############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL XNAString ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'XNAString' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/char_stream.c -o ViennaRNA/datastructures/char_stream.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/heap.c -o ViennaRNA/datastructures/heap.o ViennaRNA/datastructures/heap.c: In function 'heapify_down': ViennaRNA/datastructures/heap.c:319:22: warning: unused variable 'child_v2' [-Wunused-variable] 319 | void *child_v, *child_v2, *v; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/stream_output.c -o ViennaRNA/datastructures/stream_output.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/io/file_formats.c -o ViennaRNA/io/file_formats.o ViennaRNA/io/file_formats.c: In function 'vrna_file_helixlist': ViennaRNA/io/file_formats.c:83:9: warning: variable 'out' set but not used [-Wunused-but-set-variable] 83 | FILE *out; | ^~~ ViennaRNA/io/file_formats.c:80:15: warning: unused variable 's' [-Wunused-variable] 80 | int s; | ^ ViennaRNA/io/file_formats.c: In function 'vrna_file_connect': ViennaRNA/io/file_formats.c:104:7: warning: unused variable 'i' [-Wunused-variable] 104 | int i, power_d; | ^ ViennaRNA/io/file_formats.c: In function 'vrna_file_bpseq': ViennaRNA/io/file_formats.c:142:7: warning: unused variable 'i' [-Wunused-variable] 142 | int i; | ^ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/landscape/findpath.c -o ViennaRNA/landscape/findpath.o ViennaRNA/landscape/findpath.c: In function 'vrna_path_direct_ub': ViennaRNA/landscape/findpath.c:451:34: warning: unused variable 'd' [-Wunused-variable] 451 | int E, d; | ^ ViennaRNA/landscape/findpath.c:451:31: warning: unused variable 'E' [-Wunused-variable] 451 | int E, d; | ^ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/landscape/move.c -o ViennaRNA/landscape/move.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/landscape/neighbor.c -o ViennaRNA/landscape/neighbor.o ViennaRNA/landscape/neighbor.c: In function 'generate_local_nb_insertion': ViennaRNA/landscape/neighbor.c:2527:20: warning: unused variable 'j' [-Wunused-variable] 2527 | int i, j; | ^ ViennaRNA/landscape/neighbor.c: In function 'generate_conflicts_local_nb_insertion': ViennaRNA/landscape/neighbor.c:2879:20: warning: unused variable 'j' [-Wunused-variable] 2879 | int i, j; | ^ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/io/io_utils.c -o ViennaRNA/io/io_utils.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external.c -o ViennaRNA/loops/external.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal.c -o ViennaRNA/loops/internal.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external_bt.c -o ViennaRNA/loops/external_bt.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin_pf.c -o ViennaRNA/loops/hairpin_pf.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal_bt.c -o ViennaRNA/loops/internal_bt.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch_pf.c -o ViennaRNA/loops/multibranch_pf.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin.c -o ViennaRNA/loops/hairpin.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch.c -o ViennaRNA/loops/multibranch.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external_pf.c -o ViennaRNA/loops/external_pf.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin_bt.c -o ViennaRNA/loops/hairpin_bt.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal_pf.c -o ViennaRNA/loops/internal_pf.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch_bt.c -o ViennaRNA/loops/multibranch_bt.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/params/default.c -o ViennaRNA/params/default.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/params/io.c -o ViennaRNA/params/io.o ViennaRNA/params/io.c: In function 'rd_1dim_slice': ViennaRNA/params/io.c:782:9: warning: variable 'cp' set but not used [-Wunused-but-set-variable] 782 | char *cp; | ^~ ViennaRNA/params/io.c: At top level: ViennaRNA/params/io.c:967:1: warning: 'rd_6dim' defined but not used [-Wunused-function] 967 | rd_6dim(char **content, | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/params/params.c -o ViennaRNA/params/params.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/search/BoyerMoore.c -o ViennaRNA/search/BoyerMoore.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/2Dfold.c -o ViennaRNA/2Dfold.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/part_func.c -o ViennaRNA/part_func.o ViennaRNA/part_func.c: In function 'vrna_pf_dimer': ViennaRNA/part_func.c:263:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 263 | if (n > 1600) | ^ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/snofold.c -o ViennaRNA/snofold.o ViennaRNA/snofold.c: In function 'snofold': ViennaRNA/snofold.c:360:30: warning: variable 'bonus_cnt' set but not used [-Wunused-but-set-variable] 360 | int length, energy, bonus, bonus_cnt, s; | ^~~~~~~~~ ViennaRNA/snofold.c:360:23: warning: variable 'bonus' set but not used [-Wunused-but-set-variable] 360 | int length, energy, bonus, bonus_cnt, s; | ^~~~~ ViennaRNA/snofold.c: In function 'alifill_arrays': ViennaRNA/snofold.c:587:7: warning: variable 'bonus' set but not used [-Wunused-but-set-variable] 587 | int bonus, n_seq, s; | ^~~~~ ViennaRNA/snofold.c: In function 'alibacktrack': ViennaRNA/snofold.c:747:34: warning: variable 'j1' set but not used [-Wunused-but-set-variable] 747 | int ml, ss, cij, traced, i1, j1, p, q; | ^~ ViennaRNA/snofold.c:747:30: warning: variable 'i1' set but not used [-Wunused-but-set-variable] 747 | int ml, ss, cij, traced, i1, j1, p, q; | ^~ ViennaRNA/snofold.c:734:7: warning: variable 'bonus' set but not used [-Wunused-but-set-variable] 734 | int bonus, n_seq, *type; | ^~~~~ ViennaRNA/snofold.c: In function 'backtrack': ViennaRNA/snofold.c:1097:30: warning: variable 'j1' set but not used [-Wunused-but-set-variable] 1097 | int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q; | ^~ ViennaRNA/snofold.c:1097:26: warning: variable 'i1' set but not used [-Wunused-but-set-variable] 1097 | int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q; | ^~ ViennaRNA/snofold.c: At top level: ViennaRNA/snofold.c:153:15: warning: 'alpha' defined but not used [-Wunused-variable] 153 | PRIVATE char alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz"; | ^~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/2Dpfold.c -o ViennaRNA/2Dpfold.o ViennaRNA/2Dpfold.c: In function 'pf2D_linear': ViennaRNA/2Dpfold.c:4163:32: warning: 'l_max_post' may be used uninitialized [-Wmaybe-uninitialized] 4163 | (*max_l)[d1] = MAX2((*max_l)[d1], d2); | ^ ViennaRNA/2Dpfold.c:967:49: note: 'l_max_post' was declared here 967 | int k_min_post, k_max_post, *l_min_post, *l_max_post; | ^~~~~~~~~~ ViennaRNA/2Dpfold.c:4162:32: warning: 'l_min_post' may be used uninitialized [-Wmaybe-uninitialized] 4162 | (*min_l)[d1] = MIN2((*min_l)[d1], d2); | ^ ViennaRNA/2Dpfold.c:967:36: note: 'l_min_post' was declared here 967 | int k_min_post, k_max_post, *l_min_post, *l_max_post; | ^~~~~~~~~~ ViennaRNA/2Dpfold.c:4163:32: warning: 'l_max_post_m' may be used uninitialized [-Wmaybe-uninitialized] 4163 | (*max_l)[d1] = MAX2((*max_l)[d1], d2); | ^ ViennaRNA/2Dpfold.c:665:55: note: 'l_max_post_m' was declared here 665 | int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m; | ^~~~~~~~~~~~ ViennaRNA/2Dpfold.c:4162:32: warning: 'l_min_post_m' may be used uninitialized [-Wmaybe-uninitialized] 4162 | (*min_l)[d1] = MIN2((*min_l)[d1], d2); | ^ ViennaRNA/2Dpfold.c:665:40: note: 'l_min_post_m' was declared here 665 | int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m; | ^~~~~~~~~~~~ ViennaRNA/2Dpfold.c:4163:32: warning: 'l_max_post_b' may be used uninitialized [-Wmaybe-uninitialized] 4163 | (*max_l)[d1] = MAX2((*max_l)[d1], d2); | ^ ViennaRNA/2Dpfold.c:446:57: note: 'l_max_post_b' was declared here 446 | int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b; | ^~~~~~~~~~~~ ViennaRNA/2Dpfold.c:4162:32: warning: 'l_min_post_b' may be used uninitialized [-Wmaybe-uninitialized] 4162 | (*min_l)[d1] = MIN2((*min_l)[d1], d2); | ^ ViennaRNA/2Dpfold.c:446:42: note: 'l_min_post_b' was declared here 446 | int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b; | ^~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/boltzmann_sampling.c -o ViennaRNA/boltzmann_sampling.o In file included from ViennaRNA/boltzmann_sampling.c:32: ../src/ViennaRNA/data_structures_nonred.inc: In function 'free_all_nrll': ../src/ViennaRNA/data_structures_nonred.inc:1153:7: warning: unused variable 'i' [-Wunused-variable] 1153 | int i; | ^ ViennaRNA/boltzmann_sampling.c: In function 'backtrack_ext_loop': ViennaRNA/boltzmann_sampling.c:428:70: warning: variable 'q1k' set but not used [-Wunused-but-set-variable] 428 | FLT_OR_DBL r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale; | ^~~ ViennaRNA/boltzmann_sampling.c:428:61: warning: variable 'q' set but not used [-Wunused-but-set-variable] 428 | FLT_OR_DBL r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale; | ^ ViennaRNA/boltzmann_sampling.c:427:50: warning: unused variable 'u' [-Wunused-variable] 427 | int ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext; | ^ ViennaRNA/boltzmann_sampling.c:427:47: warning: unused variable 'k' [-Wunused-variable] 427 | int ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext; | ^ ViennaRNA/boltzmann_sampling.c: In function 'backtrack_qm': ViennaRNA/boltzmann_sampling.c:826:40: warning: variable 'span' set but not used [-Wunused-but-set-variable] 826 | int k, u, cnt, span, turn, is_unpaired, *my_iindx, *jindx, *hc_up_ml, ret; | ^~~~ ViennaRNA/boltzmann_sampling.c: In function 'backtrack': ViennaRNA/boltzmann_sampling.c:1434:25: warning: 'type' may be used uninitialized [-Wmaybe-uninitialized] 1434 | q_temp *= exp_E_IntLoop(u1, | ^~~~~~~~~~~~~~~~~ 1435 | u2, | ~~~ 1436 | type, | ~~~~~ 1437 | type_2, | ~~~~~~~ 1438 | S1[i + 1], | ~~~~~~~~~~ 1439 | S1[j - 1], | ~~~~~~~~~~ 1440 | S1[k - 1], | ~~~~~~~~~~ 1441 | S1[l + 1], | ~~~~~~~~~~ 1442 | pf_params); | ~~~~~~~~~~ ViennaRNA/boltzmann_sampling.c:1253:49: note: 'type' was declared here 1253 | unsigned int **a2s, s, n_seq, n, type, type_2, *types, u1_local, u2_local; | ^~~~ In function 'pbacktrack_circ', inlined from 'vrna_pbacktrack5_resume_cb' at ViennaRNA/boltzmann_sampling.c:238:11: ViennaRNA/boltzmann_sampling.c:1786:32: warning: 'type' may be used uninitialized [-Wmaybe-uninitialized] 1786 | q_temp *= exp_E_IntLoop(ln2 + ln3, | ^~~~~~~~~~~~~~~~~~~~~~~~ 1787 | ln1, | ~~~~ 1788 | type2, | ~~~~~~ 1789 | type, | ~~~~~ 1790 | S1[l + 1], | ~~~~~~~~~~ 1791 | S1[k - 1], | ~~~~~~~~~~ 1792 | S1[i - 1], | ~~~~~~~~~~ 1793 | S1[j + 1], | ~~~~~~~~~~ 1794 | pf_params); | ~~~~~~~~~~ ViennaRNA/boltzmann_sampling.c: In function 'vrna_pbacktrack5_resume_cb': ViennaRNA/boltzmann_sampling.c:1651:29: note: 'type' was declared here 1651 | unsigned int type, type2, *tt, s, n_seq, **a2s, u1_local, | ^~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/dist_vars.c -o ViennaRNA/dist_vars.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/part_func_up.c -o ViennaRNA/part_func_up.o ViennaRNA/part_func_up.c: In function 'pf_interact': ViennaRNA/part_func_up.c:911:69: warning: 'p_c2_S' may be used uninitialized [-Wmaybe-uninitialized] 911 | tt = qint_4[i][j][a][b] * p_c_S[add_i5][add_i3] * p_c2_S[j][b] * scalew * rev_d; | ^ ViennaRNA/part_func_up.c:594:49: note: 'p_c2_S' was declared here 594 | double temp, Z, rev_d, E, Z2, **p_c_S, **p_c2_S, int_scale; | ^~~~~~ ViennaRNA/part_func_up.c: In function 'Up_plot': ViennaRNA/part_func_up.c:1615:10: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] 1615 | return ret; | ^~~ ViennaRNA/part_func_up.c:1587:11: note: 'ret' was declared here 1587 | int ret; | ^~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/special_const.c -o ViennaRNA/special_const.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/bs_wrappers.c -o ViennaRNA/bs_wrappers.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/dp_matrices.c -o ViennaRNA/dp_matrices.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/c_plex.c -o ViennaRNA/c_plex.o ViennaRNA/c_plex.c: In function 'duplexfold_CXS': ViennaRNA/c_plex.c:347:41: warning: variable 'bonus_x' set but not used [-Wunused-but-set-variable] 347 | int dx_5, dx_3, dy_5, dy_3, dGx, dGy, bonus_x; | ^~~~~~~ ViennaRNA/c_plex.c: In function 'find_max_CXS': ViennaRNA/c_plex.c:866:13: warning: variable 'max' set but not used [-Wunused-but-set-variable] 866 | int max; | ^~~ ViennaRNA/c_plex.c:864:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable] 864 | int max_pos_j; | ^~~~~~~~~ ViennaRNA/c_plex.c: In function 'duplexfold_C': ViennaRNA/c_plex.c:982:19: warning: variable 'l1' set but not used [-Wunused-but-set-variable] 982 | int i, j, l1, Emin = INF, i_min = 0, j_min = 0; | ^~ ViennaRNA/c_plex.c: In function 'find_max_C': ViennaRNA/c_plex.c:1528:13: warning: variable 'max' set but not used [-Wunused-but-set-variable] 1528 | int max; | ^~~ ViennaRNA/c_plex.c:1526:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable] 1526 | int max_pos_j; | ^~~~~~~~~ ViennaRNA/c_plex.c: In function 'Lduplexfold_CXS': ViennaRNA/c_plex.c:947:54: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized] 947 | int end_q = MIN2(n2 - 9, max_pos_j + alignment_length - 2); | ^ ViennaRNA/c_plex.c:517:13: note: 'max_pos_j' was declared here 517 | int max_pos_j; | ^~~~~~~~~ In function 'plot_max_CXS', inlined from 'Lduplexfold_CXS' at ViennaRNA/c_plex.c:804:5: ViennaRNA/c_plex.c:948:72: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized] 948 | char *s3 = (char *)vrna_alloc(sizeof(char) * (end_t - begin_t + 2)); | ~~~~~~^~~~~~~~~ ViennaRNA/c_plex.c: In function 'Lduplexfold_CXS': ViennaRNA/c_plex.c:516:13: note: 'max_pos' was declared here 516 | int max_pos; /* get position of the best hit */ | ^~~~~~~ ViennaRNA/c_plex.c:780:27: warning: 'min_j_colonne' may be used uninitialized [-Wmaybe-uninitialized] 780 | position_j[i + delta] = min_j_colonne; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ ViennaRNA/c_plex.c:519:13: note: 'min_j_colonne' was declared here 519 | int min_j_colonne; | ^~~~~~~~~~~~~ ViennaRNA/c_plex.c: In function 'Lduplexfold_C': ViennaRNA/c_plex.c:1602:55: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized] 1602 | int end_t = MIN2(n1 - 10, max_pos + 1); | ^ ViennaRNA/c_plex.c:1235:7: note: 'max_pos' was declared here 1235 | int max_pos; /* get position of the best hit */ | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_window.c -o ViennaRNA/mfe_window.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/perturbation_fold.c -o ViennaRNA/perturbation_fold.o ViennaRNA/perturbation_fold.c: In function 'pairing_probabilities_from_sampling': ViennaRNA/perturbation_fold.c:212:25: warning: unused variable 's' [-Wunused-variable] 212 | int length, i, j, s; | ^ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/subopt.c -o ViennaRNA/subopt.o ViennaRNA/subopt.c: In function 'vrna_subopt_cb': ViennaRNA/subopt.c:833:28: warning: variable 'se' set but not used [-Wunused-but-set-variable] 833 | unsigned int *so, *ss, *se; | ^~ ViennaRNA/subopt.c: At top level: ViennaRNA/subopt.c:429:1: warning: 'print_stack' defined but not used [-Wunused-function] 429 | print_stack(LIST *list) | ^~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/equilibrium_probs.c -o ViennaRNA/equilibrium_probs.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_window_wrappers.c -o ViennaRNA/mfe_window_wrappers.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/pf_fold.c -o ViennaRNA/pf_fold.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/eval.c -o ViennaRNA/eval.o ViennaRNA/eval.c: In function 'vrna_eval_loop_pt_v': ViennaRNA/eval.c:245:28: warning: variable 'ss' set but not used [-Wunused-but-set-variable] 245 | unsigned int *sn, *so, *ss; | ^~ ViennaRNA/eval.c:245:23: warning: variable 'so' set but not used [-Wunused-but-set-variable] 245 | unsigned int *sn, *so, *ss; | ^~ ViennaRNA/eval.c: In function 'en_corr_of_loop_gquad': ViennaRNA/eval.c:697:18: warning: variable 'sequence' set but not used [-Wunused-but-set-variable] 697 | char *sequence; | ^~~~~~~~ ViennaRNA/eval.c: In function 'stack_energy': ViennaRNA/eval.c:882:18: warning: variable 'string' set but not used [-Wunused-but-set-variable] 882 | char *string; | ^~~~~~ ViennaRNA/eval.c:880:28: warning: variable 'ss' set but not used [-Wunused-but-set-variable] 880 | unsigned int *sn, *so, *ss; | ^~ ViennaRNA/eval.c:880:23: warning: variable 'so' set but not used [-Wunused-but-set-variable] 880 | unsigned int *sn, *so, *ss; | ^~ ViennaRNA/eval.c: In function 'en_corr_of_loop_gquad_ali': ViennaRNA/eval.c:1822:18: warning: unused variable 'sequence' [-Wunused-variable] 1822 | char *sequence = vc->cons_seq; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_wrappers.c -o ViennaRNA/mfe_wrappers.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/plex.c -o ViennaRNA/plex.o ViennaRNA/plex.c: In function 'duplexfold_XS': ViennaRNA/plex.c:425:41: warning: variable 'bonus_x' set but not used [-Wunused-but-set-variable] 425 | int dx_5, dx_3, dy_5, dy_3, dGx, dGy, bonus_x; | ^~~~~~~ ViennaRNA/plex.c: In function 'fduplexfold_XS': ViennaRNA/plex.c:748:11: warning: unused variable 'jdiff' [-Wunused-variable] 748 | int jdiff = j_pos + j - 11; | ^~~~~ ViennaRNA/plex.c:996:7: warning: variable 'endy' set but not used [-Wunused-but-set-variable] 996 | int endy; | ^~~~ ViennaRNA/plex.c:994:7: warning: variable 'endx' set but not used [-Wunused-but-set-variable] 994 | int endx; | ^~~~ ViennaRNA/plex.c:613:13: warning: variable 'maxPenalty' set but not used [-Wunused-but-set-variable] 613 | int maxPenalty[4]; | ^~~~~~~~~~ ViennaRNA/plex.c: In function 'fbacktrack_XS': ViennaRNA/plex.c:1091:13: warning: variable 'maxPenalty' set but not used [-Wunused-but-set-variable] 1091 | int maxPenalty[4]; | ^~~~~~~~~~ ViennaRNA/plex.c: In function 'Lduplexfold_XS': ViennaRNA/plex.c:1922:13: warning: variable 'maxPenalty' set but not used [-Wunused-but-set-variable] 1922 | int maxPenalty[4]; | ^~~~~~~~~~ ViennaRNA/plex.c: In function 'find_max_XS': ViennaRNA/plex.c:2381:13: warning: variable 'max' set but not used [-Wunused-but-set-variable] 2381 | int max; | ^~~ ViennaRNA/plex.c:2379:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable] 2379 | int max_pos_j; | ^~~~~~~~~ ViennaRNA/plex.c:2434:15: warning: unused variable 'l1' [-Wunused-variable] 2434 | int l1 = strchr(test.structure, '&') - test.structure; | ^~ ViennaRNA/plex.c: In function 'plot_max_XS': ViennaRNA/plex.c:2545:13: warning: unused variable 'l1' [-Wunused-variable] 2545 | int l1 = strchr(test.structure, '&') - test.structure; | ^~ ViennaRNA/plex.c: In function 'duplexfold': ViennaRNA/plex.c:2583:19: warning: variable 'l1' set but not used [-Wunused-but-set-variable] 2583 | int i, j, l1, Emin = INF, i_min = 0, j_min = 0; | ^~ ViennaRNA/plex.c: In function 'fduplexfold': ViennaRNA/plex.c:2770:39: warning: variable 'l1' set but not used [-Wunused-but-set-variable] 2770 | int i, j, Emin, i_min, j_min, l1; | ^~ ViennaRNA/plex.c: In function 'find_max': ViennaRNA/plex.c:4075:13: warning: variable 'max' set but not used [-Wunused-but-set-variable] 4075 | int max; | ^~~ ViennaRNA/plex.c:4073:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable] 4073 | int max_pos_j; | ^~~~~~~~~ ViennaRNA/plex.c:4117:15: warning: unused variable 'l1' [-Wunused-variable] 4117 | int l1 = strchr(test.structure, '&') - test.structure; | ^~ ViennaRNA/plex.c:4239:15: warning: unused variable 'l1' [-Wunused-variable] 4239 | int l1 = strchr(test.structure, '&') - test.structure; | ^~ ViennaRNA/plex.c: In function 'plot_max': ViennaRNA/plex.c:4287:13: warning: unused variable 'l1' [-Wunused-variable] 4287 | int l1 = strchr(test.structure, '&') - test.structure; | ^~ ViennaRNA/plex.c:4306:9: warning: unused variable 'l1' [-Wunused-variable] 4306 | int l1 = strchr(test.structure, '&') - test.structure; | ^~ In file included from ViennaRNA/plex.c:43: ../src/ViennaRNA/utils/basic.h: In function 'fduplexfold': ../src/ViennaRNA/utils/basic.h:121:42: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized] 