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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'GenomicAlignments' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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 'parse_cigar_ranges',
    inlined from 'cigar_ranges' at cigar_utils.c:660:12:
cigar_utils.c:213:21: warning: 'range_buf1' may be used uninitialized [-Wmaybe-uninitialized]
  213 |         buf_nelt0 = IntPairAE_get_nelt(range_buf);
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
      |                    ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicAlignments)