Package Installation Error

[phoman14]

🐛 Bug

I am having trouble installing immunarch using both
devtools::install_github("immunomind/immunarch")
and
devtools::install_github("immunomind/immunarch", ref="dev")

But I keep getting the same error

Any advice or insight would be appreciated

> devtools::install_github("immunomind/immunarch") Registered S3 methods overwritten by 'htmltools': method from print.html tools:rstudio print.shiny.tag tools:rstudio print.shiny.tag.list tools:rstudio Registered S3 method overwritten by 'htmlwidgets': method from print.htmlwidget tools:rstudio Downloading GitHub repo immunomind/immunarch@HEAD Error: Failed to install 'unknown package' 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: ‘gcc-8 (Homebrew GCC 8.5.0) 8.5.0’
using SDK: ‘’
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c foo.c -o foo.o
gcc-8 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
-macosx_version_min has been renamed to -macos_version_min
ld: warning: ignoring duplicate libraries: '-lSystem'
ld: unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/usr/local/Cellar/gcc@8/8.5.0/lib/gcc/8/libgcc_ext.10.5.dylib'
collect2: error: ld returned 1 exit status
make: *** [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.`

Additional context

R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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

other attached packages:
[1] devtools_2.4.5 usethis_2.2.2

loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 compiler_4.3.2 promises_1.2.1 Rcpp_1.0.12 stringr_1.5.1 callr_3.7.3
[7] later_1.3.2 fastmap_1.1.1 mime_0.12 R6_2.5.1 curl_5.2.0 knitr_1.45
[13] htmlwidgets_1.6.4 desc_1.4.3 profvis_0.3.8 shiny_1.8.0 rlang_1.1.3 cachem_1.0.8
[19] stringi_1.8.3 httpuv_1.6.13 xfun_0.41 fs_1.6.3 pkgload_1.3.4 memoise_2.0.1
[25] cli_3.6.2 magrittr_2.0.3 ps_1.7.6 processx_3.8.3 digest_0.6.34 rstudioapi_0.15.0
[31] xtable_1.8-4 remotes_2.4.2.1 lifecycle_1.0.4 vctrs_0.6.5 glue_1.7.0 urlchecker_1.0.1
[37] sessioninfo_1.2.2 pkgbuild_1.4.3 purrr_1.0.2 tools_4.3.2 ellipsis_0.3.2 htmltools_0.5.7

[vadimnazarov]

Hi phoman14, this is the first time I see the error you encountered. I searched and even asked ChatGPT about it, this is what it said to me:

The error message you're encountering indicates an issue with the build tools necessary to compile R packages from source, particularly those involving C/C++ code. This is a common issue on macOS, where the necessary compilers and command-line tools might not be properly set up or compatible with your R installation.

Here are some steps to diagnose and potentially resolve the problem:

1. Check Xcode Command Line Tools:

   • macOS uses Xcode's command-line tools for compiling software. Ensure they are installed and up to date.
   • Open Terminal and run:

     xcode-select --install

   • This command will prompt you to install the command-line tools if they're not already installed. If they are installed, it will tell you so.

2. Install/Update Homebrew and GCC:

   • Homebrew is a package manager for macOS, and GCC is the GNU Compiler Collection which includes C/C++ compilers.
   • If not already installed, install Homebrew by following instructions on brew.sh.
   • Then, install GCC with Homebrew:

     brew install gcc

3. Linking the Correct Compiler:

   • The error message shows gcc-8 being used. Depending on your Homebrew installation and the current GCC version, you might have a newer version of GCC.
   • Check the installed GCC version:

     gcc --version

   • Ensure your system is using the correct version of GCC. Sometimes, R might not point to the correct version automatically.

4. Configure R to Use the Correct Compilers:

   • Create or modify the ~/.R/Makevars file to set the correct paths for the compilers.
   • You can open this file in a text editor and add lines like:

     CC=gcc-x
     CXX=g++-x
     

     Replace x with your installed GCC version number.

5. Reinstall immunarch:

   • After ensuring that the build tools are correctly set up, try reinstalling immunarch:

     devtools::install_github("immunomind/immunarch")

6. Check for Other Dependency Issues:

   • Sometimes, specific package dependencies might cause installation issues. Ensure that all dependencies are installed and updated.

7. Use a Binary Version (if available):

   • If compiling from source continues to be problematic, check if a binary version of immunarch is available for your version of R and macOS. Installing binary packages bypasses the need to compile from source.

Looks legit, I too have some issues with compiling libraries on mac from time to time. Could you try it and get back to me please?