl.h error on my MacOS Github action. >>> What do you recommend as the fix? My current script is here: >>> >>> https://github.com/dmurdoch/parseLatex/blob/main/.github/workflows/R-CMD-check.yaml >>> >>> I've tried a couple of things (install using brew: fails because it is >>> already installed, but R isn't looking there; install using the curl >>> command below: fails because of permissions. >>> >> For the latter - did you forget sudo in front of the tar? >> Without exact output we can only guess ... >> Cheers, >> Simon >>> Duncan Murdoch >>> >>> >>> On 2025-04-19 5:40 p.m., Simon Urbanek 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 >>>>> >>>> _______________________________________________ >>>> 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 -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd....@cbs.dk Priv: pda...@gmail.com _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
