Created
August 14, 2022 23:51
-
-
Save rsangole/3a82e6fd17a0cee97ea8f97a5191311f to your computer and use it in GitHub Desktop.
Error while trying to install topicmodels on my MacOS 12.5
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
> 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’ |
Author
rsangole
commented
Aug 14, 2022
> 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
>
> cat ~/.R/Makevars
OBJCXX = clang++
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment