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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:XNAString.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings XNAString_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/XNAString.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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 ... NOTE
  installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
* 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 ‘/home/biocbuild/bbs-3.14-bioc/R/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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/XNAString.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL XNAString
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘XNAString’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.o
ViennaRNA/utils/higher_order_functions.c: In function ‘zip_add_min_dispatcher’:
ViennaRNA/utils/higher_order_functions.c:116:1: warning: label ‘exec_fun_zip_add_min’ defined but not used [-Wunused-label]
  116 | exec_fun_zip_add_min:
      | ^~~~~~~~~~~~~~~~~~~~
ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable ‘features’ [-Wunused-variable]
   96 |   unsigned int features = vrna_cpu_simd_capabilities();
      |                ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_utils.o
ViennaRNA/utils/string_utils.c: In function ‘vrna_strjoin’:
ViennaRNA/utils/string_utils.c:391:36: warning: unused variable ‘num_strings’ [-Wunused-variable]
  391 |   size_t      n, offset, *lengths, num_strings, mem_strings, total_length;
      |                                    ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/utils.o
ViennaRNA/utils/utils.c:60:15: warning: ‘scale2’ defined but not used [-Wunused-variable]
   60 | PRIVATE char  scale2[]  = "....,....5....,....6....,....7....,....8";
      |               ^~~~~~
ViennaRNA/utils/utils.c:59:15: warning: ‘scale1’ defined but not used [-Wunused-variable]
   59 | PRIVATE char  scale1[]  = "....,....1....,....2....,....3....,....4";
      |               ^~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/constraints/SHAPE.c -o ViennaRNA/constraints/SHAPE.o
ViennaRNA/constraints/SHAPE.c: In function ‘vrna_constraints_add_SHAPE’:
ViennaRNA/constraints/SHAPE.c:202:10: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  202 |   method = shape_method;
      |          ^
ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer
  206 |   vrna_file_SHAPE_read(shape_file, length, method == 'W' ? 0 : -1, sequence, values);
      |                                                   ^~
ViennaRNA/constraints/SHAPE.c:208:14: warning: comparison between pointer and integer
  208 |   if (method == 'D') {
      |              ^~
ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer
  210 |   } else if (method == 'Z') {
      |                     ^~
ViennaRNA/constraints/SHAPE.c: In function ‘sc_parse_parameters’:
ViennaRNA/constraints/SHAPE.c:612:15: warning: unused variable ‘warning’ [-Wunused-variable]
  612 |   const char  warning[] = "SHAPE method parameters not recognized! Using default parameters!";
      |               ^~~~~~~
ViennaRNA/constraints/SHAPE.c: In function ‘vrna_constraints_add_SHAPE’:
ViennaRNA/constraints/SHAPE.c:209:11: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  209 |     (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/constraints/SHAPE.c:209:11: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.o
In file included from ViennaRNA/constraints/hard.c:37:
ViennaRNA/constraints/hc_depot.inc: In function ‘hc_depot_store_bp’:
ViennaRNA/constraints/hc_depot.inc:229:38: warning: unused variable ‘entry’ [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |                                      ^~~~~
ViennaRNA/constraints/hc_depot.inc:229:16: warning: unused variable ‘old_size’ [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |                ^~~~~~~~
ViennaRNA/constraints/hc_depot.inc:229:13: warning: unused variable ‘k’ [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |             ^
ViennaRNA/constraints/hc_depot.inc: In function ‘hc_depot_free’:
ViennaRNA/constraints/hc_depot.inc:263:25: warning: unused variable ‘n’ [-Wunused-variable]
  263 |   unsigned int    s, i, n;
      |                         ^
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_update’:
ViennaRNA/constraints/hard.c:211:20: warning: variable ‘maxdist’ set but not used [-Wunused-but-set-variable]
  211 |   unsigned int  n, maxdist;
      |                    ^~~~~~~
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_up_strand_batch’:
ViennaRNA/constraints/hard.c:386:46: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable]
  386 |   unsigned int  i, strand, pos, n_pos, *ss, *sn;
      |                                              ^~
ViennaRNA/constraints/hard.c:386:41: warning: variable ‘ss’ set but not used [-Wunused-but-set-variable]
  386 |   unsigned int  i, strand, pos, n_pos, *ss, *sn;
      |                                         ^~
