############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 XNAString ### ############################################################################## ############################################################################## * checking for file ‘XNAString/DESCRIPTION’ ... OK * preparing ‘XNAString’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘XNAString’ ... ** this is package ‘XNAString’ version ‘1.17.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.o ViennaRNA/utils/higher_order_functions.c: In function ‘zip_add_min_dispatcher’: ViennaRNA/utils/higher_order_functions.c:116:1: warning: label ‘exec_fun_zip_add_min’ defined but not used [-Wunused-label] 116 | exec_fun_zip_add_min: | ^~~~~~~~~~~~~~~~~~~~ ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable ‘features’ [-Wunused-variable] 96 | unsigned int features = vrna_cpu_simd_capabilities(); | ^~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_utils.o ViennaRNA/utils/string_utils.c: In function ‘vrna_strjoin’: ViennaRNA/utils/string_utils.c:391:36: warning: unused variable ‘num_strings’ [-Wunused-variable] 391 | size_t n, offset, *lengths, num_strings, mem_strings, total_length; | ^~~~~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/utils.o ViennaRNA/utils/utils.c:60:15: warning: ‘scale2’ defined but not used [-Wunused-variable] 60 | PRIVATE char scale2[] = "....,....5....,....6....,....7....,....8"; | ^~~~~~ ViennaRNA/utils/utils.c:59:15: warning: ‘scale1’ defined but not used [-Wunused-variable] 59 | PRIVATE char scale1[] = "....,....1....,....2....,....3....,....4"; | ^~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/constraints/SHAPE.c -o ViennaRNA/constraints/SHAPE.o ViennaRNA/constraints/SHAPE.c: In function ‘vrna_constraints_add_SHAPE’: ViennaRNA/constraints/SHAPE.c:202:10: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 202 | method = shape_method; | ^ ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer 206 | vrna_file_SHAPE_read(shape_file, length, method == 'W' ? 0 : -1, sequence, values); | ^~ ViennaRNA/constraints/SHAPE.c:208:14: warning: comparison between pointer and integer 208 | if (method == 'D') { | ^~ ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer 210 | } else if (method == 'Z') { | ^~ ViennaRNA/constraints/SHAPE.c: In function ‘sc_parse_parameters’: ViennaRNA/constraints/SHAPE.c:612:15: warning: unused variable ‘warning’ [-Wunused-variable] 612 | const char warning[] = "SHAPE method parameters not recognized! Using default parameters!"; | ^~~~~~~ ViennaRNA/constraints/SHAPE.c: In function ‘vrna_constraints_add_SHAPE’: ViennaRNA/constraints/SHAPE.c:209:11: warning: ‘p2’ may be used uninitialized [-Wmaybe-uninitialized] 209 | (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ViennaRNA/constraints/SHAPE.c:196:15: note: ‘p2’ was declared here 196 | float p1, p2; | ^~ ViennaRNA/constraints/SHAPE.c:209:11: warning: ‘p1’ may be used uninitialized [-Wmaybe-uninitialized] 209 | (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ViennaRNA/constraints/SHAPE.c:196:11: note: ‘p1’ was declared here 196 | float p1, p2; | ^~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.o In file included from ViennaRNA/constraints/hard.c:37: ViennaRNA/constraints/hc_depot.inc: In function ‘hc_depot_store_bp’: ViennaRNA/constraints/hc_depot.inc:229:38: warning: unused variable ‘entry’ [-Wunused-variable] 229 | size_t k, old_size, next_entry, entry; | ^~~~~ ViennaRNA/constraints/hc_depot.inc:229:16: warning: unused variable ‘old_size’ [-Wunused-variable] 229 | size_t k, old_size, next_entry, entry; | ^~~~~~~~ ViennaRNA/constraints/hc_depot.inc:229:13: warning: unused variable ‘k’ [-Wunused-variable] 229 | size_t k, old_size, next_entry, entry; | ^ ViennaRNA/constraints/hc_depot.inc: In function ‘hc_depot_free’: ViennaRNA/constraints/hc_depot.inc:263:25: warning: unused variable ‘n’ [-Wunused-variable] 263 | unsigned int s, i, n; | ^ ViennaRNA/constraints/hard.c: In function ‘vrna_hc_update’: ViennaRNA/constraints/hard.c:211:20: warning: variable ‘maxdist’ set but not used [-Wunused-but-set-variable] 211 | unsigned int n, maxdist; | ^~~~~~~ ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_up_strand_batch’: ViennaRNA/constraints/hard.c:386:46: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable] 386 | unsigned int i, strand, pos, n_pos, *ss, *sn; | ^~ ViennaRNA/constraints/hard.c:386:41: warning: variable ‘ss’ set but not used [-Wunused-but-set-variable] 386 | unsigned int i, strand, pos, n_pos, *ss, *sn; | ^~ ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp_nonspecific’: ViennaRNA/constraints/hard.c:437:17: warning: unused variable ‘p’ [-Wunused-variable] 437 | int p; | ^ ViennaRNA/constraints/hard.c:436:49: warning: variable ‘se’ set but not used [-Wunused-but-set-variable] 436 | unsigned int n, strand, actual_i, *sn, *ss, *se; | ^~ ViennaRNA/constraints/hard.c:436:17: warning: variable ‘n’ set but not used [-Wunused-but-set-variable] 436 | unsigned int n, strand, actual_i, *sn, *ss, *se; | ^ ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp_strand’: ViennaRNA/constraints/hard.c:476:48: warning: unused variable ‘l’ [-Wunused-variable] 476 | unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; | ^ ViennaRNA/constraints/hard.c:476:45: warning: unused variable ‘k’ [-Wunused-variable] 476 | unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; | ^ ViennaRNA/constraints/hard.c:476:31: warning: variable ‘ss’ set but not used [-Wunused-but-set-variable] 476 | unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; | ^~ ViennaRNA/constraints/hard.c:476:26: warning: variable ‘se’ set but not used [-Wunused-but-set-variable] 476 | unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; | ^~ ViennaRNA/constraints/hard.c:476:21: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable] 476 | unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; | ^~ ViennaRNA/constraints/hard.c:476:17: warning: unused variable ‘n’ [-Wunused-variable] 476 | unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; | ^ ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp’: ViennaRNA/constraints/hard.c:533:20: warning: unused variable ‘l’ [-Wunused-variable] 533 | int k, l, ret; | ^ ViennaRNA/constraints/hard.c:533:17: warning: unused variable ‘k’ [-Wunused-variable] 533 | int k, l, ret; | ^ ViennaRNA/constraints/hard.c:532:26: warning: variable ‘se’ set but not used [-Wunused-but-set-variable] 532 | unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j; | ^~ ViennaRNA/constraints/hard.c:532:17: warning: variable ‘n’ set but not used [-Wunused-but-set-variable] 532 | unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j; | ^ ViennaRNA/constraints/hard.c: In function ‘vrna_hc_free’: ViennaRNA/constraints/hard.c:588:20: warning: unused variable ‘i’ [-Wunused-variable] 588 | unsigned int i; | ^ ViennaRNA/constraints/hard.c: In function ‘default_hc_up’: ViennaRNA/constraints/hard.c:841:20: warning: unused variable ‘depot’ [-Wunused-variable] 841 | vrna_hc_depot_t *depot; | ^~~~~ ViennaRNA/constraints/hard.c: In function ‘prepare_hc_bp’: ViennaRNA/constraints/hard.c:1011:25: warning: unused variable ‘ij’ [-Wunused-variable] 1011 | int *idx, ij; | ^~ ViennaRNA/constraints/hard.c:1010:109: warning: variable ‘se’ set but not used [-Wunused-but-set-variable] 1010 | unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se; | ^~ ViennaRNA/constraints/hard.c:1010:99: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable] 1010 | unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se; | ^~ ViennaRNA/constraints/hard.c:1010:88: warning: unused variable ‘t_end’ [-Wunused-variable] 1010 | unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se; | ^~~~~ ViennaRNA/constraints/hard.c:1010:79: warning: unused variable ‘t_start’ [-Wunused-variable] 1010 | unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se; | ^~~~~~~ ViennaRNA/constraints/hard.c:1010:74: warning: unused variable ‘end’ [-Wunused-variable] 1010 | unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se; | ^~~ ViennaRNA/constraints/hard.c:1010:67: warning: unused variable ‘start’ [-Wunused-variable] 1010 | unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se; | ^~~~~ ViennaRNA/constraints/hard.c:1009:27: warning: unused variable ‘type’ [-Wunused-variable] 1009 | unsigned char option, type; | ^~~~ ViennaRNA/constraints/hard.c: In function ‘populate_hc_bp’: ViennaRNA/constraints/hard.c:1122:39: warning: unused variable ‘t2’ [-Wunused-variable] 1122 | unsigned char constraint, type, t1, t2; | ^~ ViennaRNA/constraints/hard.c:1122:35: warning: unused variable ‘t1’ [-Wunused-variable] 1122 | unsigned char constraint, type, t1, t2; | ^~ ViennaRNA/constraints/hard.c: In function ‘hc_update_up’: ViennaRNA/constraints/hard.c:1887:23: warning: unused variable ‘u’ [-Wunused-variable] 1887 | unsigned int i, n, u; | ^ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o ViennaRNA/datastructures/lists.c:97:1: error: conflicting types for ‘lst_kill’; have ‘void(LIST *, void (*)(void *))’ 97 | lst_kill (LIST * l, void (*freeNode) (void *node)) | ^~~~~~~~ In file included from ViennaRNA/datastructures/lists.c:33: ../src/ViennaRNA/datastructures/lists.h:58:6: note: previous declaration of ‘lst_kill’ with type ‘void(LIST *, void (*)(void))’ 58 | void lst_kill (LIST * l, void (*freeNode) ()); | ^~~~~~~~ ViennaRNA/datastructures/lists.c:284:1: error: conflicting types for ‘lst_mergesort’; have ‘void(LIST *, int (*)(void *, void *))’ 284 | lst_mergesort (LIST * l, int (*cmp_func) (void *, void *)) | ^~~~~~~~~~~~~ ../src/ViennaRNA/datastructures/lists.h:63:6: note: previous declaration of ‘lst_mergesort’ with type ‘void(LIST *, int (*)(void))’ 63 | void lst_mergesort (LIST * l, int (*cmp_func) ()); | ^~~~~~~~~~~~~ make: *** [/home/biocbuild/bbs-3.22-bioc/R/etc/Makeconf:202: ViennaRNA/datastructures/lists.o] Error 1 ERROR: compilation failed for package ‘XNAString’ * removing ‘/tmp/Rtmp15gW3s/Rinst2a943b3f8fce3a/XNAString’ ----------------------------------- ERROR: package installation failed