##############################################################################
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###
### Running command:
###
### rm -rf XNAString.buildbin-libdir && mkdir XNAString.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XNAString_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R XNAString.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XNAString.buildbin-libdir XNAString_1.14.0.tar.gz'
>>>>>>>
* installing *source* package ‘XNAString’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:116:1: warning: unused label 'exec_fun_zip_add_min' [-Wunused-label]
exec_fun_zip_add_min:
^~~~~~~~~~~~~~~~~~~~~
ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable 'features' [-Wunused-variable]
unsigned int features = vrna_cpu_simd_capabilities();
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:229:16: 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:229:13: warning: unused variable 'k' [-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:436:49: 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: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: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:476:45: warning: unused variable 'k' [-Wunused-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:476:48: warning: unused variable 'l' [-Wunused-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: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:533:20: warning: unused variable 'l' [-Wunused-variable]
int k, l, ret;
^
ViennaRNA/constraints/hard.c:533:17: warning: unused variable 'k' [-Wunused-variable]
int k, l, ret;
^
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: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:1010:109: 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: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:1010:79: 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:1010:67: 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: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/char_stream.c -o ViennaRNA/datastructures/char_stream.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/heap.c -o ViennaRNA/datastructures/heap.o
ViennaRNA/datastructures/heap.c:319:22: warning: unused variable 'child_v2' [-Wunused-variable]
void *child_v, *child_v2, *v;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/datastructures/stream_output.c -o ViennaRNA/datastructures/stream_output.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/io/file_formats.c -o ViennaRNA/io/file_formats.o
ViennaRNA/io/file_formats.c:80:15: warning: unused variable 's' [-Wunused-variable]
int s;
^
ViennaRNA/io/file_formats.c:83:9: warning: variable 'out' set but not used [-Wunused-but-set-variable]
FILE *out;
^
ViennaRNA/io/file_formats.c:104:7: warning: unused variable 'i' [-Wunused-variable]
int i, power_d;
^
ViennaRNA/io/file_formats.c:142:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/landscape/findpath.c -o ViennaRNA/landscape/findpath.o
ViennaRNA/landscape/findpath.c:451:31: warning: unused variable 'E' [-Wunused-variable]
int E, d;
^
ViennaRNA/landscape/findpath.c:451:34: warning: unused variable 'd' [-Wunused-variable]
int E, d;
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/landscape/move.c -o ViennaRNA/landscape/move.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/landscape/neighbor.c -o ViennaRNA/landscape/neighbor.o
ViennaRNA/landscape/neighbor.c:2527:20: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
ViennaRNA/landscape/neighbor.c:2879:20: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
ViennaRNA/landscape/neighbor.c:2498:1: warning: unused function 'deletions_range_cb' [-Wunused-function]
deletions_range_cb(vrna_fold_compound_t *fc,
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/io/io_utils.c -o ViennaRNA/io/io_utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/external.c -o ViennaRNA/loops/external.o
ViennaRNA/loops/external.c:1890:48: warning: variable 'si1' is uninitialized when used here [-Wuninitialized]
for (i = j - turn - 1; i > 1; i--, ij--, si1--) {
^~~
ViennaRNA/loops/external.c:1818:35: note: initialize the variable 'si1' to silence this warning
short *S, *si1, sj1, **SS, **S5, **S3, *s3j1, *ssj1;
^
= NULL
