############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL IRanges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘IRanges’ ... ** this is package ‘IRanges’ version ‘2.43.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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) | ^~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 RleViews_utils.c: In function ‘C_summarize_RleViews’: RleViews_utils.c:325:54: warning: ‘max’ may be used uninitialized in this function [-Wmaybe-uninitialized] 325 | if (!max_is_initialized || v > max) { | ~~^~~~~ RleViews_utils.c:316:21: note: ‘max’ was declared here 316 | int max; /* uninitialized */ | ^~~ RleViews_utils.c:293:54: warning: ‘min’ may be used uninitialized in this function [-Wmaybe-uninitialized] 293 | if (!min_is_initialized || v < min) { | ~~^~~~~ RleViews_utils.c:284:21: note: ‘min’ was declared here 284 | int min; /* uninitialized */ | ^~~ RleViews_utils.c:67:54: warning: ‘max’ may be used uninitialized in this function [-Wmaybe-uninitialized] 67 | if (!max_is_initialized || v > max) { | ~~^~~~~ RleViews_utils.c:54:21: note: ‘max’ was declared here 54 | int max; /* uninitialized */ | ^~~ RleViews_utils.c:36:54: warning: ‘min’ may be used uninitialized in this function [-Wmaybe-uninitialized] 36 | if (!min_is_initialized || v < min) { | ~~^~~~~ RleViews_utils.c:23:21: note: ‘min’ was declared here 23 | int min; /* uninitialized */ | ^~~ gcc -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’: coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized] 579 | if (*out_ranges_are_tiles && x_end != cvg_len) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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:66:33: warning: ‘split_partitions_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized] 66 | IntAE_insert_at(split_partitions_buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 | IntAE_get_nelt(split_partitions_buf), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | q_prev_end); | ~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-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 gcc -shared -L/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-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)