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This page was generated on 2024-02-22 11:37:28 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2256/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XNAString 1.10.0  (landing page)
Marianna Plucinska
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/XNAString
git_branch: RELEASE_3_18
git_last_commit: 2237ef8
git_last_commit_date: 2023-10-24 11:33:33 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for XNAString on palomino4


To the developers/maintainers of the XNAString package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XNAString.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: XNAString
Version: 1.10.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:XNAString.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings XNAString_1.10.0.tar.gz
StartedAt: 2024-02-22 07:46:58 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 07:54:55 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 477.1 seconds
RetCode: 0
Status:   OK  
CheckDir: XNAString.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:XNAString.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings XNAString_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/XNAString.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'XNAString/DESCRIPTION' ... OK
* this is package 'XNAString' version '1.10.0'
* 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 whether package 'XNAString' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/XNAString/libs/x64/XNAString.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  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 nor [v]sprintf. 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
XNAVmatchPattern 13.74   0.11   13.84
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/XNAString.Rcheck/00check.log'
for details.



Installation output

XNAString.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL XNAString
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'XNAString' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++11
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.o
ViennaRNA/utils/higher_order_functions.c: In function 'zip_add_min_dispatcher':
ViennaRNA/utils/higher_order_functions.c:116:1: warning: label 'exec_fun_zip_add_min' defined but not used [-Wunused-label]
  116 | exec_fun_zip_add_min:
      | ^~~~~~~~~~~~~~~~~~~~
ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable 'features' [-Wunused-variable]
   96 |   unsigned int features = vrna_cpu_simd_capabilities();
      |                ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_utils.o
ViennaRNA/utils/string_utils.c: In function 'vrna_strjoin':
ViennaRNA/utils/string_utils.c:391:36: warning: unused variable 'num_strings' [-Wunused-variable]
  391 |   size_t      n, offset, *lengths, num_strings, mem_strings, total_length;
      |                                    ^~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/utils.o
ViennaRNA/utils/utils.c:60:15: warning: 'scale2' defined but not used [-Wunused-variable]
   60 | PRIVATE char  scale2[]  = "....,....5....,....6....,....7....,....8";
      |               ^~~~~~
ViennaRNA/utils/utils.c:59:15: warning: 'scale1' defined but not used [-Wunused-variable]
   59 | PRIVATE char  scale1[]  = "....,....1....,....2....,....3....,....4";
      |               ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/constraints/SHAPE.c -o ViennaRNA/constraints/SHAPE.o
ViennaRNA/constraints/SHAPE.c: In function 'vrna_constraints_add_SHAPE':
ViennaRNA/constraints/SHAPE.c:202:10: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
  202 |   method = shape_method;
      |          ^
ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer
  206 |   vrna_file_SHAPE_read(shape_file, length, method == 'W' ? 0 : -1, sequence, values);
      |                                                   ^~
ViennaRNA/constraints/SHAPE.c:208:14: warning: comparison between pointer and integer
  208 |   if (method == 'D') {
      |              ^~
ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer
  210 |   } else if (method == 'Z') {
      |                     ^~
ViennaRNA/constraints/SHAPE.c: In function 'sc_parse_parameters':
ViennaRNA/constraints/SHAPE.c:612:15: warning: unused variable 'warning' [-Wunused-variable]
  612 |   const char  warning[] = "SHAPE method parameters not recognized! Using default parameters!";
      |               ^~~~~~~
ViennaRNA/constraints/SHAPE.c: In function 'vrna_constraints_add_SHAPE':
ViennaRNA/constraints/SHAPE.c:209:11: warning: 'p2' may be used uninitialized [-Wmaybe-uninitialized]
  209 |     (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/constraints/SHAPE.c:196:15: note: 'p2' was declared here
  196 |   float   p1, p2;
      |               ^~
ViennaRNA/constraints/SHAPE.c:209:11: warning: 'p1' may be used uninitialized [-Wmaybe-uninitialized]
  209 |     (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/constraints/SHAPE.c:196:11: note: 'p1' was declared here
  196 |   float   p1, p2;
      |           ^~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.o
In file included from ViennaRNA/constraints/hard.c:37:
ViennaRNA/constraints/hc_depot.inc: In function 'hc_depot_store_bp':
ViennaRNA/constraints/hc_depot.inc:229:38: warning: unused variable 'entry' [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |                                      ^~~~~
ViennaRNA/constraints/hc_depot.inc:229:16: warning: unused variable 'old_size' [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |                ^~~~~~~~
ViennaRNA/constraints/hc_depot.inc:229:13: warning: unused variable 'k' [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |             ^
ViennaRNA/constraints/hc_depot.inc: In function 'hc_depot_free':
ViennaRNA/constraints/hc_depot.inc:263:25: warning: unused variable 'n' [-Wunused-variable]
  263 |   unsigned int    s, i, n;
      |                         ^
ViennaRNA/constraints/hard.c: In function 'vrna_hc_update':
ViennaRNA/constraints/hard.c:211:20: warning: variable 'maxdist' set but not used [-Wunused-but-set-variable]
  211 |   unsigned int  n, maxdist;
      |                    ^~~~~~~
ViennaRNA/constraints/hard.c: In function 'vrna_hc_add_up_strand_batch':
ViennaRNA/constraints/hard.c:386:46: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
  386 |   unsigned int  i, strand, pos, n_pos, *ss, *sn;
      |                                              ^~
ViennaRNA/constraints/hard.c:386:41: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
  386 |   unsigned int  i, strand, pos, n_pos, *ss, *sn;
      |                                         ^~
ViennaRNA/constraints/hard.c: In function 'vrna_hc_add_bp_nonspecific':
ViennaRNA/constraints/hard.c:437:17: warning: unused variable 'p' [-Wunused-variable]
  437 |   int           p;
      |                 ^
ViennaRNA/constraints/hard.c:436:49: warning: variable 'se' set but not used [-Wunused-but-set-variable]
  436 |   unsigned int  n, strand, actual_i, *sn, *ss, *se;
      |                                                 ^~
ViennaRNA/constraints/hard.c:436:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  436 |   unsigned int  n, strand, actual_i, *sn, *ss, *se;
      |                 ^
ViennaRNA/constraints/hard.c: In function 'vrna_hc_add_bp_strand':
ViennaRNA/constraints/hard.c:476:48: warning: unused variable 'l' [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                                                ^
ViennaRNA/constraints/hard.c:476:45: warning: unused variable 'k' [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                                             ^
ViennaRNA/constraints/hard.c:476:31: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                               ^~
ViennaRNA/constraints/hard.c:476:26: warning: variable 'se' set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                          ^~
ViennaRNA/constraints/hard.c:476:21: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                     ^~
ViennaRNA/constraints/hard.c:476:17: warning: unused variable 'n' [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                 ^
ViennaRNA/constraints/hard.c: In function 'vrna_hc_add_bp':
ViennaRNA/constraints/hard.c:533:20: warning: unused variable 'l' [-Wunused-variable]
  533 |   int           k, l, ret;
      |                    ^
ViennaRNA/constraints/hard.c:533:17: warning: unused variable 'k' [-Wunused-variable]
  533 |   int           k, l, ret;
      |                 ^
ViennaRNA/constraints/hard.c:532:26: warning: variable 'se' set but not used [-Wunused-but-set-variable]
  532 |   unsigned int  n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
      |                          ^~
ViennaRNA/constraints/hard.c:532:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  532 |   unsigned int  n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
      |                 ^
ViennaRNA/constraints/hard.c: In function 'vrna_hc_free':
ViennaRNA/constraints/hard.c:588:20: warning: unused variable 'i' [-Wunused-variable]
  588 |       unsigned int i;
      |                    ^
ViennaRNA/constraints/hard.c: In function 'default_hc_up':
ViennaRNA/constraints/hard.c:841:20: warning: unused variable 'depot' [-Wunused-variable]
  841 |   vrna_hc_depot_t *depot;
      |                    ^~~~~
ViennaRNA/constraints/hard.c: In function 'prepare_hc_bp':
ViennaRNA/constraints/hard.c:1011:25: warning: unused variable 'ij' [-Wunused-variable]
 1011 |   int             *idx, ij;
      |                         ^~
ViennaRNA/constraints/hard.c:1010:109: warning: variable 'se' set but not used [-Wunused-but-set-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                                             ^~
ViennaRNA/constraints/hard.c:1010:99: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                                   ^~
ViennaRNA/constraints/hard.c:1010:88: warning: unused variable 't_end' [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                        ^~~~~