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/internal.c -o ViennaRNA/loops/internal.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/external_bt.c -o ViennaRNA/loops/external_bt.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/hairpin_pf.c -o ViennaRNA/loops/hairpin_pf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/internal_bt.c -o ViennaRNA/loops/internal_bt.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/multibranch_pf.c -o ViennaRNA/loops/multibranch_pf.o
ViennaRNA/loops/multibranch_pf.c:340:31: warning: variable 'kl' is uninitialized when used here [-Wuninitialized]
for (; k <= j - 1; k++, kl--)
^~
ViennaRNA/loops/multibranch_pf.c:246:38: note: initialize the variable 'kl' to silence this warning
int ij, k, kl, *my_iindx, *jindx, *rtype, tt;
^
= 0
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/hairpin.c -o ViennaRNA/loops/hairpin.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/multibranch.c -o ViennaRNA/loops/multibranch.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/external_pf.c -o ViennaRNA/loops/external_pf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/hairpin_bt.c -o ViennaRNA/loops/hairpin_bt.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/internal_pf.c -o ViennaRNA/loops/internal_pf.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/loops/multibranch_bt.c -o ViennaRNA/loops/multibranch_bt.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/params/default.c -o ViennaRNA/params/default.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/params/io.c -o ViennaRNA/params/io.o
ViennaRNA/params/io.c:782:9: warning: variable 'cp' set but not used [-Wunused-but-set-variable]
char *cp;
^
ViennaRNA/params/io.c:967:1: warning: unused function 'rd_6dim' [-Wunused-function]
rd_6dim(char **content,
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/params/params.c -o ViennaRNA/params/params.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/search/BoyerMoore.c -o ViennaRNA/search/BoyerMoore.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/2Dfold.c -o ViennaRNA/2Dfold.o
ViennaRNA/2Dfold.c:3941:1: warning: unused function 'prepareArray2' [-Wunused-function]
prepareArray2(unsigned long ***array,
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/part_func.c -o ViennaRNA/part_func.o
ViennaRNA/part_func.c:296:5: warning: add explicit braces to avoid dangling else [-Wdangling-else]
} else {
^
ViennaRNA/part_func.c:263:7: warning: variable 'X' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
if (n > 1600)
^~~~~~~~
ViennaRNA/part_func.c:323:10: note: uninitialized use occurs here
return X;
^
ViennaRNA/part_func.c:263:3: note: remove the 'if' if its condition is always true
if (n > 1600)
^~~~~~~~~~~~~
ViennaRNA/part_func.c:193:3: note: variable 'X' is declared here
vrna_dimer_pf_t X;
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/snofold.c -o ViennaRNA/snofold.o
ViennaRNA/snofold.c:360:23: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
int length, energy, bonus, bonus_cnt, s;
^
ViennaRNA/snofold.c:360:30: warning: variable 'bonus_cnt' set but not used [-Wunused-but-set-variable]
int length, energy, bonus, bonus_cnt, s;
^
ViennaRNA/snofold.c:587:7: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
int bonus, n_seq, s;
^
ViennaRNA/snofold.c:747:34: warning: variable 'j1' set but not used [-Wunused-but-set-variable]
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]
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]
int bonus, n_seq, *type;
^
ViennaRNA/snofold.c:876:7: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
int bonus;
^
ViennaRNA/snofold.c:1097:26: warning: variable 'i1' set but not used [-Wunused-but-set-variable]
int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;
^
ViennaRNA/snofold.c:1097:30: warning: variable 'j1' set but not used [-Wunused-but-set-variable]
int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;
^
ViennaRNA/snofold.c:153:15: warning: unused variable 'alpha' [-Wunused-variable]
PRIVATE char alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
^
10 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/2Dpfold.c -o ViennaRNA/2Dpfold.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -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:1153:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
ViennaRNA/boltzmann_sampling.c:427:50: warning: unused variable 'u' [-Wunused-variable]
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]
int ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext;
^
ViennaRNA/boltzmann_sampling.c:428:70: warning: variable 'q1k' set but not used [-Wunused-but-set-variable]
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]