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp_nonspecific’:
ViennaRNA/constraints/hard.c:437:17: warning: unused variable ‘p’ [-Wunused-variable]
  437 |   int           p;
      |                 ^
ViennaRNA/constraints/hard.c:436:49: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
  436 |   unsigned int  n, strand, actual_i, *sn, *ss, *se;
      |                                                 ^~
ViennaRNA/constraints/hard.c:436:17: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
  436 |   unsigned int  n, strand, actual_i, *sn, *ss, *se;
      |                 ^
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp_strand’:
ViennaRNA/constraints/hard.c:476:48: warning: unused variable ‘l’ [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                                                ^
ViennaRNA/constraints/hard.c:476:45: warning: unused variable ‘k’ [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                                             ^
ViennaRNA/constraints/hard.c:476:31: warning: variable ‘ss’ set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                               ^~
ViennaRNA/constraints/hard.c:476:26: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                          ^~
ViennaRNA/constraints/hard.c:476:21: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                     ^~
ViennaRNA/constraints/hard.c:476:17: warning: unused variable ‘n’ [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                 ^
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp’:
ViennaRNA/constraints/hard.c:533:20: warning: unused variable ‘l’ [-Wunused-variable]
  533 |   int           k, l, ret;
      |                    ^
ViennaRNA/constraints/hard.c:533:17: warning: unused variable ‘k’ [-Wunused-variable]
  533 |   int           k, l, ret;
      |                 ^
ViennaRNA/constraints/hard.c:532:26: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
  532 |   unsigned int  n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
      |                          ^~
ViennaRNA/constraints/hard.c:532:17: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
  532 |   unsigned int  n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
      |                 ^
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_free’:
ViennaRNA/constraints/hard.c:588:20: warning: unused variable ‘i’ [-Wunused-variable]
  588 |       unsigned int i;
      |                    ^
ViennaRNA/constraints/hard.c: In function ‘default_hc_up’:
ViennaRNA/constraints/hard.c:841:20: warning: unused variable ‘depot’ [-Wunused-variable]
  841 |   vrna_hc_depot_t *depot;
      |                    ^~~~~
ViennaRNA/constraints/hard.c: In function ‘prepare_hc_bp’:
ViennaRNA/constraints/hard.c:1011:25: warning: unused variable ‘ij’ [-Wunused-variable]
 1011 |   int             *idx, ij;
      |                         ^~
ViennaRNA/constraints/hard.c:1010:109: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                                             ^~
ViennaRNA/constraints/hard.c:1010:99: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                                   ^~
ViennaRNA/constraints/hard.c:1010:88: warning: unused variable ‘t_end’ [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                        ^~~~~
ViennaRNA/constraints/hard.c:1010:79: warning: unused variable ‘t_start’ [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                               ^~~~~~~
ViennaRNA/constraints/hard.c:1010:74: warning: unused variable ‘end’ [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                          ^~~
ViennaRNA/constraints/hard.c:1010:67: warning: unused variable ‘start’ [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                   ^~~~~
ViennaRNA/constraints/hard.c:1009:27: warning: unused variable ‘type’ [-Wunused-variable]
 1009 |   unsigned char   option, type;
      |                           ^~~~
ViennaRNA/constraints/hard.c: In function ‘populate_hc_bp’:
ViennaRNA/constraints/hard.c:1122:39: warning: unused variable ‘t2’ [-Wunused-variable]
 1122 |   unsigned char constraint, type, t1, t2;
      |                                       ^~
ViennaRNA/constraints/hard.c:1122:35: warning: unused variable ‘t1’ [-Wunused-variable]
 1122 |   unsigned char constraint, type, t1, t2;
      |                                   ^~
ViennaRNA/constraints/hard.c: In function ‘hc_update_up’:
ViennaRNA/constraints/hard.c:1887:23: warning: unused variable ‘u’ [-Wunused-variable]
 1887 |   unsigned int  i, n, u;
      |                       ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/datastructures/char_stream.c -o ViennaRNA/datastructures/char_stream.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/datastructures/heap.c -o ViennaRNA/datastructures/heap.o
ViennaRNA/datastructures/heap.c: In function ‘heapify_down’:
ViennaRNA/datastructures/heap.c:319:22: warning: unused variable ‘child_v2’ [-Wunused-variable]
  319 |   void    *child_v, *child_v2, *v;
      |                      ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/datastructures/stream_output.c -o ViennaRNA/datastructures/stream_output.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/io/file_formats.c -o ViennaRNA/io/file_formats.o
ViennaRNA/io/file_formats.c: In function ‘vrna_file_helixlist’:
ViennaRNA/io/file_formats.c:83:9: warning: variable ‘out’ set but not used [-Wunused-but-set-variable]
   83 |   FILE *out;
      |         ^~~
ViennaRNA/io/file_formats.c:80:15: warning: unused variable ‘s’ [-Wunused-variable]
   80 |   int         s;
      |               ^
ViennaRNA/io/file_formats.c: In function ‘vrna_file_connect’:
ViennaRNA/io/file_formats.c:104:7: warning: unused variable ‘i’ [-Wunused-variable]
  104 |   int i, power_d;
      |       ^
ViennaRNA/io/file_formats.c: In function ‘vrna_file_bpseq’:
ViennaRNA/io/file_formats.c:142:7: warning: unused variable ‘i’ [-Wunused-variable]
  142 |   int i;
      |       ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/landscape/findpath.c -o ViennaRNA/landscape/findpath.o
ViennaRNA/landscape/findpath.c: In function ‘vrna_path_direct_ub’:
ViennaRNA/landscape/findpath.c:451:34: warning: unused variable ‘d’ [-Wunused-variable]
  451 |   int                         E, d;
      |                                  ^
ViennaRNA/landscape/findpath.c:451:31: warning: unused variable ‘E’ [-Wunused-variable]
  451 |   int                         E, d;
      |                               ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/landscape/move.c -o ViennaRNA/landscape/move.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/landscape/neighbor.c -o ViennaRNA/landscape/neighbor.o
ViennaRNA/landscape/neighbor.c: In function ‘generate_local_nb_insertion’:
ViennaRNA/landscape/neighbor.c:2527:20: warning: unused variable ‘j’ [-Wunused-variable]
 2527 |   int           i, j;
      |                    ^
ViennaRNA/landscape/neighbor.c: In function ‘generate_conflicts_local_nb_insertion’:
ViennaRNA/landscape/neighbor.c:2879:20: warning: unused variable ‘j’ [-Wunused-variable]
 2879 |   int           i, j;
      |                    ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/io/io_utils.c -o ViennaRNA/io/io_utils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/external.c -o ViennaRNA/loops/external.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/internal.c -o ViennaRNA/loops/internal.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/external_bt.c -o ViennaRNA/loops/external_bt.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/hairpin_pf.c -o ViennaRNA/loops/hairpin_pf.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/internal_bt.c -o ViennaRNA/loops/internal_bt.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/multibranch_pf.c -o ViennaRNA/loops/multibranch_pf.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/hairpin.c -o ViennaRNA/loops/hairpin.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/multibranch.c -o ViennaRNA/loops/multibranch.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/external_pf.c -o ViennaRNA/loops/external_pf.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/hairpin_bt.c -o ViennaRNA/loops/hairpin_bt.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/internal_pf.c -o ViennaRNA/loops/internal_pf.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/loops/multibranch_bt.c -o ViennaRNA/loops/multibranch_bt.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/params/default.c -o ViennaRNA/params/default.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/params/io.c -o ViennaRNA/params/io.o
ViennaRNA/params/io.c: In function ‘rd_1dim_slice’:
ViennaRNA/params/io.c:782:9: warning: variable ‘cp’ set but not used [-Wunused-but-set-variable]
  782 |   char *cp;
      |         ^~
At top level:
ViennaRNA/params/io.c:967:1: warning: ‘rd_6dim’ defined but not used [-Wunused-function]
  967 | rd_6dim(char    **content,
      | ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/params/params.c -o ViennaRNA/params/params.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/search/BoyerMoore.c -o ViennaRNA/search/BoyerMoore.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/2Dfold.c -o ViennaRNA/2Dfold.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/part_func.c -o ViennaRNA/part_func.o
ViennaRNA/part_func.c: In function ‘vrna_pf_dimer’:
ViennaRNA/part_func.c:263:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
  263 |   if (n > 1600)
      |      ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/snofold.c -o ViennaRNA/snofold.o
ViennaRNA/snofold.c: In function ‘snofold’:
ViennaRNA/snofold.c:360:30: warning: variable ‘bonus_cnt’ set but not used [-Wunused-but-set-variable]
  360 |   int length, energy, bonus, bonus_cnt, s;
      |                              ^~~~~~~~~
ViennaRNA/snofold.c:360:23: warning: variable ‘bonus’ set but not used [-Wunused-but-set-variable]
  360 |   int length, energy, bonus, bonus_cnt, s;
      |                       ^~~~~
