##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VegaMC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘VegaMC’ ...
** this is package ‘VegaMC’ version ‘3.49.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c:144:62: warning: data argument not used by format string [-Wformat-extra-args]
  144 |     Rprintf("\tAberration Matrices Successfully Computed\n", num_seg_regions);
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ^
run_vegaMC.c:150:13: warning: data argument not used by format string [-Wformat-extra-args]
  149 |     Rprintf("\tStatistical Analysis Successfully Completed\n",
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  150 |             num_seg_regions);
      |             ^
run_vegaMC.c:317:17: warning: variable 'tot_baf' set but not used [-Wunused-but-set-variable]
  317 |             int tot_baf = 0;
      |                 ^
run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
  491 |             elem = strtok('\0', sep);
      |                           ^~~~
run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
  526 |             elem = strtok('\0', sep);
      |                           ^~~~
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
  618 |     char *elem, *brkt;
      |                  ^~~~
6 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sort_data.c -o sort_data.o
sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
  131 |             elem = strtok('\0', sep);
      |                           ^~~~
sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
  180 |             elem = strtok('\0', sep);
      |                           ^~~~
2 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vegaMC.c -o vegaMC.o
vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
  235 |     node deleted;
      |          ^
vegaMC.c:458:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  458 |     lambda_gradient = abs(lambda);
      |                       ^
vegaMC.c:458:23: note: use function 'fabsf' instead
  458 |     lambda_gradient = abs(lambda);
      |                       ^~~
      |                       fabsf
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
  592 |     int i, j, index;
      |               ^
3 warnings generated.
clang -arch arm64 -std=gnu23 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-VegaMC/00new/VegaMC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'useMart(mart_database, ': unused argument (archive = TRUE) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (VegaMC)