FLT_OR_DBL r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale;
^
ViennaRNA/boltzmann_sampling.c:826:40: warning: variable 'span' set but not used [-Wunused-but-set-variable]
int k, u, cnt, span, turn, is_unpaired, *my_iindx, *jindx, *hc_up_ml, ret;
^
6 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/dist_vars.c -o ViennaRNA/dist_vars.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/part_func_up.c -o ViennaRNA/part_func_up.o
ViennaRNA/part_func_up.c:594:34: warning: variable 'Z2' set but not used [-Wunused-but-set-variable]
double temp, Z, rev_d, E, Z2, **p_c_S, **p_c2_S, int_scale;
^
ViennaRNA/part_func_up.c:601:15: warning: variable 'Z_int' set but not used [-Wunused-but-set-variable]
double Z_int, temp_int, temppfs;
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/special_const.c -o ViennaRNA/special_const.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/bs_wrappers.c -o ViennaRNA/bs_wrappers.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/dp_matrices.c -o ViennaRNA/dp_matrices.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/c_plex.c -o ViennaRNA/c_plex.o
ViennaRNA/c_plex.c:347:41: warning: variable 'bonus_x' set but not used [-Wunused-but-set-variable]
int dx_5, dx_3, dy_5, dy_3, dGx, dGy, bonus_x;
^
ViennaRNA/c_plex.c:864:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^
ViennaRNA/c_plex.c:866:13: warning: variable 'max' set but not used [-Wunused-but-set-variable]
int max;
^
ViennaRNA/c_plex.c:982:19: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
int i, j, l1, Emin = INF, i_min = 0, j_min = 0;
^
ViennaRNA/c_plex.c:1526:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^
ViennaRNA/c_plex.c:1528:13: warning: variable 'max' set but not used [-Wunused-but-set-variable]
int max;
^
6 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/mfe_window.c -o ViennaRNA/mfe_window.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/perturbation_fold.c -o ViennaRNA/perturbation_fold.o
ViennaRNA/perturbation_fold.c:212:25: warning: unused variable 's' [-Wunused-variable]
int length, i, j, s;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/subopt.c -o ViennaRNA/subopt.o
ViennaRNA/subopt.c:833:28: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int *so, *ss, *se;
^
ViennaRNA/subopt.c:429:1: warning: unused function 'print_stack' [-Wunused-function]
print_stack(LIST *list)
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/equilibrium_probs.c -o ViennaRNA/equilibrium_probs.o
ViennaRNA/equilibrium_probs.c:2428:1: warning: unused function 'ud_outside_hp_loops2' [-Wunused-function]
ud_outside_hp_loops2(vrna_fold_compound_t *vc)
^
ViennaRNA/equilibrium_probs.c:2696:1: warning: unused function 'ud_outside_int_loops2' [-Wunused-function]
ud_outside_int_loops2(vrna_fold_compound_t *vc)
^
ViennaRNA/equilibrium_probs.c:3156:1: warning: unused function 'ud_outside_mb_loops2' [-Wunused-function]
ud_outside_mb_loops2(vrna_fold_compound_t *vc)
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/mfe_window_wrappers.c -o ViennaRNA/mfe_window_wrappers.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/pf_fold.c -o ViennaRNA/pf_fold.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/eval.c -o ViennaRNA/eval.o
ViennaRNA/eval.c:245:28: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
unsigned int *sn, *so, *ss;
^
ViennaRNA/eval.c:245:23: warning: variable 'so' set but not used [-Wunused-but-set-variable]
unsigned int *sn, *so, *ss;
^
ViennaRNA/eval.c:697:18: warning: variable 'sequence' set but not used [-Wunused-but-set-variable]
char *sequence;
^
ViennaRNA/eval.c:880:23: warning: variable 'so' set but not used [-Wunused-but-set-variable]
unsigned int *sn, *so, *ss;
^
ViennaRNA/eval.c:882:18: warning: variable 'string' set but not used [-Wunused-but-set-variable]
char *string;
^
ViennaRNA/eval.c:880:28: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
unsigned int *sn, *so, *ss;
^
ViennaRNA/eval.c:1822:18: warning: unused variable 'sequence' [-Wunused-variable]
char *sequence = vc->cons_seq;
^
ViennaRNA/eval.c:2026:34: warning: variable 'up_mis' set but not used [-Wunused-but-set-variable]
int num_elem, num_g, up_mis;
^
8 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/mfe_wrappers.c -o ViennaRNA/mfe_wrappers.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/plex.c -o ViennaRNA/plex.o
ViennaRNA/plex.c:425:41: warning: variable 'bonus_x' set but not used [-Wunused-but-set-variable]