ViennaRNA/snofold.c: In function ‘alifill_arrays’:
ViennaRNA/snofold.c:587:7: warning: variable ‘bonus’ set but not used [-Wunused-but-set-variable]
  587 |   int bonus, n_seq, s;
      |       ^~~~~
ViennaRNA/snofold.c: In function ‘alibacktrack’:
ViennaRNA/snofold.c:747:34: warning: variable ‘j1’ set but not used [-Wunused-but-set-variable]
  747 |     int ml, ss, cij, traced, i1, j1, p, q;
      |                                  ^~
ViennaRNA/snofold.c:747:30: warning: variable ‘i1’ set but not used [-Wunused-but-set-variable]
  747 |     int ml, ss, cij, traced, i1, j1, p, q;
      |                              ^~
ViennaRNA/snofold.c:734:7: warning: variable ‘bonus’ set but not used [-Wunused-but-set-variable]
  734 |   int bonus, n_seq, *type;
      |       ^~~~~
ViennaRNA/snofold.c: In function ‘backtrack’:
ViennaRNA/snofold.c:1097:30: warning: variable ‘j1’ set but not used [-Wunused-but-set-variable]
 1097 |     int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;
      |                              ^~
ViennaRNA/snofold.c:1097:26: warning: variable ‘i1’ set but not used [-Wunused-but-set-variable]
 1097 |     int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;
      |                          ^~
At top level:
ViennaRNA/snofold.c:153:15: warning: ‘alpha’ defined but not used [-Wunused-variable]
  153 | PRIVATE char  alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
      |               ^~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/2Dpfold.c -o ViennaRNA/2Dpfold.o
ViennaRNA/2Dpfold.c: In function ‘pf2D_linear’:
ViennaRNA/2Dpfold.c:967:49: warning: ‘l_max_post’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  967 |       int k_min_post, k_max_post, *l_min_post, *l_max_post;
      |                                                 ^~~~~~~~~~
ViennaRNA/2Dpfold.c:967:36: warning: ‘l_min_post’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  967 |       int k_min_post, k_max_post, *l_min_post, *l_max_post;
      |                                    ^~~~~~~~~~
ViennaRNA/2Dpfold.c:668:58: warning: ‘l_max_post_m1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  668 |       int k_min_post_m1, k_max_post_m1, *l_min_post_m1, *l_max_post_m1;
      |                                                          ^~~~~~~~~~~~~
ViennaRNA/2Dpfold.c:668:42: warning: ‘l_min_post_m1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  668 |       int k_min_post_m1, k_max_post_m1, *l_min_post_m1, *l_max_post_m1;
      |                                          ^~~~~~~~~~~~~
ViennaRNA/2Dpfold.c:665:55: warning: ‘l_max_post_m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  665 |       int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m;
      |                                                       ^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:665:40: warning: ‘l_min_post_m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  665 |       int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m;
      |                                        ^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4163:32: warning: ‘l_max_post_b’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 4163 |   (*max_l)[d1]  = MAX2((*max_l)[d1], d2);
      |                                ^
ViennaRNA/2Dpfold.c:446:57: note: ‘l_max_post_b’ was declared here
  446 |         int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b;
      |                                                         ^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4162:32: warning: ‘l_min_post_b’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 4162 |   (*min_l)[d1]  = MIN2((*min_l)[d1], d2);
      |                                ^
ViennaRNA/2Dpfold.c:446:42: note: ‘l_min_post_b’ was declared here
  446 |         int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b;
      |                                          ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/boltzmann_sampling.c -o ViennaRNA/boltzmann_sampling.o
In file included from ViennaRNA/boltzmann_sampling.c:32:
../src/ViennaRNA/data_structures_nonred.inc: In function ‘free_all_nrll’:
../src/ViennaRNA/data_structures_nonred.inc:1153:7: warning: unused variable ‘i’ [-Wunused-variable]
 1153 |   int i;
      |       ^
ViennaRNA/boltzmann_sampling.c: In function ‘backtrack_ext_loop’:
ViennaRNA/boltzmann_sampling.c:428:70: warning: variable ‘q1k’ set but not used [-Wunused-but-set-variable]
  428 |   FLT_OR_DBL                r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale;
      |                                                                      ^~~
ViennaRNA/boltzmann_sampling.c:428:61: warning: variable ‘q’ set but not used [-Wunused-but-set-variable]
  428 |   FLT_OR_DBL                r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale;
      |                                                             ^
ViennaRNA/boltzmann_sampling.c:427:50: warning: unused variable ‘u’ [-Wunused-variable]
