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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL XNAString
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* 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)