############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL cigarillo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘cigarillo’ ... ** this is package ‘cigarillo’ version ‘0.99.1’ ** 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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_init_cigarillo.c -o R_init_cigarillo.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c cigar_extent.c -o cigar_extent.o cigar_extent.c: In function ‘C_cigar_extent’: cigar_extent.c:44:29: warning: ‘flags_elt’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if (*flags_elt == NA_INTEGER) { | ^~~~~~~~~~ cigar_extent.c:34:20: note: ‘flags_elt’ was declared here 34 | const int *flags_elt; | ^~~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c cigar_ops_visibility.c -o cigar_ops_visibility.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c cigars_as_ranges.c -o cigars_as_ranges.o cigars_as_ranges.c: In function ‘C_cigars_as_ranges’: cigars_as_ranges.c:327:48: warning: ‘range_buf2’ may be used uninitialized [-Wmaybe-uninitialized] 327 | range_buf1 = range_buf2->elts[*f_p - 1]; | ~~~~~~~~~~^~~~~~ cigars_as_ranges.c:260:22: note: ‘range_buf2’ was declared here 260 | IntPairAEAE *range_buf2; | ^~~~~~~~~~ cigars_as_ranges.c:295:29: warning: ‘flags_p’ may be used uninitialized [-Wmaybe-uninitialized] 295 | if (*flags_p == NA_INTEGER) { | ^~~~~~~~ cigars_as_ranges.c:250:20: note: ‘flags_p’ was declared here 250 | const int *flags_p; | ^~~~~~~ cigars_as_ranges.c:344:38: warning: ‘breakpoints’ may be used uninitialized [-Wmaybe-uninitialized] 344 | *(breakpoints++) = IntPairAE_get_nelt(range_buf1); | ~~~~~~~~~~~~^~~ cigars_as_ranges.c:262:14: note: ‘breakpoints’ was declared here 262 | int *breakpoints; | ^~~~~~~~~~~ cigars_as_ranges.c:325:29: warning: ‘f_p’ may be used uninitialized [-Wmaybe-uninitialized] 325 | if (*f_p == NA_INTEGER) | ^~~~ cigars_as_ranges.c:264:20: note: ‘f_p’ was declared here 264 | const int *f_p; | ^~~ In function ‘parse_cigar_ranges’, inlined from ‘C_cigars_as_ranges’ at cigars_as_ranges.c:329:24: cigars_as_ranges.c:142:25: warning: ‘range_buf1’ may be used uninitialized [-Wmaybe-uninitialized] 142 | int buf_nelt0 = IntPairAE_get_nelt(range_buf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cigars_as_ranges.c: In function ‘C_cigars_as_ranges’: cigars_as_ranges.c:259:20: note: ‘range_buf1’ was declared here 259 | IntPairAE *range_buf1; | ^~~~~~~~~~ In file included from /home/biocbuild/bbs-3.22-bioc/R/include/Rdefines.h:41, from cigars_as_ranges.h:4, from cigars_as_ranges.c:1: In function ‘make_CompressedIRangesList’, inlined from ‘C_cigars_as_ranges’ at cigars_as_ranges.c:352:3: /home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:388:25: warning: ‘ans_breakpoints’ may be used uninitialized [-Wmaybe-uninitialized] 388 | #define PROTECT(s) Rf_protect(s) | ^~~~~~~~~~~~~ cigars_as_ranges.c:204:17: note: in expansion of macro ‘PROTECT’ 204 | PROTECT(new_PartitioningByEnd("PartitioningByEnd", | ^~~~~~~ cigars_as_ranges.c: In function ‘C_cigars_as_ranges’: cigars_as_ranges.c:261:14: note: ‘ans_breakpoints’ was declared here 261 | SEXP ans_breakpoints; | ^~~~~~~~~~~~~~~ In function ‘make_list_of_IRanges’, inlined from ‘C_cigars_as_ranges’ at cigars_as_ranges.c:350:10: /home/biocbuild/bbs-3.22-bioc/R/include/Rdefines.h:146:33: warning: ‘f_levels’ may be used uninitialized [-Wmaybe-uninitialized] 146 | #define SET_NAMES(x, n) Rf_setAttrib(x, R_NamesSymbol, n) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cigars_as_ranges.c:176:9: note: in expansion of macro ‘SET_NAMES’ 176 | SET_NAMES(ans, names); | ^~~~~~~~~ cigars_as_ranges.c: In function ‘C_cigars_as_ranges’: cigars_as_ranges.c:263:14: note: ‘f_levels’ was declared here 263 | SEXP f_levels; | ^~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c explode_cigars.c -o explode_cigars.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c map_ref_ranges_to_query.c -o map_ref_ranges_to_query.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c project_positions.c -o project_positions.o project_positions.c: In function ‘_to_ref’: project_positions.c:67:6: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized] 67 | if (n == 0) | ^ project_positions.c:20:7: note: ‘n’ was declared here 20 | int n, offset = 0, OPL, query_consumed = 0; | ^ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c tabulate_cigar_ops.c -o tabulate_cigar_ops.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c trim_cigars.c -o trim_cigars.o In function ‘trim_along_ref’, inlined from ‘C_trim_cigars_along_ref’ at trim_cigars.c:178:24: trim_cigars.c:130:12: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized] 130 | if (Roffset < Loffset) { | ^ trim_cigars.c: In function ‘C_trim_cigars_along_ref’: trim_cigars.c:118:13: note: ‘Loffset’ was declared here 118 | int Loffset; | ^~~~~~~ In function ‘trim_along_ref’, inlined from ‘C_trim_cigars_along_ref’ at trim_cigars.c:178:24: trim_cigars.c:130:12: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized] 130 | if (Roffset < Loffset) { | ^ trim_cigars.c: In function ‘C_trim_cigars_along_ref’: trim_cigars.c:125:13: note: ‘Roffset’ was declared here 125 | int Roffset; | ^~~~~~~ In function ‘trim_along_query’, inlined from ‘C_trim_cigars_along_query’ at trim_cigars.c:364:24: trim_cigars.c:311:12: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized] 311 | if (Roffset < Loffset) { | ^ trim_cigars.c: In function ‘C_trim_cigars_along_query’: trim_cigars.c:299:13: note: ‘Loffset’ was declared here 299 | int Loffset; | ^~~~~~~ In function ‘trim_along_query’, inlined from ‘C_trim_cigars_along_query’ at trim_cigars.c:364:24: trim_cigars.c:311:12: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized] 311 | if (Roffset < Loffset) { | ^ trim_cigars.c: In function ‘C_trim_cigars_along_query’: trim_cigars.c:306:13: note: ‘Roffset’ was declared here 306 | int Roffset; | ^~~~~~~ gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o cigarillo.so IRanges_stubs.o R_init_cigarillo.o S4Vectors_stubs.o cigar_extent.o cigar_ops_visibility.o cigars_as_ranges.o explode_cigars.o map_ref_ranges_to_query.o project_positions.o tabulate_cigar_ops.o trim_cigars.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-cigarillo/00new/cigarillo/libs ** R ** 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 (cigarillo)