  427 |   int                       ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext;
      |                                                  ^
ViennaRNA/boltzmann_sampling.c:427:47: warning: unused variable ‘k’ [-Wunused-variable]
  427 |   int                       ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext;
      |                                               ^
ViennaRNA/boltzmann_sampling.c: In function ‘backtrack_qm’:
ViennaRNA/boltzmann_sampling.c:826:40: warning: variable ‘span’ set but not used [-Wunused-but-set-variable]
  826 |   int                       k, u, cnt, span, turn, is_unpaired, *my_iindx, *jindx, *hc_up_ml, ret;
      |                                        ^~~~
In file included from ../src/ViennaRNA/loops/all.h:33,
                 from ViennaRNA/boltzmann_sampling.c:21:
ViennaRNA/boltzmann_sampling.c: In function ‘backtrack’:
../src/ViennaRNA/loops/internal.h:587:69: warning: ‘type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  587 |   if ((noGUclosure) && ((type2 == 3) || (type2 == 4) || (type == 3) || (type == 4)))
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/boltzmann_sampling.c:1253:49: note: ‘type’ was declared here
 1253 |   unsigned int              **a2s, s, n_seq, n, type, type_2, *types, u1_local, u2_local;
      |                                                 ^~~~
In file included from ../src/ViennaRNA/loops/all.h:33,
                 from ViennaRNA/boltzmann_sampling.c:21:
ViennaRNA/boltzmann_sampling.c: In function ‘vrna_pbacktrack5_resume_cb’:
../src/ViennaRNA/loops/internal.h:587:38: warning: ‘type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  587 |   if ((noGUclosure) && ((type2 == 3) || (type2 == 4) || (type == 3) || (type == 4)))
      |                         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/boltzmann_sampling.c:1651:29: note: ‘type’ was declared here
 1651 |   unsigned int              type, type2, *tt, s, n_seq, **a2s, u1_local,
      |                             ^~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/dist_vars.c -o ViennaRNA/dist_vars.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/part_func_up.c -o ViennaRNA/part_func_up.o
ViennaRNA/part_func_up.c: In function ‘pf_interact’:
ViennaRNA/part_func_up.c:911:69: warning: ‘p_c2_S’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  911 |             tt = qint_4[i][j][a][b] * p_c_S[add_i5][add_i3] * p_c2_S[j][b] * scalew * rev_d;
      |                                                                     ^
ViennaRNA/part_func_up.c: In function ‘Up_plot’:
ViennaRNA/part_func_up.c:1615:10: warning: ‘ret’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1615 |   return ret;
      |          ^~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/special_const.c -o ViennaRNA/special_const.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/bs_wrappers.c -o ViennaRNA/bs_wrappers.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/dp_matrices.c -o ViennaRNA/dp_matrices.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/c_plex.c -o ViennaRNA/c_plex.o
ViennaRNA/c_plex.c: In function ‘duplexfold_CXS’:
ViennaRNA/c_plex.c:347:41: warning: variable ‘bonus_x’ set but not used [-Wunused-but-set-variable]
  347 |   int dx_5, dx_3, dy_5, dy_3, dGx, dGy, bonus_x;
      |                                         ^~~~~~~
ViennaRNA/c_plex.c: In function ‘find_max_CXS’:
ViennaRNA/c_plex.c:866:13: warning: variable ‘max’ set but not used [-Wunused-but-set-variable]
  866 |         int max;
      |             ^~~
ViennaRNA/c_plex.c:864:13: warning: variable ‘max_pos_j’ set but not used [-Wunused-but-set-variable]
  864 |         int max_pos_j;
      |             ^~~~~~~~~
ViennaRNA/c_plex.c: In function ‘duplexfold_C’:
ViennaRNA/c_plex.c:982:19: warning: variable ‘l1’ set but not used [-Wunused-but-set-variable]
  982 |   int       i, j, l1, Emin = INF, i_min = 0, j_min = 0;
      |                   ^~
ViennaRNA/c_plex.c: In function ‘find_max_C’:
ViennaRNA/c_plex.c:1528:13: warning: variable ‘max’ set but not used [-Wunused-but-set-variable]
 1528 |         int max;
      |             ^~~
ViennaRNA/c_plex.c:1526:13: warning: variable ‘max_pos_j’ set but not used [-Wunused-but-set-variable]
 1526 |         int max_pos_j;
      |             ^~~~~~~~~
ViennaRNA/c_plex.c: In function ‘Lduplexfold_CXS’:
ViennaRNA/c_plex.c:947:54: warning: ‘max_pos_j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  947 |     int   end_q             = MIN2(n2 - 9, max_pos_j + alignment_length - 2);
      |                                                      ^
ViennaRNA/c_plex.c:517:13: note: ‘max_pos_j’ was declared here
  517 |   int       max_pos_j;
      |             ^~~~~~~~~
ViennaRNA/c_plex.c:948:72: warning: ‘max_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  948 |     char  *s3               = (char *)vrna_alloc(sizeof(char) * (end_t - begin_t + 2));
      |                                                                  ~~~~~~^~~~~~~~~