121 | #define MAX2(A, B) ((A) > (B) ? (A) : (B)) | ^ ViennaRNA/plex.c:2781:13: note: 'max_pos_j' was declared here 2781 | int max_pos_j; | ^~~~~~~~~ In function 'fbacktrack', inlined from 'fduplexfold' at ViennaRNA/plex.c:3029:11: ViennaRNA/plex.c:3101:20: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized] 3101 | type = pair[S1[i]][S2[j]]; | ^ ViennaRNA/plex.c: In function 'fduplexfold': ViennaRNA/plex.c:2780:13: note: 'max_pos' was declared here 2780 | int max_pos; /* get position of the best hit */ | ^~~~~~~ ViennaRNA/plex.c: In function 'fduplexfold_XS': ViennaRNA/plex.c:1009:10: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized] 1009 | j_min--; | ~~~~~^~ ViennaRNA/plex.c:608:13: note: 'max_pos_j' was declared here 608 | int max_pos_j; | ^~~~~~~~~ In function 'fbacktrack_XS', inlined from 'fduplexfold_XS' at ViennaRNA/plex.c:975:11: ViennaRNA/plex.c:1110:20: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized] 1110 | type = pair[S1[i]][S2[j]]; | ^ ViennaRNA/plex.c: In function 'fduplexfold_XS': ViennaRNA/plex.c:607:13: note: 'max_pos' was declared here 607 | int max_pos; /* get position of the best hit */ | ^~~~~~~ ViennaRNA/plex.c: In function 'Lduplexfold_XS': ViennaRNA/plex.c:2298:27: warning: 'min_j_colonne' may be used uninitialized [-Wmaybe-uninitialized] 2298 | position_j[i + delta] = min_j_colonne; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ ViennaRNA/plex.c:1918:13: note: 'min_j_colonne' was declared here 1918 | int min_j_colonne; | ^~~~~~~~~~~~~ ViennaRNA/plex.c: In function 'Lduplexfold': ViennaRNA/plex.c:3999:27: warning: 'min_j_colonne' may be used uninitialized [-Wmaybe-uninitialized] 3999 | position_j[i + delta] = min_j_colonne; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ ViennaRNA/plex.c:3698:13: note: 'min_j_colonne' was declared here 3698 | int min_j_colonne; | ^~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/eval_wrappers.c -o ViennaRNA/eval_wrappers.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mm.c -o ViennaRNA/mm.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/plex_functions.c -o ViennaRNA/plex_functions.o In function 'backtrack_XS', inlined from 'duplexfold_XS' at ViennaRNA/plex_functions.c:201:15, inlined from 'PKLduplexfold_XS' at ViennaRNA/plex_functions.c:349:3: ViennaRNA/plex_functions.c:303:12: warning: 'type2' may be used uninitialized [-Wmaybe-uninitialized] 303 | E -= vrna_E_ext_stem(type2, ((k < i) ? SS1[k + 1] : -1), ((l > j - 1) ? SS1[l - 1] : -1), P); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ViennaRNA/plex_functions.c: In function 'PKLduplexfold_XS': ViennaRNA/plex_functions.c:253:21: note: 'type2' was declared here 253 | int p, q, type, type2, E, traced, i0, j0; | ^~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/units.c -o ViennaRNA/units.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ali_plex.c -o ViennaRNA/ali_plex.o ViennaRNA/ali_plex.c: In function 'alifind_max': ViennaRNA/ali_plex.c:850:13: warning: variable 'max' set but not used [-Wunused-but-set-variable] 850 | int max; | ^~~ ViennaRNA/ali_plex.c:848:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable] 848 | int max_pos_j; | ^~~~~~~~~ ViennaRNA/ali_plex.c:891:15: warning: unused variable 'l1' [-Wunused-variable] 891 | int l1 = strchr(test.structure, '&') - test.structure; | ^~ ViennaRNA/ali_plex.c: In function 'aliplot_max': ViennaRNA/ali_plex.c:944:13: warning: unused variable 'l1' [-Wunused-variable] 944 | int l1 = strchr(test.structure, '&') - test.structure; | ^~ ViennaRNA/ali_plex.c: In function 'aliLduplexfold': ViennaRNA/ali_plex.c:928:43: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized] 928 | int end_q = MIN2(n2 - 10, max_pos_j + alignment_length - 1); | ^ ViennaRNA/ali_plex.c:456:9: note: 'max_pos_j' was declared here 456 | int max_pos_j; | ^~~~~~~~~ ViennaRNA/ali_plex.c:925:38: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized] 925 | int begin_t = MAX2(11, max_pos - alignment_length + 