############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL IRanges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘IRanges’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c CompressedList_class.c -o CompressedList_class.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c Grouping_class.c -o Grouping_class.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -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 -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c Ranges_class.c -o Ranges_class.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -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 -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -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 -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -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 -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)