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error installing Azimuth Mac #238

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el-hodiri opened this issue Oct 4, 2024 · 0 comments
Open

error installing Azimuth Mac #238

el-hodiri opened this issue Oct 4, 2024 · 0 comments

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@el-hodiri
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el-hodiri commented Oct 4, 2024

I think I've seen this error before, so pardon me if this is a repeat.

I'm unable to install Azimuth on a Mac with Intel CPU running MacOS Sonoma 14.6.1. I get an error that seems to indicate that the installer/compiler is looking for llvm v16.0.2, whereas the indicated folder (/usr/local/cellar) contains llvm v18.1.8. I've tried installing the Mac version of RTools but that didn't help. Any suggestions?

I've gotten this to work before but this is now after upgrades to MacOS, R and R Studio.

Thanks in advance.

Heithem

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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remotes::install_github('satijalab/azimuth', ref = 'master')
Using GitHub PAT from the git credential store.
Downloading GitHub repo satijalab/azimuth@master
Error: Failed to install 'Azimuth' 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
sh: /usr/local/Cellar/llvm/16.0.2/bin/clang: No such file or directory
using SDK: ‘’
/usr/local/Cellar/llvm/16.0.2/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/icu4c/include -I/usr/local/opt/libxml2/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/libpng/include/ -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openblas/include -I/usr/local/opt/lapack/include -I/usr/local/opt/tcl-tk/include -I/usr/local/opt/udunits/include/ -I/usr/local/opt/expat/include -I/usr/local/opt/krb5/include -I/usr/local/opt/libpq/include -I/usr/local/opt/qt@5/include -fPIC -I/usr/local/include -c foo.c -o foo.o
/bin/sh: /usr/local/Cellar/llvm/16.0.2/bin/clang: No such file or directory
make: *** [foo.o] Error 127
Error: Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

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: America/New_York
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] utf8_1.2.4 R6_2.5.1 tidyselect_1.2.1 magrittr_2.0.3 remotes_2.5.0 glue_1.8.0 tibble_3.2.1
[8] pkgconfig_2.0.3 dplyr_1.1.4 generics_0.1.3 lifecycle_1.0.4 ps_1.7.7 cli_3.6.3 processx_3.8.4
[15] fansi_1.0.6 callr_3.7.6 vctrs_0.6.5 compiler_4.4.1 plyr_1.8.9 rstudioapi_0.16.0 tools_4.4.1
[22] pkgbuild_1.4.4 curl_5.2.2 pillar_1.9.0 Rcpp_1.0.13 rlang_1.1.4

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