##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GraphAlignment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘GraphAlignment’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c GA_alloc.c -o GA_alloc.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c GA_matrix.c -o GA_matrix.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c GA_matrix_R.c -o GA_matrix_R.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c GA_message.c -o GA_message.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c GA_vector.c -o GA_vector.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c: In function ‘GA_clamp_mode_from_R’:
GA_vector_R.c:139:9: warning: unused variable ‘size’ [-Wunused-variable]
  139 |     int size = LENGTH(robj);
      |         ^~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function ‘GA_encode_directed_graph’:
GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
  138 |                 if (matrix->elts[i][j] == 1)
      |                    ^
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
  159 |                 if (matrix->elts[i][j] == 1)
      |                    ^
GraphAlignment.c: In function ‘GA_directed_mode_from_R’:
GraphAlignment.c:264:9: warning: unused variable ‘size’ [-Wunused-variable]
  264 |     int size = LENGTH(robj);
      |         ^~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c lap.c -o lap.o
lap.c: In function ‘LAP_checklap’:
lap.c:348:9: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  348 |         scanf("%c", &wait);
      |         ^~~~~~~~~~~~~~~~~~
lap.c:358:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  358 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:371:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  371 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:384:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  384 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:394:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  394 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c: In function ‘LAP_lap’:
lap.c:64:30: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   64 |   col  j, j1, j2, endofpath, last, low, up, *collist, *matches;
      |                              ^~~~
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o GraphAlignment.so GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GraphAlignment/00new/GraphAlignment/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 (GraphAlignment)