##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XNAString.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XNAString_1.2.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/XNAString.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XNAString/DESCRIPTION’ ... OK
* this is package ‘XNAString’ version ‘1.2.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘XNAString’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XNAString/libs/XNAString.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/XNAString.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL XNAString
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘XNAString’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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')
  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')
  if (method == 'D') {
      ~~~~~~ ^  ~~~
ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer ('char *' and 'int')
  } 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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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:229:38: 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:229:16: warning: unused variable 'old_size' [-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:437:17: warning: unused variable 'p' [-Wunused-variable]
  int           p;
                ^
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:476:17: warning: unused variable 'n' [-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: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: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: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:1010:79: 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:1009:27: warning: unused variable 'type' [-Wunused-variable]
  unsigned char   option, type;
                          ^
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:1011:25: warning: unused variable 'ij' [-Wunused-variable]
  int             *idx, ij;
                        ^
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: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;
                      ^
21 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/datastructures/char_stream.c -o ViennaRNA/datastructures/char_stream.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/datastructures/stream_output.c -o ViennaRNA/datastructures/stream_output.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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: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;
      ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/landscape/findpath.c -o ViennaRNA/landscape/findpath.o
ViennaRNA/landscape/findpath.c:451:34: warning: unused variable 'd' [-Wunused-variable]
  int                         E, d;
                                 ^
ViennaRNA/landscape/findpath.c:451:31: warning: unused variable 'E' [-Wunused-variable]
  int                         E, d;
                              ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/landscape/move.c -o ViennaRNA/landscape/move.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/io/io_utils.c -o ViennaRNA/io/io_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/internal.c -o ViennaRNA/loops/internal.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/external_bt.c -o ViennaRNA/loops/external_bt.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/hairpin_pf.c -o ViennaRNA/loops/hairpin_pf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/internal_bt.c -o ViennaRNA/loops/internal_bt.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/hairpin.c -o ViennaRNA/loops/hairpin.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/multibranch.c -o ViennaRNA/loops/multibranch.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/external_pf.c -o ViennaRNA/loops/external_pf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/hairpin_bt.c -o ViennaRNA/loops/hairpin_bt.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/internal_pf.c -o ViennaRNA/loops/internal_pf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/loops/multibranch_bt.c -o ViennaRNA/loops/multibranch_bt.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/params/default.c -o ViennaRNA/params/default.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/params/io.c -o ViennaRNA/params/io.o
ViennaRNA/params/io.c:967:1: warning: unused function 'rd_6dim' [-Wunused-function]
rd_6dim(char    **content,
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/params/params.c -o ViennaRNA/params/params.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/search/BoyerMoore.c -o ViennaRNA/search/BoyerMoore.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/snofold.c -o ViennaRNA/snofold.o
ViennaRNA/snofold.c:153:15: warning: unused variable 'alpha' [-Wunused-variable]
PRIVATE char  alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
              ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/2Dpfold.c -o ViennaRNA/2Dpfold.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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;
                                              ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/dist_vars.c -o ViennaRNA/dist_vars.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/part_func_up.c -o ViennaRNA/part_func_up.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/special_const.c -o ViennaRNA/special_const.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/bs_wrappers.c -o ViennaRNA/bs_wrappers.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/dp_matrices.c -o ViennaRNA/dp_matrices.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/c_plex.c -o ViennaRNA/c_plex.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/mfe_window.c -o ViennaRNA/mfe_window.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/subopt.c -o ViennaRNA/subopt.o
ViennaRNA/subopt.c:429:1: warning: unused function 'print_stack' [-Wunused-function]
print_stack(LIST *list)
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/mfe_window_wrappers.c -o ViennaRNA/mfe_window_wrappers.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/pf_fold.c -o ViennaRNA/pf_fold.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/eval.c -o ViennaRNA/eval.o
ViennaRNA/eval.c:1822:18: warning: unused variable 'sequence' [-Wunused-variable]
  char          *sequence     = vc->cons_seq;
                 ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/mfe_wrappers.c -o ViennaRNA/mfe_wrappers.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/plex.c -o ViennaRNA/plex.o
ViennaRNA/plex.c:748:11: warning: unused variable 'jdiff' [-Wunused-variable]
      int jdiff = j_pos + j - 11;
          ^
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: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;
        ^
7 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/eval_wrappers.c -o ViennaRNA/eval_wrappers.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/mm.c -o ViennaRNA/mm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/plex_functions.c -o ViennaRNA/plex_functions.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/units.c -o ViennaRNA/units.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/ali_plex.c -o ViennaRNA/ali_plex.o
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;
            ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/combinatorics.c -o ViennaRNA/combinatorics.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/fold.c -o ViennaRNA/fold.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/model.c -o ViennaRNA/model.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/commands.c -o ViennaRNA/commands.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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;
                 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ViennaRNA/unstructured_domains.c -o ViennaRNA/unstructured_domains.o
clang++ -mmacosx-version-min=10.13 -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/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c predict_mfe.cpp -o predict_mfe.o
clang++ -mmacosx-version-min=10.13 -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/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-XNAString/00new/XNAString/libs
** 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
** 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)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(testthat)
> library(XNAString)

Attaching package: 'XNAString'

The following object is masked from 'package:base':

    objects

> 
> test_check("XNAString")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 161 ]
> 
> proc.time()
   user  system elapsed 
102.861   5.192 108.072