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@rsangole
Created August 14, 2022 23:51
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Error while trying to install topicmodels on my MacOS 12.5
> renv::install("topicmodels")
Retrieving 'https://cran.microsoft.com/snapshot/2022-06-25/src/contrib/topicmodels_0.2-12.tar.gz' ...
OK [file is up to date]
Installing topicmodels [0.2-12] ...
FAILED
Error installing package 'topicmodels':
=======================================
* installing to library ‘/Users/rahul/github/github.com/blog/quarto/renv/staging/1’
* installing *source* package ‘topicmodels’ ...
** package ‘topicmodels’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c cokus.c -o cokus.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c common.c -o common.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c ctm.c -o ctm.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c dataset.cpp -o dataset.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c gsl-wrappers.c -o gsl-wrappers.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c inference.c -o inference.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c init.c -o init.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c lda-alpha.c -o lda-alpha.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c lda-inference.c -o lda-inference.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c lda-model.c -o lda-model.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c model.cpp -o model.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c rGibbslda.cpp -o rGibbslda.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c rctm.c -o rctm.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c rlda.c -o rlda.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c utilities.cpp -o utilities.o
clang -I"/usr/local/Cellar/r/4.2.1_2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -Wno-implicit-function-declaration -c utils.c -o utils.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/4.2.1_2/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/xz/lib -L/usr/local/lib -o topicmodels.so cokus.o common.o ctm.o dataset.o gsl-wrappers.o inference.o init.o lda-alpha.o lda-inference.o lda-model.o model.o rGibbslda.o rctm.o rlda.o utilities.o utils.o -lgsl -lgslcblas -L/usr/local/Cellar/r/4.2.1_2/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /Users/rahul/github/github.com/blog/quarto/renv/staging/1/00LOCK-topicmodels/00new/topicmodels/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/rahul/renv_cache/v5/R-4.2/x86_64-apple-darwin21.5.0/slam/0.1-50/e25793551cbdb843154152e5ee88cbd6/slam/libs/slam.so':
dlopen(/Users/rahul/renv_cache/v5/R-4.2/x86_64-apple-darwin21.5.0/slam/0.1-50/e25793551cbdb843154152e5ee88cbd6/slam/libs/slam.so, 0x0006): Library not loaded: '/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib'
Referenced from: '/Users/rahul/renv_cache/v5/R-4.2/x86_64-apple-darwin21.5.0/slam/0.1-50/e25793551cbdb843154152e5ee88cbd6/slam/libs/slam.so'
Reason: tried: '/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/usr/local/Cellar/r/4.2.1_2/lib/R/lib/libgfortran.5.dylib' (no such file)
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘topicmodels’
@rsangole
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> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin21.5.0 (64-bit)
Running under: macOS Monterey 12.5

Matrix products: default
LAPACK: /usr/local/Cellar/r/4.2.1_2/lib/R/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.2.1 tools_4.2.1    renv_0.15.2   

@rsangole
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> system("gcc --version")
Apple clang version 13.1.6 (clang-1316.0.21.2.5)
Target: x86_64-apple-darwin21.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
> 

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> cat ~/.R/Makevars                                                                                                                                                                                                                                                                                                                       

OBJCXX = clang++

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