##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL GenomicAlignments
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function ‘cigar_ranges’:
cigar_utils.c:676:9: warning: ‘f_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  676 |    f_elt++;
      |    ~~~~~^~
cigar_utils.c:674:22: warning: ‘range_buf1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  674 |    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:674:16: warning: ‘breakpoint’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  674 |    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |     ~~~~~~~~~~~^~~
cigar_utils.c:626:8: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  626 |    if (*flag_elt == NA_INTEGER) {
      |        ^~~~~~~~~
cigar_utils.c: In function ‘cigar_width’:
cigar_utils.c:708:8: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  708 |    if (*flag_elt == NA_INTEGER) {
      |        ^~~~~~~~~
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:883:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  883 |   if (offset == Roffset)
      |      ^
cigar_utils.c:854:15: note: ‘Roffset’ was declared here
  854 |  int Loffset, Roffset, buf_offset;
      |               ^~~~~~~
cigar_utils.c:881:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  881 |   if (offset == Loffset)
      |      ^
cigar_utils.c:854:6: note: ‘Loffset’ was declared here
  854 |  int Loffset, Roffset, buf_offset;
      |      ^~~~~~~
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1074:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1074 |   if (offset == Roffset)
      |      ^
cigar_utils.c:1045:15: note: ‘Roffset’ was declared here
 1045 |  int Loffset, Roffset, buf_offset;
      |               ^~~~~~~
cigar_utils.c:1072:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1072 |   if (offset == Loffset)
      |      ^
cigar_utils.c:1045:6: note: ‘Loffset’ was declared here
 1045 |  int Loffset, Roffset, buf_offset;
      |      ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function ‘overlap_encoding’:
encodeOverlaps_methods.c:180:33: warning: ‘out_nelt0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  180 |  CharAE_set_nelt(out, out_nelt0 + j2 * nrow);
      |                       ~~~~~~~~~~^~~~~~~~~~~
encodeOverlaps_methods.c:99:6: note: ‘out_nelt0’ was declared here
   99 |  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      |      ^~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-GenomicAlignments/00new/GenomicAlignments/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 (GenomicAlignments)