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### Running command:
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###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL GenomicAlignments
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* installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/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:676:30: warning: ‘f_elt’ may be used uninitialized [-Wmaybe-uninitialized]
  676 |                         f_elt++;
      |                         ~~~~~^~
cigar_utils.c:593:41: note: ‘f_elt’ was declared here
  593 |         const int *flag_elt, *pos_elt, *f_elt;
      |                                         ^~~~~
In function ‘drop_or_append_or_merge_range’,
    inlined from ‘parse_cigar_ranges’ at cigar_utils.c:221:4,
    inlined from ‘cigar_ranges’ at cigar_utils.c:660:12:
cigar_utils.c:180:44: warning: ‘range_buf1’ may be used uninitialized [-Wmaybe-uninitialized]
  180 |                                   range_buf->b->elts[buf_nelt_minus_1];
      |                                   ~~~~~~~~~^~~
cigar_utils.c: In function ‘cigar_ranges’:
cigar_utils.c:590:20: note: ‘range_buf1’ was declared here
  590 |         IntPairAE *range_buf1;
      |                    ^~~~~~~~~~
cigar_utils.c:674:37: warning: ‘breakpoint’ may be used uninitialized [-Wmaybe-uninitialized]
  674 |                         *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |                          ~~~~~~~~~~~^~~
cigar_utils.c:588:62: note: ‘breakpoint’ was declared here
  588 |         int cigar_len, space0, pos_len, f_is_NULL, ans_len, *breakpoint,
      |                                                              ^~~~~~~~~~
cigar_utils.c:542:25: warning: ‘ans_breakpoints’ may be used uninitialized [-Wmaybe-uninitialized]
  542 |                         new_PartitioningByEnd("PartitioningByEnd",
      |                         ^~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:587:19: note: ‘ans_breakpoints’ was declared here
  587 |         SEXP ans, ans_breakpoints, f_levels, cigar_elt;
      |                   ^~~~~~~~~~~~~~~
cigar_utils.c:626:29: warning: ‘flag_elt’ may be used uninitialized [-Wmaybe-uninitialized]
  626 |                         if (*flag_elt == NA_INTEGER) {
      |                             ^~~~~~~~~
cigar_utils.c:593:20: note: ‘flag_elt’ was declared here
  593 |         const int *flag_elt, *pos_elt, *f_elt;
      |                    ^~~~~~~~
cigar_utils.c: In function ‘cigar_width’:
cigar_utils.c:708:29: warning: ‘flag_elt’ may be used uninitialized [-Wmaybe-uninitialized]
  708 |                         if (*flag_elt == NA_INTEGER) {
      |                             ^~~~~~~~~
cigar_utils.c:698:20: note: ‘flag_elt’ was declared here
  698 |         const int *flag_elt;
      |                    ^~~~~~~~
In function ‘narrow_cigar_string’,
    inlined from ‘cigar_narrow’ at cigar_utils.c:920:12:
cigar_utils.c:879:39: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized]
  879 |         for (offset = Loffset; offset <= Roffset; offset += n) {
      |                                ~~~~~~~^~~~~~~~~~
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:854:22: note: ‘Roffset’ was declared here
  854 |         int Loffset, Roffset, buf_offset;
      |                      ^~~~~~~
In function ‘narrow_cigar_string’,
    inlined from ‘cigar_narrow’ at cigar_utils.c:920:12:
cigar_utils.c:881:20: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized]
  881 |                 if (offset == Loffset)
      |                    ^
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:854:13: note: ‘Loffset’ was declared here
  854 |         int Loffset, Roffset, buf_offset;
      |             ^~~~~~~
In function ‘qnarrow_cigar_string’,
    inlined from ‘cigar_qnarrow’ at cigar_utils.c:1116:12:
cigar_utils.c:1070:39: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized]
 1070 |         for (offset = Loffset; offset <= Roffset; offset += n) {
      |                                ~~~~~~~^~~~~~~~~~
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1045:22: note: ‘Roffset’ was declared here
 1045 |         int Loffset, Roffset, buf_offset;
      |                      ^~~~~~~
In function ‘qnarrow_cigar_string’,
    inlined from ‘cigar_qnarrow’ at cigar_utils.c:1116:12:
cigar_utils.c:1072:20: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized]
 1072 |                 if (offset == Loffset)
      |                    ^
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1045:13: note: ‘Loffset’ was declared here
 1045 |         int Loffset, Roffset, buf_offset;
      |             ^~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function ‘to_query’:
coordinate_mapping_methods.c:64:26: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
   64 |   if (query_loc < 0 || n == 0)
      |                        ~~^~~~
coordinate_mapping_methods.c:17:7: note: ‘n’ was declared here
   17 |   int n, offset = 0, OPL, query_consumed = 0;
      |       ^
coordinate_mapping_methods.c: In function ‘to_ref’:
coordinate_mapping_methods.c:219:6: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
  219 |   if (n == 0)
      |      ^
coordinate_mapping_methods.c:172:7: note: ‘n’ was declared here
  172 |   int n, offset = 0, OPL, query_consumed = 0;
      |       ^
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -shared -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
installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/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)