Hi Bioconductor team, I meet an error when install DESeq2 package on MAC M1 using Rstudio. It is very weird that I can load DESeq2 in the terminal.

BiocManager::install("DESeq2",type = "source",force = TRUE)

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Installing package(s) 'DESeq2'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/DESeq2_1.40.0.tar.gz'
Content type 'application/x-gzip' length 2132760 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘DESeq2’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DESeq2.cpp -o DESeq2.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o DESeq2.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0'
ld: warning: directory not found for option '-L/opt/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [DESeq2.so] Error 1
ERROR: compilation failed for package ‘DESeq2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DESeq2’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/DESeq2’

The downloaded source packages are in
    ‘/private/var/folders/4l/6tt1kfzs2598dq49yqmt_1lc0000gn/T/Rtmpeo9xYh/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

I have tried install gcc, but it doesn't work.

gcc --version
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
Target: arm64-apple-darwin22.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Best, Dorcas

Please try and search and look for other questions as well: See load failed for ‘DESeq2’ and DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17) . New binaries should be available by the end of the week