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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R 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 ‘1.17.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.o
ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable 'features' [-Wunused-variable]
unsigned int features = vrna_cpu_simd_capabilities();
^
ViennaRNA/utils/higher_order_functions.c:116:1: warning: unused label 'exec_fun_zip_add_min' [-Wunused-label]
exec_fun_zip_add_min:
^~~~~~~~~~~~~~~~~~~~~
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_utils.o
ViennaRNA/utils/string_utils.c:391:36: warning: unused variable 'num_strings' [-Wunused-variable]
size_t n, offset, *lengths, num_strings, mem_strings, total_length;
^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/utils.o
ViennaRNA/utils/utils.c:59:15: warning: unused variable 'scale1' [-Wunused-variable]
PRIVATE char scale1[] = "....,....1....,....2....,....3....,....4";
^
ViennaRNA/utils/utils.c:60:15: warning: unused variable 'scale2' [-Wunused-variable]
PRIVATE char scale2[] = "....,....5....,....6....,....7....,....8";
^
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/SHAPE.c -o ViennaRNA/constraints/SHAPE.o
ViennaRNA/constraints/SHAPE.c:202:10: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
method = shape_method;
^ ~~~~~~~~~~~~
ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer ('char *' and 'int') [-Wpointer-integer-compare]
vrna_file_SHAPE_read(shape_file, length, method == 'W' ? 0 : -1, sequence, values);
~~~~~~ ^ ~~~
ViennaRNA/constraints/SHAPE.c:208:14: warning: comparison between pointer and integer ('char *' and 'int') [-Wpointer-integer-compare]
if (method == 'D') {
~~~~~~ ^ ~~~
ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer ('char *' and 'int') [-Wpointer-integer-compare]
} else if (method == 'Z') {
~~~~~~ ^ ~~~
ViennaRNA/constraints/SHAPE.c:209:64: warning: variable 'p1' is uninitialized when used here [-Wuninitialized]
(void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
^~
ViennaRNA/constraints/SHAPE.c:196:13: note: initialize the variable 'p1' to silence this warning
float p1, p2;
^
= 0.0
ViennaRNA/constraints/SHAPE.c:209:68: warning: variable 'p2' is uninitialized when used here [-Wuninitialized]
(void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
^~
ViennaRNA/constraints/SHAPE.c:196:17: note: initialize the variable 'p2' to silence this warning
float p1, p2;
^
= 0.0
ViennaRNA/constraints/SHAPE.c:612:15: warning: unused variable 'warning' [-Wunused-variable]
const char warning[] = "SHAPE method parameters not recognized! Using default parameters!";
^
7 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.o
In file included from ViennaRNA/constraints/hard.c:37:
ViennaRNA/constraints/hc_depot.inc:229:13: warning: unused variable 'k' [-Wunused-variable]
size_t k, old_size, next_entry, entry;
^
ViennaRNA/constraints/hc_depot.inc:229:16: warning: unused variable 'old_size' [-Wunused-variable]
size_t k, old_size, next_entry, entry;
^
ViennaRNA/constraints/hc_depot.inc:229:38: warning: unused variable 'entry' [-Wunused-variable]
size_t k, old_size, next_entry, entry;
^
ViennaRNA/constraints/hc_depot.inc:263:25: warning: unused variable 'n' [-Wunused-variable]
unsigned int s, i, n;
^
ViennaRNA/constraints/hard.c:211:20: warning: variable 'maxdist' set but not used [-Wunused-but-set-variable]
unsigned int n, maxdist;
^
ViennaRNA/constraints/hard.c:386:41: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
unsigned int i, strand, pos, n_pos, *ss, *sn;
^
ViennaRNA/constraints/hard.c:386:46: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
unsigned int i, strand, pos, n_pos, *ss, *sn;
^
ViennaRNA/constraints/hard.c:436:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
unsigned int n, strand, actual_i, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c:436:49: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, strand, actual_i, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c:437:17: warning: unused variable 'p' [-Wunused-variable]
int p;
^
ViennaRNA/constraints/hard.c:476:17: warning: unused variable 'n' [-Wunused-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:21: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:26: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:31: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:45: warning: unused variable 'k' [-Wunused-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:48: warning: unused variable 'l' [-Wunused-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:532:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
^
ViennaRNA/constraints/hard.c:532:26: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
^
ViennaRNA/constraints/hard.c:533:17: warning: unused variable 'k' [-Wunused-variable]
int k, l, ret;
^
ViennaRNA/constraints/hard.c:533:20: warning: unused variable 'l' [-Wunused-variable]
int k, l, ret;
^
ViennaRNA/constraints/hard.c:588:20: warning: unused variable 'i' [-Wunused-variable]
unsigned int i;
^
ViennaRNA/constraints/hard.c:841:20: warning: unused variable 'depot' [-Wunused-variable]
vrna_hc_depot_t *depot;
^
ViennaRNA/constraints/hard.c:1009:27: warning: unused variable 'type' [-Wunused-variable]
unsigned char option, type;
^
ViennaRNA/constraints/hard.c:1010:67: warning: unused variable 'start' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c:1010:74: warning: unused variable 'end' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c:1010:79: warning: unused variable 't_start' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c:1010:88: warning: unused variable 't_end' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c:1010:99: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c:1010:109: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c:1011:25: warning: unused variable 'ij' [-Wunused-variable]
int *idx, ij;
^
ViennaRNA/constraints/hard.c:1122:35: warning: unused variable 't1' [-Wunused-variable]
unsigned char constraint, type, t1, t2;
^
ViennaRNA/constraints/hard.c:1122:39: warning: unused variable 't2' [-Wunused-variable]
unsigned char constraint, type, t1, t2;
^
ViennaRNA/constraints/hard.c:1887:23: warning: unused variable 'u' [-Wunused-variable]
unsigned int i, n, u;
^
33 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
ViennaRNA/datastructures/lists.c:97:1: error: conflicting types for 'lst_kill'
lst_kill (LIST * l, void (*freeNode) (void *node))
^
../src/ViennaRNA/datastructures/lists.h:58:6: note: previous declaration is here
void lst_kill (LIST * l, void (*freeNode) ());
^
ViennaRNA/datastructures/lists.c:284:1: error: conflicting types for 'lst_mergesort'
lst_mergesort (LIST * l, int (*cmp_func) (void *, void *))
^
../src/ViennaRNA/datastructures/lists.h:63:6: note: previous declaration is here
void lst_mergesort (LIST * l, int (*cmp_func) ());
^
2 errors generated.
make: *** [ViennaRNA/datastructures/lists.o] Error 1
ERROR: compilation failed for package ‘XNAString’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpdxJkMv/Rinstc7f26ba68d40/XNAString’
-----------------------------------
ERROR: package installation failed