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### Running command:
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### chmod a+r XNAString -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data XNAString
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* checking for file 'XNAString/DESCRIPTION' ... OK
* preparing 'XNAString':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package 'XNAString' ...
** this is package 'XNAString' version '1.15.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++11
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
ViennaRNA/datastructures/lists.c:97:1: error: conflicting types for 'lst_kill'; have 'void(LIST *, void (*)(void *))'
97 | lst_kill (LIST * l, void (*freeNode) (void *node))
| ^~~~~~~~
In file included from ViennaRNA/datastructures/lists.c:33:
../src/ViennaRNA/datastructures/lists.h:58:6: note: previous declaration of 'lst_kill' with type 'void(LIST *, void (*)(void))'
58 | void lst_kill (LIST * l, void (*freeNode) ());
| ^~~~~~~~
ViennaRNA/datastructures/lists.c:284:1: error: conflicting types for 'lst_mergesort'; have 'void(LIST *, int (*)(void *, void *))'
284 | lst_mergesort (LIST * l, int (*cmp_func) (void *, void *))
| ^~~~~~~~~~~~~
../src/ViennaRNA/datastructures/lists.h:63:6: note: previous declaration of 'lst_mergesort' with type 'void(LIST *, int (*)(void))'
63 | void lst_mergesort (LIST * l, int (*cmp_func) ());
| ^~~~~~~~~~~~~
make: *** [E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:289: ViennaRNA/datastructures/lists.o] Error 1
ERROR: compilation failed for package 'XNAString'
* removing 'E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpcxFjOz/Rinst105687fb47a82/XNAString'
-----------------------------------
ERROR: package installation failed