ViennaRNA/c_plex.c:516:13: note: ‘max_pos’ was declared here
  516 |   int       max_pos;                  /* get position of the best hit */
      |             ^~~~~~~
ViennaRNA/c_plex.c:780:27: warning: ‘min_j_colonne’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  780 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/c_plex.c: In function ‘Lduplexfold_C’:
ViennaRNA/c_plex.c:1602:55: warning: ‘max_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1602 |     int     end_t             = MIN2(n1 - 10, max_pos + 1);
      |                                                       ^
ViennaRNA/c_plex.c:1235:7: note: ‘max_pos’ was declared here
 1235 |   int max_pos;                                    /* get position of the best hit */
      |       ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/mfe_window.c -o ViennaRNA/mfe_window.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/perturbation_fold.c -o ViennaRNA/perturbation_fold.o
ViennaRNA/perturbation_fold.c: In function ‘pairing_probabilities_from_sampling’:
ViennaRNA/perturbation_fold.c:212:25: warning: unused variable ‘s’ [-Wunused-variable]
  212 |   int     length, i, j, s;
      |                         ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/subopt.c -o ViennaRNA/subopt.o
ViennaRNA/subopt.c: In function ‘vrna_subopt_cb’:
ViennaRNA/subopt.c:833:28: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
  833 |   unsigned int  *so, *ss, *se;
      |                            ^~
At top level:
ViennaRNA/subopt.c:429:1: warning: ‘print_stack’ defined but not used [-Wunused-function]
  429 | print_stack(LIST *list)
      | ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/equilibrium_probs.c -o ViennaRNA/equilibrium_probs.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/mfe_window_wrappers.c -o ViennaRNA/mfe_window_wrappers.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/pf_fold.c -o ViennaRNA/pf_fold.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/eval.c -o ViennaRNA/eval.o
ViennaRNA/eval.c: In function ‘vrna_eval_loop_pt_v’:
ViennaRNA/eval.c:245:28: warning: variable ‘ss’ set but not used [-Wunused-but-set-variable]
  245 |   unsigned int  *sn, *so, *ss;
      |                            ^~
ViennaRNA/eval.c:245:23: warning: variable ‘so’ set but not used [-Wunused-but-set-variable]
  245 |   unsigned int  *sn, *so, *ss;
      |                       ^~
ViennaRNA/eval.c: In function ‘en_corr_of_loop_gquad’:
ViennaRNA/eval.c:697:18: warning: variable ‘sequence’ set but not used [-Wunused-but-set-variable]
  697 |   char          *sequence;
      |                  ^~~~~~~~
ViennaRNA/eval.c: In function ‘stack_energy’:
ViennaRNA/eval.c:882:18: warning: variable ‘string’ set but not used [-Wunused-but-set-variable]
  882 |   char          *string;
      |                  ^~~~~~
ViennaRNA/eval.c:880:28: warning: variable ‘ss’ set but not used [-Wunused-but-set-variable]
  880 |   unsigned int  *sn, *so, *ss;
      |                            ^~
ViennaRNA/eval.c:880:23: warning: variable ‘so’ set but not used [-Wunused-but-set-variable]
  880 |   unsigned int  *sn, *so, *ss;
      |                       ^~
ViennaRNA/eval.c: In function ‘en_corr_of_loop_gquad_ali’:
ViennaRNA/eval.c:1822:18: warning: unused variable ‘sequence’ [-Wunused-variable]
 1822 |   char          *sequence     = vc->cons_seq;
      |                  ^~~~~~~~
ViennaRNA/eval.c:1963:42: warning: ‘elem_j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1963 |                      (elem_i - r - 1 + s - elem_j - 1 - up_mis) * P->MLbase;
      |                       ~~~~~~~~~~~~~~~~~~~^~~~~~~~
ViennaRNA/eval.c:1963:30: warning: ‘elem_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1963 |                      (elem_i - r - 1 + s - elem_j - 1 - up_mis) * P->MLbase;
      |                       ~~~~~~~^~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/mfe_wrappers.c -o ViennaRNA/mfe_wrappers.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/plex.c -o ViennaRNA/plex.o
ViennaRNA/plex.c: In function ‘duplexfold_XS’:
ViennaRNA/plex.c:425:41: warning: variable ‘bonus_x’ set but not used [-Wunused-but-set-variable]
  425 |   int dx_5, dx_3, dy_5, dy_3, dGx, dGy, bonus_x;
      |                                         ^~~~~~~
ViennaRNA/plex.c: In function ‘fduplexfold_XS’:
ViennaRNA/plex.c:748:11: warning: unused variable ‘jdiff’ [-Wunused-variable]
  748 |       int jdiff = j_pos + j - 11;
      |           ^~~~~
ViennaRNA/plex.c:996:7: warning: variable ‘endy’ set but not used [-Wunused-but-set-variable]
  996 |   int endy;
      |       ^~~~
ViennaRNA/plex.c:994:7: warning: variable ‘endx’ set but not used [-Wunused-but-set-variable]
  994 |   int endx;
      |       ^~~~
ViennaRNA/plex.c:613:13: warning: variable ‘maxPenalty’ set but not used [-Wunused-but-set-variable]
  613 |   int       maxPenalty[4];
      |             ^~~~~~~~~~
ViennaRNA/plex.c: In function ‘fbacktrack_XS’:
ViennaRNA/plex.c:1091:13: warning: variable ‘maxPenalty’ set but not used [-Wunused-but-set-variable]