1); | ^ ViennaRNA/ali_plex.c:455:9: note: 'max_pos' was declared here 455 | int max_pos; /* get position of the best hit */ | ^~~~~~~ ViennaRNA/ali_plex.c:777:27: warning: 'min_j_colonne' may be used uninitialized [-Wmaybe-uninitialized] 777 | position_j[i + delta] = min_j_colonne; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ ViennaRNA/ali_plex.c:458:9: note: 'min_j_colonne' was declared here 458 | int min_j_colonne; | ^~~~~~~~~~~~~ ViennaRNA/ali_plex.c: In function 'aliLduplexfold_XS': ViennaRNA/ali_plex.c:1770:45: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized] 1770 | int end_q = MIN2(n2 - 10, max_pos_j + alignment_length - 1); | ^ ViennaRNA/ali_plex.c:1261:9: note: 'max_pos_j' was declared here 1261 | int max_pos_j; | ^~~~~~~~~ ViennaRNA/ali_plex.c:1767:38: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized] 1767 | int begin_t = MAX2(11, max_pos - alignment_length); /* only get the position that binds.. */ | ^ ViennaRNA/ali_plex.c:1260:9: note: 'max_pos' was declared here 1260 | int max_pos; /* get position of the best hit */ | ^~~~~~~ ViennaRNA/ali_plex.c:1601:27: warning: 'min_j_colonne' may be used uninitialized [-Wmaybe-uninitialized] 1601 | position_j[i + delta] = min_j_colonne; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ ViennaRNA/ali_plex.c:1263:9: note: 'min_j_colonne' was declared here 1263 | int min_j_colonne; | ^~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/combinatorics.c -o ViennaRNA/combinatorics.o ViennaRNA/combinatorics.c: In function 'vrna_rotational_symmetry_db_pos': ViennaRNA/combinatorics.c:489:7: warning: 'shifts' may be used uninitialized [-Wmaybe-uninitialized] 489 | free(shifts); | ^~~~~~~~~~~~ ViennaRNA/combinatorics.c:381:22: note: 'shifts' declared here 381 | unsigned int *shifts, s, r, i, j, ii, jj, string_permutations; | ^~~~~~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/fold.c -o ViennaRNA/fold.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/model.c -o ViennaRNA/model.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/commands.c -o ViennaRNA/commands.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/fold_compound.c -o ViennaRNA/fold_compound.o ViennaRNA/fold_compound.c: In function 'set_fold_compound': ViennaRNA/fold_compound.c:613:24: warning: unused variable 'seq2' [-Wunused-variable] 613 | char *seq, *seq2; | ^~~~ ViennaRNA/fold_compound.c:613:18: warning: unused variable 'seq' [-Wunused-variable] 613 | char *seq, *seq2; | ^~~ ViennaRNA/fold_compound.c:612:17: warning: variable 'cp' set but not used [-Wunused-but-set-variable] 612 | int cp; | ^~ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/sequence.c -o ViennaRNA/sequence.o ViennaRNA/sequence.c: In function 'set_sequence': ViennaRNA/sequence.c:529:22: warning: unused variable 'p' [-Wunused-variable] 529 | for (size_t i = 1, p = 0; i < obj->length; i++) { | ^ gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/unstructured_domains.c -o ViennaRNA/unstructured_domains.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c predict_mfe.cpp -o predict_mfe.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o C:\rtools43\x86_64-w64-mingw32.static.posix\bin\nm.exe: Warning: '.' is a directory g++ -shared -s -static-libgcc -o XNAString.dll tmp.def ./ViennaRNA/utils/cpu.o ./ViennaRNA/utils/msa_utils.o ./ViennaRNA/utils/structure_tree.o ./ViennaRNA/utils/higher_order_functions.o ./ViennaRNA/utils/string_utils.o ./ViennaRNA/utils/structure_utils.o ./ViennaRNA/utils/utils.o ./ViennaRNA/constraints/SHAPE.o ./ViennaRNA/constraints/constraints.o ./ViennaRNA/constraints/soft.o ./ViennaRNA/constraints/hard.o ./ViennaRNA/constraints/ligand.o ./ViennaRNA/datastructures/basic_datastructures.o ./ViennaRNA/datastructures/lists.o ./ViennaRNA/datastructures/char_stream.o ./ViennaRNA/datastructures/heap.o ./ViennaRNA/datastructures/stream_output.o ./ViennaRNA/io/file_formats.o ./ViennaRNA/landscape/findpath.o ./ViennaRNA/landscape/move.o ./ViennaRNA/landscape/neighbor.o ./ViennaRNA/io/io_utils.o ./ViennaRNA/loops/external.o ./ViennaRNA/loops/internal.o ./ViennaRNA/loops/external_bt.o ./ViennaRNA/loops/hairpin_pf.o ./ViennaRNA/loops/internal_bt.o ./ViennaRNA/loops/multibranch_pf.o ./ViennaRNA/loops/hairpin.o ./ViennaRNA/loops/multibranch.o ./ViennaRNA/loops/external_pf.o ./ViennaRNA/loops/hairpin_bt.o ./ViennaRNA/loops/internal_pf.o ./ViennaRNA/loops/multibranch_bt.o ./ViennaRNA/params/default.o ./ViennaRNA/params/io.o ./ViennaRNA/params/params.o ./ViennaRNA/search/BoyerMoore.o ./ViennaRNA/2Dfold.o ./ViennaRNA/concentrations.o ./ViennaRNA/gquad.o ./ViennaRNA/part_func.o ./ViennaRNA/snofold.o ./ViennaRNA/2Dpfold.o ./ViennaRNA/alphabet.o ./ViennaRNA/grammar.o ./ViennaRNA/boltzmann_sampling.o ./ViennaRNA/dist_vars.o ./ViennaRNA/part_func_up.o ./ViennaRNA/special_const.o ./ViennaRNA/Lfold.o ./ViennaRNA/bs_wrappers.o ./ViennaRNA/dp_matrices.o ./ViennaRNA/mfe.o ./ViennaRNA/MEA.o ./ViennaRNA/c_plex.o ./ViennaRNA/duplex.o ./ViennaRNA/mfe_window.o ./ViennaRNA/perturbation_fold.o ./ViennaRNA/subopt.o ./ViennaRNA/ProfileAln.o ./ViennaRNA/centroid.o ./ViennaRNA/equilibrium_probs.o ./ViennaRNA/mfe_window_wrappers.o ./ViennaRNA/pf_fold.o ./ViennaRNA/cofold.o ./ViennaRNA/eval.o ./ViennaRNA/mfe_wrappers.o ./ViennaRNA/plex.o ./ViennaRNA/RNAstruct.o ./ViennaRNA/eval_wrappers.o ./ViennaRNA/mm.o ./ViennaRNA/plex_functions.o ./ViennaRNA/units.o ./ViennaRNA/ali_plex.o ./ViennaRNA/combinatorics.o ./ViennaRNA/fold.o ./ViennaRNA/model.o ./ViennaRNA/ribo.o ./ViennaRNA/commands.o ./ViennaRNA/fold_compound.o ./ViennaRNA/sequence.o ./ViennaRNA/unstructured_domains.o predict_mfe.o RcppExports.o -L../src -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-XNAString/00new/XNAString/libs/x64 ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading in method for 'name' with signature '"XNAString"': no definition for class "XNAString" in method for 'name<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'base' with signature '"XNAString"': no definition for class "XNAString" in method for 'base<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'sugar' with signature '"XNAString"': no definition for class "XNAString" in method for 'sugar<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'backbone' with signature '"XNAString"': no definition for class "XNAString" in method for 'backbone<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'target' with signature '"XNAString"': no definition for class "XNAString" in method for 'target<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'conjugate5' with signature '"XNAString"': no definition for class "XNAString" in method for 'conjugate5<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'conjugate3' with signature '"XNAString"': no definition for class "XNAString" in method for 'conjugate3<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'dictionary' with signature '"XNAString"': no definition for class "XNAString" in method for 'dictionary<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'secondary_structure' with signature '"XNAString"': no definition for class "XNAString" in method for 'secondary_structure<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'compl_dictionary' with signature '"XNAString"': no definition for class "XNAString" in method for 'compl_dictionary<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'duplex_structure' with signature '"XNAString"': no definition for class "XNAString" in method for 'duplex_structure<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'default_sugar' with signature '"XNAString"': no definition for class "XNAString" in method for 'default_sugar<-' with signature '"XNAString"': no definition for class "XNAString" in method for 'default_backbone' with signature '"XNAString"': no definition for class "XNAString" in method for 'default_backbone<-' with signature '"XNAString"': no definition for class "XNAString" Creating a new generic function for 'objects' in package 'XNAString' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XNAString)