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Errors to install the monocle3 in Macbook #727

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mainharryHR opened this issue Jul 1, 2024 · 0 comments
Open

Errors to install the monocle3 in Macbook #727

mainharryHR opened this issue Jul 1, 2024 · 0 comments

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@mainharryHR
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mainharryHR commented Jul 1, 2024

Dear everyone,

It seems many people have the issues to install the package for Mac. Is there any easy or straightforward way to resolve this problems?

devtools::install_github('cole-trapnell-lab/monocle3')

Using github PAT from envvar GITHUB_PAT. Use gitcreds::gitcreds_set() and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead.
Downloading GitHub repo cole-trapnell-lab/monocle3@HEAD
Error: Failed to install 'monocle3' from GitHub:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

pkgbuild::check_build_tools(debug = TRUE)
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘clang version 14.0.6’
using 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 foo.c -o foo.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: library 'System' not found
clang-14: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [/Library/Frameworks/R.framework/Resources/share/make/shlib.mk:10: foo.so] Error 1
Error: Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

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