 1091 |   int       maxPenalty[4];
      |             ^~~~~~~~~~
ViennaRNA/plex.c: In function ‘Lduplexfold_XS’:
ViennaRNA/plex.c:1922:13: warning: variable ‘maxPenalty’ set but not used [-Wunused-but-set-variable]
 1922 |   int       maxPenalty[4];
      |             ^~~~~~~~~~
ViennaRNA/plex.c: In function ‘find_max_XS’:
ViennaRNA/plex.c:2381:13: warning: variable ‘max’ set but not used [-Wunused-but-set-variable]
 2381 |         int max;
      |             ^~~
ViennaRNA/plex.c:2379:13: warning: variable ‘max_pos_j’ set but not used [-Wunused-but-set-variable]
 2379 |         int max_pos_j;
      |             ^~~~~~~~~
ViennaRNA/plex.c:2434:15: warning: unused variable ‘l1’ [-Wunused-variable]
 2434 |           int l1 = strchr(test.structure, '&') - test.structure;
      |               ^~
ViennaRNA/plex.c: In function ‘plot_max_XS’:
ViennaRNA/plex.c:2545:13: warning: unused variable ‘l1’ [-Wunused-variable]
 2545 |     int     l1 = strchr(test.structure, '&') - test.structure;
      |             ^~
ViennaRNA/plex.c: In function ‘duplexfold’:
ViennaRNA/plex.c:2583:19: warning: variable ‘l1’ set but not used [-Wunused-but-set-variable]
 2583 |   int       i, j, l1, Emin = INF, i_min = 0, j_min = 0;
      |                   ^~
ViennaRNA/plex.c: In function ‘fduplexfold’:
ViennaRNA/plex.c:2770:39: warning: variable ‘l1’ set but not used [-Wunused-but-set-variable]
 2770 |   int       i, j, Emin, i_min, j_min, l1;
      |                                       ^~
ViennaRNA/plex.c: In function ‘find_max’:
ViennaRNA/plex.c:4075:13: warning: variable ‘max’ set but not used [-Wunused-but-set-variable]
 4075 |         int max;
      |             ^~~
ViennaRNA/plex.c:4073:13: warning: variable ‘max_pos_j’ set but not used [-Wunused-but-set-variable]
 4073 |         int max_pos_j;
      |             ^~~~~~~~~
ViennaRNA/plex.c:4117:15: warning: unused variable ‘l1’ [-Wunused-variable]
 4117 |           int l1 = strchr(test.structure, '&') - test.structure;
      |               ^~
ViennaRNA/plex.c:4239:15: warning: unused variable ‘l1’ [-Wunused-variable]
 4239 |           int l1 = strchr(test.structure, '&') - test.structure;
      |               ^~
ViennaRNA/plex.c: In function ‘plot_max’:
ViennaRNA/plex.c:4287:13: warning: unused variable ‘l1’ [-Wunused-variable]
 4287 |     int     l1 = strchr(test.structure, '&') - test.structure;
      |             ^~
ViennaRNA/plex.c:4306:9: warning: unused variable ‘l1’ [-Wunused-variable]
 4306 |     int l1 = strchr(test.structure, '&') - test.structure;
      |         ^~
ViennaRNA/plex.c: In function ‘fduplexfold’:
ViennaRNA/plex.c:3034:10: warning: ‘max_pos_j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3034 |     j_min--;
      |     ~~~~~^~
ViennaRNA/plex.c:3031:10: warning: ‘max_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3031 |     i_min++;
      |     ~~~~~^~
ViennaRNA/plex.c: In function ‘fduplexfold_XS’:
ViennaRNA/plex.c:1009:10: warning: ‘max_pos_j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1009 |     j_min--;
      |     ~~~~~^~
ViennaRNA/plex.c:1006:10: warning: ‘max_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1006 |     i_min++;
      |     ~~~~~^~
ViennaRNA/plex.c: In function ‘Lduplexfold_XS’:
ViennaRNA/plex.c:2532:45: warning: ‘max_pos_j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2532 |     int   end_q   = MIN2(n2 - 10, max_pos_j + alignment_length2 - 1);
      |                                             ^
ViennaRNA/plex.c:1917:13: note: ‘max_pos_j’ was declared here
 1917 |   int       max_pos_j;
      |             ^~~~~~~~~
ViennaRNA/plex.c:2530:43: warning: ‘max_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2530 |     int   end_t   = MIN2(n1 - 10, max_pos + 1);
      |                                           ^
ViennaRNA/plex.c:1916:13: note: ‘max_pos’ was declared here
 1916 |   int       max_pos;
      |             ^~~~~~~
ViennaRNA/plex.c:2298:27: warning: ‘min_j_colonne’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2298 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/plex.c: In function ‘Lduplexfold’:
ViennaRNA/plex.c:3999:27: warning: ‘min_j_colonne’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3999 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/plex.c:4272:43: warning: ‘max_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 4272 |     int   end_t   = MIN2(n1 - 10, max_pos + 1);
      |                                           ^
ViennaRNA/plex.c:3695:13: note: ‘max_pos’ was declared here
 3695 |   int       max_pos;                                    /* get position of the best hit */
      |             ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/eval_wrappers.c -o ViennaRNA/eval_wrappers.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/mm.c -o ViennaRNA/mm.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/plex_functions.c -o ViennaRNA/plex_functions.o
ViennaRNA/plex_functions.c: In function ‘PKLduplexfold_XS’:
