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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL IRanges
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘IRanges’ ...
** this is package ‘IRanges’ version ‘2.42.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IPosRanges_comparison.c -o IPosRanges_comparison.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c NCList.c -o NCList.o
NCList.c:1173:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
 1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
  202 | static const NCList *next_top_down(const NCList *nclist)
      |                      ^~~~~~~~~~~~~
NCList.c: In function ‘C_find_overlaps_in_groups_NCList’:
NCList.c:1608:24: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized]
 1608 |                 return ans;
      |                        ^~~
NCList.c:1546:14: note: ‘ans’ was declared here
 1546 |         SEXP ans;
      |              ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Ranges_class.c -o Ranges_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c RleViews_utils.c -o RleViews_utils.o
In function ‘viewWhichMaxs_int_RleViews’,
    inlined from ‘viewWhichMaxs_RleViews’ at RleViews_utils.c:579:3,
    inlined from ‘C_summarize_RleViews’ at RleViews_utils.c:694:9:
RleViews_utils.c:325:54: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized]
  325 |                         if (!max_is_initialized || v > max) {
      |                                                    ~~^~~~~
RleViews_utils.c: In function ‘C_summarize_RleViews’:
RleViews_utils.c:316:21: note: ‘max’ was declared here
  316 |                 int max;  /* uninitialized */
      |                     ^~~
In function ‘viewWhichMins_int_RleViews’,
    inlined from ‘viewWhichMins_RleViews’ at RleViews_utils.c:546:3,
    inlined from ‘C_summarize_RleViews’ at RleViews_utils.c:686:9:
RleViews_utils.c:293:54: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
  293 |                         if (!min_is_initialized || v < min) {
      |                                                    ~~^~~~~
RleViews_utils.c: In function ‘C_summarize_RleViews’:
RleViews_utils.c:284:21: note: ‘min’ was declared here
  284 |                 int min;  /* uninitialized */
      |                     ^~~
In function ‘viewMaxs_int_RleViews’,
    inlined from ‘viewMaxs_RleViews’ at RleViews_utils.c:443:3,
    inlined from ‘C_summarize_RleViews’ at RleViews_utils.c:665:9:
RleViews_utils.c:67:54: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized]
   67 |                         if (!max_is_initialized || v > max) {
      |                                                    ~~^~~~~
RleViews_utils.c: In function ‘C_summarize_RleViews’:
RleViews_utils.c:54:21: note: ‘max’ was declared here
   54 |                 int max;  /* uninitialized */
      |                     ^~~
In function ‘viewMins_int_RleViews’,
    inlined from ‘viewMins_RleViews’ at RleViews_utils.c:413:3,
    inlined from ‘C_summarize_RleViews’ at RleViews_utils.c:660:9:
RleViews_utils.c:36:54: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
   36 |                         if (!min_is_initialized || v < min) {
      |                                                    ~~^~~~~
RleViews_utils.c: In function ‘C_summarize_RleViews’:
RleViews_utils.c:23:21: note: ‘min’ was declared here
   23 |                 int min;  /* uninitialized */
      |                     ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c coverage_methods.c -o coverage_methods.o
In function ‘shift_and_clip_ranges’,
    inlined from ‘compute_coverage_from_IRanges_holder’ at coverage_methods.c:609:12:
coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized [-Wmaybe-uninitialized]
  579 |         if (*out_ranges_are_tiles && x_end != cvg_len)
      |             ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:495:28: note: ‘x_end’ was declared here
  495 |             i, j, x_start, x_end, shift_elt, tmp;
      |                            ^~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function ‘C_find_partition_overlaps’:
extractListFragments.c:85:25: warning: ‘split_partitions_buf’ may be used uninitialized [-Wmaybe-uninitialized]
   85 |                         IntAE_insert_at(split_partitions_buf,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   86 |                                 IntAE_get_nelt(split_partitions_buf),
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   87 |                                 q_prev_end);
      |                                 ~~~~~~~~~~~
extractListFragments.c:35:16: note: ‘split_partitions_buf’ was declared here
   35 |         IntAE *split_partitions_buf;
      |                ^~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function ‘reduce_ranges.isra’:
inter_range_methods.c:156:35: warning: ‘max_end’ may be used uninitialized [-Wmaybe-uninitialized]
  156 |                         width_inc = end_j - max_end;
      |                         ~~~~~~~~~~^~~~~~~~~~~~~~~~~
inter_range_methods.c:102:29: note: ‘max_end’ was declared here
  102 |             append_or_drop, max_end, gapwidth, delta, width_inc;
      |                             ^~~~~~~
inter_range_methods.c:165:33: warning: ‘revmap_elt’ may be used uninitialized [-Wmaybe-uninitialized]
  165 |                                 IntAE_insert_at(revmap_elt,
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~
  166 |                                                 IntAE_get_nelt(revmap_elt),
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
  167 |                                                 j + 1);
      |                                                 ~~~~~~
inter_range_methods.c:103:22: note: ‘revmap_elt’ was declared here
  103 |         IntAE *tmp, *revmap_elt;
      |                      ^~~~~~~~~~
inter_range_methods.c:154:39: warning: ‘gapwidth’ may be used uninitialized [-Wmaybe-uninitialized]
  154 |                                 delta += gapwidth;
      |                                 ~~~~~~^~~~~~~~~~~
inter_range_methods.c:102:38: note: ‘gapwidth’ was declared here
  102 |             append_or_drop, max_end, gapwidth, delta, width_inc;
      |                                      ^~~~~~~~
inter_range_methods.c:154:39: warning: ‘delta’ may be used uninitialized [-Wmaybe-uninitialized]
  154 |                                 delta += gapwidth;
      |                                 ~~~~~~^~~~~~~~~~~
inter_range_methods.c:102:48: note: ‘delta’ was declared here
  102 |             append_or_drop, max_end, gapwidth, delta, width_inc;
      |                                                ^~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
** 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 (IRanges)