Package loading fails after seemingly successful compilation with macOS brew R

[uhkeller]

I'm using the homebrew version of R 4.2.0 on macOS 12.4 (Intel). Previous versions of collapse installed just fine. Today when updating to collapse 1.8.4 it seemed it compiled but then I got an error:

trying URL 'https://cloud.r-project.org/src/contrib/collapse_1.8.4.tar.gz'
Content type 'application/x-gzip' length 1162757 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘collapse’ ...
** package ‘collapse’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 ExportSymbols.c -o ExportSymbols.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 TRA.c -o TRA.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 base_radixsort.c -o base_radixsort.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 data.table_init.c -o data.table_init.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 data.table_rbindlist.c -o data.table_rbindlist.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 data.table_subset.c -o data.table_subset.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 data.table_utils.c -o data.table_utils.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 extptr.c -o extptr.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c fbetween_fwithin.cpp -o fbetween_fwithin.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c fbstats.cpp -o fbstats.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 fcumsum.c -o fcumsum.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c fdiff_fgrowth.cpp -o fdiff_fgrowth.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 ffirst.c -o ffirst.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c flag.cpp -o flag.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 flast.c -o flast.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 fmean.c -o fmean.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 fmin_fmax.c -o fmin_fmax.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 fmode.c -o fmode.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 fndistinct.c -o fndistinct.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 fnobs.c -o fnobs.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c fnth_fmedian.cpp -o fnth_fmedian.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 fprod.c -o fprod.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c fscale.cpp -o fscale.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 fsum.c -o fsum.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c fvar_fsd.cpp -o fvar_fsd.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 gsplit.c -o gsplit.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 handle_attributes.c -o handle_attributes.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 kit_dup.c -o kit_dup.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c mrtl_mctl.cpp -o mrtl_mctl.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 programming.c -o programming.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c psmat.cpp -o psmat.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c pwnobs.cpp -o pwnobs.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c qF_qG.cpp -o qF_qG.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c seqid_groupid.cpp -o seqid_groupid.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 small_helper.c -o small_helper.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 stats_mAR.c -o stats_mAR.o
clang -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -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 stats_pacf.c -o stats_pacf.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.2.0/lib/R/include" -DNDEBUG  -I'/Users/myuser/Library/R/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -DSTRICT_R_HEADERS -fPIC  -g -O2  -c varying.cpp -o varying.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/4.2.0/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 collapse.so ExportSymbols.o RcppExports.o TRA.o base_radixsort.o data.table_init.o data.table_rbindlist.o data.table_subset.o data.table_utils.o extptr.o fbetween_fwithin.o fbstats.o fcumsum.o fdiff_fgrowth.o ffirst.o flag.o flast.o fmean.o fmin_fmax.o fmode.o fndistinct.o fnobs.o fnth_fmedian.o fprod.o fscale.o fsum.o fvar_fsd.o gsplit.o handle_attributes.o kit_dup.o mrtl_mctl.o programming.o psmat.o pwnobs.o qF_qG.o seqid_groupid.o small_helper.o stats_mAR.o stats_pacf.o varying.o -L/usr/local/Cellar/r/4.2.0/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /Users/myuser/Library/R/library/00LOCK-collapse/00new/collapse/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘collapse’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/myuser/Library/R/library/00LOCK-collapse/00new/collapse/libs/collapse.so':
  dlopen(/Users/myuser/Library/R/library/00LOCK-collapse/00new/collapse/libs/collapse.so, 0x0006): symbol not found in flat namespace '_mymod'
Error:
! loading failed
Backtrace:
    ▆
 1. └─tools:::.test_load_package("collapse", "/Users/myuser/Library/R/library/00LOCK-collapse/00new")
Execution halted
ERROR: loading failed
* removing ‘/Users/myuser/Library/R/library/collapse’

If there is anything I can do to help fixing this please let me know.

[SebKrantz]

Hi, can you confirm you also get this error with 1.8.5: install.packages("collapse", repos = "https://fastverse.r-universe.dev")? Also perhaps manually try to remove the previous installation e.g. rm /Users/myuser/Library/R/library/00LOCK-collapse.

[uhkeller]

Thanks for your quick response! Same error with 1.8.5 unfortunately. The "00LOCK" folder gets removed automatically immediately after the failed installation attempt. Removing the previous installation also didn't help.

[SebKrantz]

It seems this issue is related to the name of a C-function called 'mymod' standing in conflict with some variable on your system. I have now renamed the function. Please tra again with the GitHub version: remotes::install_github("SebKrantz/collapse").

[uhkeller]

Sorry, no luck. Same error (just with different function name):

  dlopen(/Users/myuser/Library/R/library/00LOCK-collapse/00new/collapse/libs/collapse.so, 0x0006): symbol not found in flat namespace '_modulus_impl'

[SebKrantz]

Ok, I found another potential source of the problem, I should add a static keyword to the inline function. Please try again using remotes::install_github("SebKrantz/collapse").

[uhkeller]

Yes, that did the trick! Thanks!