I also got that missing libintl.h file issue on Mac Silicon. Instead of messing
up with Homebrew and its non-standard directories, I installed gettext from
Simon Urbanek recipies. This is really simple and libintl.h is then
automatically found by the compiler without requiring special compilation
flags. You need to start R in sudo mode.
sudo R
Then in R:
source("https://mac.R-project.org/bin/install.R";)
install.libs("gettext")
And that’s it. No more libintl.h problem.
Best,
Philippe
> Le 24 avr. 2025 à 18:40, Duncan Murdoch <murdoch.dun...@gmail.com> a écrit :
>
> I don't know about Gavin, but all I wanted was to be able to install my
> package from source on Github without an error.
>
> Duncan Murdoch
>
> On 2025-04-24 12:18 p.m., Kevin Ushey wrote:
>> Hi Gavin,
>> If you want to use gettext from Homebrew, you need to make sure the
>> compiler include paths are set up correctly. As a reference, R
>> installations from Homebrew use (among other tweaks, but I think these
>> are the most relevant):
>> CPPFLAGS = -I/opt/homebrew/opt/gettext/include
>> -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include
>> -I/opt/homebrew/include
>> LDFLAGS = -L/opt/homebrew/opt/gettext/lib
>> -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/xz/lib
>> -L/opt/homebrew/lib
>> in their etc/Makeconf, so you probably need something similar in your
>> own Makevars file (or wherever else is appropriate for you to set
>> these).
>> You might also be able to use `-I/opt/homebrew/include`, but that's a
>> bit more dangerous since (depending on what you've installed with
>> Homebrew) you could end up unintentionally shadowing certain header
>> files that were expected to be found in other locations. Adding `-H`
>> to CPPFLAGS can be useful in this scenario; it will tell the compiler
>> to dump the include paths used when resolving headers.
>> Caveat emptor and all that, but I've had success using CRAN R releases
>> on macOS with Homebrew-installed libraries. The main wrinkles come
>> when /usr/local/include gets full of "junk" that messes up compiler
>> header searches, but that's less of an issue on arm64 since Homebrew
>> stuff gets placed in /opt/homebrew, and /opt/homebrew/include is not
>> added to the compiler include search paths by default.
>> Best,
>> Kevin
>> On Wed, Apr 23, 2025 at 11:27 PM 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
>
> _______________________________________________
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..............................................<°}))><........
) ) ) ) )
( ( ( ( ( Prof. Philippe Grosjean
) ) ) ) )
( ( ( ( ( Numerical Ecology
) ) ) ) ) Mons University, Belgium
( ( ( ( (
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