##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL VegaMC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘VegaMC’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c: In function ‘run_vegaMC’:
run_vegaMC.c:144:13: warning: too many arguments for format [-Wformat-extra-args]
  144 |     Rprintf("\tAberration Matrices Successfully Computed\n", num_seg_regions);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c:149:13: warning: too many arguments for format [-Wformat-extra-args]
  149 |     Rprintf("\tStatistical Analysis Successfully Completed\n",
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c: In function ‘read_params’:
run_vegaMC.c:618:18: warning: unused variable ‘brkt’ [-Wunused-variable]
  618 |     char *elem, *brkt;
      |                  ^~~~
run_vegaMC.c: In function ‘load_data’:
run_vegaMC.c:564:14: warning: ‘first_probe’ may be used uninitialized [-Wmaybe-uninitialized]
  564 |     prev_chr = temp_probe->chromosome;
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c:481:12: note: ‘first_probe’ was declared here
  481 |     probe *first_probe, *prev_probe, *temp_probe;
      |            ^~~~~~~~~~~
run_vegaMC.c:535:30: warning: ‘position’ may be used uninitialized [-Wmaybe-uninitialized]
  535 |         temp_probe->position = position;
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
run_vegaMC.c:498:20: note: ‘position’ was declared here
  498 |         int i = 0, position, chr;
      |                    ^~~~~~~~
run_vegaMC.c:534:32: warning: ‘chr’ may be used uninitialized [-Wmaybe-uninitialized]
  534 |         temp_probe->chromosome = chr;
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:498:30: note: ‘chr’ was declared here
  498 |         int i = 0, position, chr;
      |                              ^~~
run_vegaMC.c: In function ‘call_VegaMC’:
run_vegaMC.c:435:32: warning: ‘prev_seg’ may be used uninitialized [-Wmaybe-uninitialized]
  435 |                 prev_seg->next = tmp;
      |                 ~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:373:30: note: ‘prev_seg’ was declared here
  373 |     seg_element *first_seg, *prev_seg;
      |                              ^~~~~~~~
run_vegaMC.c:461:29: warning: ‘first_seg’ may be used uninitialized [-Wmaybe-uninitialized]
  461 |         for (i = 0; i < (tmp->num_regions); i++) {
      |                         ~~~~^~~~~~~~~~~~~~
run_vegaMC.c:373:18: note: ‘first_seg’ was declared here
  373 |     seg_element *first_seg, *prev_seg;
      |                  ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort_data.c -o sort_data.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c vegaMC.c -o vegaMC.o
vegaMC.c: In function ‘heap_delete’:
vegaMC.c:235:10: warning: variable ‘deleted’ set but not used [-Wunused-but-set-variable]
  235 |     node deleted;
      |          ^~~~~~~
vegaMC.c: In function ‘init_trivial_segmentation’:
vegaMC.c:592:15: warning: variable ‘index’ set but not used [-Wunused-but-set-variable]
  592 |     int i, j, index;
      |               ^~~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-VegaMC/00new/VegaMC/libs
** R
** 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
** 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)