Updating R packages in anaconda but getting a clang-12 error-CodePudding

I'm on a mac m1 machine. I'm using RStudio in Anaconda and I wanted to update the R packages with the update button. However, I got the same error for many of the packages when I tried to update. Here is one example:

> install.packages("askpass")
trying URL 'https://cran.rstudio.com/src/contrib/askpass_1.1.tar.gz'
Content type 'application/x-gzip' length 5730 bytes
==================================================
downloaded 5730 bytes

* installing *source* package ‘askpass’ ...
** package ‘askpass’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
x86_64-apple-darwin13.4.0-clang -I"/Users/kaili/opt/anaconda3/envs/renv/lib/R/include" -DNDEBUG   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/kaili/opt/anaconda3/envs/renv/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/kaili/opt/anaconda3/envs/renv/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/kaili/opt/anaconda3/envs/renv=/usr/local/src/conda-prefix  -c askpass.c -o askpass.o
x86_64-apple-darwin13.4.0-clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/kaili/opt/anaconda3/envs/renv/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/kaili/opt/anaconda3/envs/renv/lib -L/Users/kaili/opt/anaconda3/envs/renv/lib -o askpass.dylib askpass.o -L/Users/kaili/opt/anaconda3/envs/renv/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd' for architecture x86_64
clang-12: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [/Users/kaili/opt/anaconda3/envs/renv/lib/R/share/make/shlib.mk:6: askpass.dylib] Error 1
ERROR: compilation failed for package ‘askpass’
* removing ‘/Users/kaili/opt/anaconda3/envs/renv/lib/R/library/askpass’
* restoring previous ‘/Users/kaili/opt/anaconda3/envs/renv/lib/R/library/askpass’
Warning in install.packages :
  installation of package ‘askpass’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/18/sx26824d315c28x_q4qg2t3h0000gn/T/RtmpVpPrtm/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

I'm new to R and Anaconda and have no idea where the problem might be. Any hint would be greatly appreciated. Thank you!

CodePudding user response：

It is simpler to avoid using install.packages() when using an R environment managed by Conda, especially when the package involves compilation. Instead, prefer using Conda for installation. In this particular case, use

conda install -n renv -c conda-forge r-askpass

from a shell session.