ViennaRNA/plex_functions.c:303:12: warning: ‘type2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  303 |       E -= vrna_E_ext_stem(type2, ((k < i) ? SS1[k + 1] : -1), ((l > j - 1) ? SS1[l - 1] : -1), P);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/plex_functions.c:253:21: note: ‘type2’ was declared here
  253 |   int   p, q, type, type2, E, traced, i0, j0;
      |                     ^~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/units.c -o ViennaRNA/units.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/ali_plex.c -o ViennaRNA/ali_plex.o
ViennaRNA/ali_plex.c: In function ‘alifind_max’:
ViennaRNA/ali_plex.c:850:13: warning: variable ‘max’ set but not used [-Wunused-but-set-variable]
  850 |         int max;
      |             ^~~
ViennaRNA/ali_plex.c:848:13: warning: variable ‘max_pos_j’ set but not used [-Wunused-but-set-variable]
  848 |         int max_pos_j;
      |             ^~~~~~~~~
ViennaRNA/ali_plex.c:891:15: warning: unused variable ‘l1’ [-Wunused-variable]
  891 |           int l1 = strchr(test.structure, '&') - test.structure;
      |               ^~
ViennaRNA/ali_plex.c: In function ‘aliplot_max’:
ViennaRNA/ali_plex.c:944:13: warning: unused variable ‘l1’ [-Wunused-variable]
  944 |     int     l1 = strchr(test.structure, '&') - test.structure;
      |             ^~
ViennaRNA/ali_plex.c: In function ‘aliLduplexfold’:
ViennaRNA/ali_plex.c:928:43: warning: ‘max_pos_j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  928 |     int   end_q = MIN2(n2 - 10, max_pos_j + alignment_length - 1);
      |                                           ^
ViennaRNA/ali_plex.c:456:9: note: ‘max_pos_j’ was declared here
  456 |   int   max_pos_j;
      |         ^~~~~~~~~
ViennaRNA/ali_plex.c:925:38: warning: ‘max_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  925 |     int   begin_t = MAX2(11, max_pos - alignment_length + 1);
      |                                      ^
ViennaRNA/ali_plex.c:455:9: note: ‘max_pos’ was declared here
  455 |   int   max_pos;                                    /* get position of the best hit */
      |         ^~~~~~~
ViennaRNA/ali_plex.c:777:27: warning: ‘min_j_colonne’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  777 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/ali_plex.c: In function ‘aliLduplexfold_XS’:
ViennaRNA/ali_plex.c:1774:45: warning: ‘max_pos_j’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1774 |     j_flag  = (begin_q == max_pos_j - 1 ? 1 : 0);
      |               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
ViennaRNA/ali_plex.c:1261:9: note: ‘max_pos_j’ was declared here
 1261 |   int   max_pos_j;
      |         ^~~~~~~~~
ViennaRNA/ali_plex.c:1767:38: warning: ‘max_pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1767 |     int   begin_t = MAX2(11, max_pos - alignment_length); /* only get the position that binds.. */
      |                                      ^
ViennaRNA/ali_plex.c:1260:9: note: ‘max_pos’ was declared here
 1260 |   int   max_pos;                  /* get position of the best hit */
      |         ^~~~~~~
ViennaRNA/ali_plex.c:1601:27: warning: ‘min_j_colonne’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1601 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/combinatorics.c -o ViennaRNA/combinatorics.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/fold.c -o ViennaRNA/fold.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/model.c -o ViennaRNA/model.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/commands.c -o ViennaRNA/commands.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/fold_compound.c -o ViennaRNA/fold_compound.o
ViennaRNA/fold_compound.c: In function ‘set_fold_compound’:
ViennaRNA/fold_compound.c:613:24: warning: unused variable ‘seq2’ [-Wunused-variable]
  613 |   char          *seq, *seq2;
      |                        ^~~~
ViennaRNA/fold_compound.c:613:18: warning: unused variable ‘seq’ [-Wunused-variable]
  613 |   char          *seq, *seq2;
      |                  ^~~
ViennaRNA/fold_compound.c:612:17: warning: variable ‘cp’ set but not used [-Wunused-but-set-variable]
  612 |   int           cp;
      |                 ^~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/sequence.c -o ViennaRNA/sequence.o
ViennaRNA/sequence.c: In function ‘set_sequence’:
ViennaRNA/sequence.c:529:22: warning: unused variable ‘p’ [-Wunused-variable]
  529 |   for (size_t i = 1, p = 0; i < obj->length; i++) {
      |                      ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ViennaRNA/unstructured_domains.c -o ViennaRNA/unstructured_domains.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c predict_mfe.cpp -o predict_mfe.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/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 -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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
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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 
 57.134   5.317  62.433