int dx_5, dx_3, dy_5, dy_3, dGx, dGy, bonus_x;
^
ViennaRNA/plex.c:748:11: warning: unused variable 'jdiff' [-Wunused-variable]
int jdiff = j_pos + j - 11;
^
ViennaRNA/plex.c:994:7: warning: variable 'endx' set but not used [-Wunused-but-set-variable]
int endx;
^
ViennaRNA/plex.c:993:7: warning: variable 'lengthx' set but not used [-Wunused-but-set-variable]
int lengthx;
^
ViennaRNA/plex.c:996:7: warning: variable 'endy' set but not used [-Wunused-but-set-variable]
int endy;
^
ViennaRNA/plex.c:2379:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^
ViennaRNA/plex.c:2381:13: warning: variable 'max' set but not used [-Wunused-but-set-variable]
int max;
^
ViennaRNA/plex.c:2434:15: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^
ViennaRNA/plex.c:2545:13: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^
ViennaRNA/plex.c:2583:19: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
int i, j, l1, Emin = INF, i_min = 0, j_min = 0;
^
ViennaRNA/plex.c:2770:39: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
int i, j, Emin, i_min, j_min, l1;
^
ViennaRNA/plex.c:4073:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^
ViennaRNA/plex.c:4075:13: warning: variable 'max' set but not used [-Wunused-but-set-variable]
int max;
^
ViennaRNA/plex.c:4117:15: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^
ViennaRNA/plex.c:4239:15: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^
ViennaRNA/plex.c:4287:13: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^
ViennaRNA/plex.c:4306:9: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^
17 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/eval_wrappers.c -o ViennaRNA/eval_wrappers.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/mm.c -o ViennaRNA/mm.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/plex_functions.c -o ViennaRNA/plex_functions.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/units.c -o ViennaRNA/units.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/ali_plex.c -o ViennaRNA/ali_plex.o
ViennaRNA/ali_plex.c:848:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^
ViennaRNA/ali_plex.c:850:13: warning: variable 'max' set but not used [-Wunused-but-set-variable]
int max;
^
ViennaRNA/ali_plex.c:891:15: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^
ViennaRNA/ali_plex.c:944:13: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/combinatorics.c -o ViennaRNA/combinatorics.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/fold.c -o ViennaRNA/fold.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/model.c -o ViennaRNA/model.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/commands.c -o ViennaRNA/commands.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/fold_compound.c -o ViennaRNA/fold_compound.o
ViennaRNA/fold_compound.c:613:24: warning: unused variable 'seq2' [-Wunused-variable]
char *seq, *seq2;
^
ViennaRNA/fold_compound.c:613:18: warning: unused variable 'seq' [-Wunused-variable]
char *seq, *seq2;
^
ViennaRNA/fold_compound.c:612:17: warning: variable 'cp' set but not used [-Wunused-but-set-variable]
int cp;
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/sequence.c -o ViennaRNA/sequence.o
ViennaRNA/sequence.c:529:22: warning: unused variable 'p' [-Wunused-variable]
for (size_t i = 1, p = 0; i < obj->length; i++) {
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ViennaRNA/unstructured_domains.c -o ViennaRNA/unstructured_domains.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c predict_mfe.cpp -o predict_mfe.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o XNAString.so ./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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/XNAString.buildbin-libdir/00LOCK-XNAString/00new/XNAString/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XNAString)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR XNAString.buildbin-libdir/XNAString/libs/XNAString.so
>>>>>>>
>>>>>>> Paths before fix:
XNAString.buildbin-libdir/XNAString/libs/XNAString.so:
XNAString.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "XNAString.buildbin-libdir/XNAString/libs/XNAString.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "XNAString.buildbin-libdir/XNAString/libs/XNAString.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "XNAString.buildbin-libdir/XNAString/libs/XNAString.so"
>>>>>>> Paths after fix:
XNAString.buildbin-libdir/XNAString/libs/XNAString.so:
XNAString.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
