############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data 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 ‘1.16.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.o ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable 'features' [-Wunused-variable] unsigned int features = vrna_cpu_simd_capabilities(); ^ ViennaRNA/utils/higher_order_functions.c:116:1: warning: unused label 'exec_fun_zip_add_min' [-Wunused-label] exec_fun_zip_add_min: ^~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_utils.o ViennaRNA/utils/string_utils.c:391:36: warning: unused variable 'num_strings' [-Wunused-variable] size_t n, offset, *lengths, num_strings, mem_strings, total_length; ^ 1 warning generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/utils.o ViennaRNA/utils/utils.c:59:15: warning: unused variable 'scale1' [-Wunused-variable] PRIVATE char scale1[] = "....,....1....,....2....,....3....,....4"; ^ ViennaRNA/utils/utils.c:60:15: warning: unused variable 'scale2' [-Wunused-variable] PRIVATE char scale2[] = "....,....5....,....6....,....7....,....8"; ^ 2 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/SHAPE.c -o ViennaRNA/constraints/SHAPE.o ViennaRNA/constraints/SHAPE.c:202:10: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] method = shape_method; ^ ~~~~~~~~~~~~ ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer ('char *' and 'int') [-Wpointer-integer-compare] 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 ('char *' and 'int') [-Wpointer-integer-compare] if (method == 'D') { ~~~~~~ ^ ~~~ ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer ('char *' and 'int') [-Wpointer-integer-compare] } else if (method == 'Z') { ~~~~~~ ^ ~~~ ViennaRNA/constraints/SHAPE.c:209:64: warning: variable 'p1' is uninitialized when used here [-Wuninitialized] (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type); ^~ ViennaRNA/constraints/SHAPE.c:196:13: note: initialize the variable 'p1' to silence this warning float p1, p2; ^ = 0.0 ViennaRNA/constraints/SHAPE.c:209:68: warning: variable 'p2' is uninitialized when used here [-Wuninitialized] (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type); ^~ ViennaRNA/constraints/SHAPE.c:196:17: note: initialize the variable 'p2' to silence this warning float p1, p2; ^ = 0.0 ViennaRNA/constraints/SHAPE.c:612:15: warning: unused variable 'warning' [-Wunused-variable] const char warning[] = "SHAPE method parameters not recognized! Using default parameters!"; ^ 7 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.o In file included from ViennaRNA/constraints/hard.c:37: ViennaRNA/constraints/hc_depot.inc:229:13: warning: unused variable 'k' [-Wunused-variable] size_t k, old_size, next_entry, entry; ^ ViennaRNA/constraints/hc_depot.inc:229:16: warning: unused variable 'old_size' [-Wunused-variable] size_t k, old_size, next_entry, entry; ^ ViennaRNA/constraints/hc_depot.inc:229:38: warning: unused variable 'entry' [-Wunused-variable] size_t k, old_size, next_entry, entry; ^ ViennaRNA/constraints/hc_depot.inc:263:25: warning: unused variable 'n' [-Wunused-variable] unsigned int s, i, n; ^ ViennaRNA/constraints/hard.c:211:20: warning: variable 'maxdist' set but not used [-Wunused-but-set-variable] unsigned int n, maxdist; ^ ViennaRNA/constraints/hard.c:386:41: warning: variable 'ss' set but not used [-Wunused-but-set-variable] unsigned int i, strand, pos, n_pos, *ss, *sn; ^ ViennaRNA/constraints/hard.c:386:46: warning: variable 'sn' set but not used [-Wunused-but-set-variable] unsigned int i, strand, pos, n_pos, *ss, *sn; ^ ViennaRNA/constraints/hard.c:436:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] unsigned int n, strand, actual_i, *sn, *ss, *se; ^ ViennaRNA/constraints/hard.c:436:49: warning: variable 'se' set but not used [-Wunused-but-set-variable] unsigned int n, strand, actual_i, *sn, *ss, *se; ^ ViennaRNA/constraints/hard.c:437:17: warning: unused variable 'p' [-Wunused-variable] int p; ^ ViennaRNA/constraints/hard.c:476:17: warning: unused variable 'n' [-Wunused-variable] 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] 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] 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] unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; ^ ViennaRNA/constraints/hard.c:476:45: warning: unused variable 'k' [-Wunused-variable] unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; ^ ViennaRNA/constraints/hard.c:476:48: warning: unused variable 'l' [-Wunused-variable] unsigned int n, *sn, *se, *ss, n_i, n_j, k, l; ^ ViennaRNA/constraints/hard.c:532:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j; ^ ViennaRNA/constraints/hard.c:532:26: warning: variable 'se' set but not used [-Wunused-but-set-variable] unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j; ^ ViennaRNA/constraints/hard.c:533:17: warning: unused variable 'k' [-Wunused-variable] int k, l, ret; ^ ViennaRNA/constraints/hard.c:533:20: warning: unused variable 'l' [-Wunused-variable] int k, l, ret; ^ ViennaRNA/constraints/hard.c:588:20: warning: unused variable 'i' [-Wunused-variable] unsigned int i; ^ ViennaRNA/constraints/hard.c:841:20: warning: unused variable 'depot' [-Wunused-variable] vrna_hc_depot_t *depot; ^ ViennaRNA/constraints/hard.c:1009:27: warning: unused variable 'type' [-Wunused-variable] unsigned char option, type; ^ ViennaRNA/constraints/hard.c:1010:67: warning: unused variable 'start' [-Wunused-variable] 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] 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] 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] 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] 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:1010:109: warning: variable 'se' set but not used [-Wunused-but-set-variable] 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:1011:25: warning: unused variable 'ij' [-Wunused-variable] int *idx, ij; ^ ViennaRNA/constraints/hard.c:1122:35: warning: unused variable 't1' [-Wunused-variable] unsigned char constraint, type, t1, t2; ^ ViennaRNA/constraints/hard.c:1122:39: warning: unused variable 't2' [-Wunused-variable] unsigned char constraint, type, t1, t2; ^ ViennaRNA/constraints/hard.c:1887:23: warning: unused variable 'u' [-Wunused-variable] unsigned int i, n, u; ^ 33 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o ViennaRNA/datastructures/lists.c:97:1: error: conflicting types for 'lst_kill' lst_kill (LIST * l, void (*freeNode) (void *node)) ^ ../src/ViennaRNA/datastructures/lists.h:58:6: note: previous declaration is here void lst_kill (LIST * l, void (*freeNode) ()); ^ ViennaRNA/datastructures/lists.c:284:1: error: conflicting types for 'lst_mergesort' lst_mergesort (LIST * l, int (*cmp_func) (void *, void *)) ^ ../src/ViennaRNA/datastructures/lists.h:63:6: note: previous declaration is here void lst_mergesort (LIST * l, int (*cmp_func) ()); ^ 2 errors generated. make: *** [ViennaRNA/datastructures/lists.o] Error 1 ERROR: compilation failed for package ‘XNAString’ * removing ‘/private/tmp/RtmpcvYZRL/Rinstb94c2c0adf9d/XNAString’ ----------------------------------- ERROR: package installation failed