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 <ucfagls at 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
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.