ViennaRNA/constraints/hard.c:1010:79: warning: unused variable 't_start' [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                               ^~~~~~~
ViennaRNA/constraints/hard.c:1010:74: warning: unused variable 'end' [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                          ^~~
ViennaRNA/constraints/hard.c:1010:67: warning: unused variable 'start' [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                   ^~~~~
ViennaRNA/constraints/hard.c:1009:27: warning: unused variable 'type' [-Wunused-variable]
 1009 |   unsigned char   option, type;
      |                           ^~~~
ViennaRNA/constraints/hard.c: In function 'populate_hc_bp':
ViennaRNA/constraints/hard.c:1122:39: warning: unused variable 't2' [-Wunused-variable]
 1122 |   unsigned char constraint, type, t1, t2;
      |                                       ^~
ViennaRNA/constraints/hard.c:1122:35: warning: unused variable 't1' [-Wunused-variable]
 1122 |   unsigned char constraint, type, t1, t2;
      |                                   ^~
ViennaRNA/constraints/hard.c: In function 'hc_update_up':
ViennaRNA/constraints/hard.c:1887:23: warning: unused variable 'u' [-Wunused-variable]
 1887 |   unsigned int  i, n, u;
      |                       ^
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/datastructures/char_stream.c -o ViennaRNA/datastructures/char_stream.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/datastructures/stream_output.c -o ViennaRNA/datastructures/stream_output.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/landscape/move.c -o ViennaRNA/landscape/move.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/io/io_utils.c -o ViennaRNA/io/io_utils.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/external.c -o ViennaRNA/loops/external.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/internal.c -o ViennaRNA/loops/internal.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/external_bt.c -o ViennaRNA/loops/external_bt.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/hairpin_pf.c -o ViennaRNA/loops/hairpin_pf.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/internal_bt.c -o ViennaRNA/loops/internal_bt.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/multibranch_pf.c -o ViennaRNA/loops/multibranch_pf.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/hairpin.c -o ViennaRNA/loops/hairpin.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/multibranch.c -o ViennaRNA/loops/multibranch.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/external_pf.c -o ViennaRNA/loops/external_pf.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/hairpin_bt.c -o ViennaRNA/loops/hairpin_bt.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/internal_pf.c -o ViennaRNA/loops/internal_pf.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/loops/multibranch_bt.c -o ViennaRNA/loops/multibranch_bt.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/params/default.c -o ViennaRNA/params/default.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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;
      |         ^~
ViennaRNA/params/io.c: 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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/params/params.c -o ViennaRNA/params/params.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/search/BoyerMoore.c -o ViennaRNA/search/BoyerMoore.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/2Dfold.c -o ViennaRNA/2Dfold.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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;
      |                          ^~
ViennaRNA/snofold.c: At top level:
ViennaRNA/snofold.c:153:15: warning: 'alpha' defined but not used [-Wunused-variable]
  153 | PRIVATE char  alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
      |               ^~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/2Dpfold.c -o ViennaRNA/2Dpfold.o
ViennaRNA/2Dpfold.c: In function 'pf2D_linear':
ViennaRNA/2Dpfold.c:4163:32: warning: 'l_max_post' may be used uninitialized [-Wmaybe-uninitialized]
 4163 |   (*max_l)[d1]  = MAX2((*max_l)[d1], d2);
      |                                ^
ViennaRNA/2Dpfold.c:967:49: note: 'l_max_post' was declared here
  967 |       int k_min_post, k_max_post, *l_min_post, *l_max_post;
      |                                                 ^~~~~~~~~~
ViennaRNA/2Dpfold.c:4162:32: warning: 'l_min_post' may be used uninitialized [-Wmaybe-uninitialized]
 4162 |   (*min_l)[d1]  = MIN2((*min_l)[d1], d2);
      |                                ^
ViennaRNA/2Dpfold.c:967:36: note: 'l_min_post' was declared here
  967 |       int k_min_post, k_max_post, *l_min_post, *l_max_post;
      |                                    ^~~~~~~~~~
ViennaRNA/2Dpfold.c:4163:32: warning: 'l_max_post_m' may be used uninitialized [-Wmaybe-uninitialized]
 4163 |   (*max_l)[d1]  = MAX2((*max_l)[d1], d2);
      |                                ^
ViennaRNA/2Dpfold.c:665:55: note: 'l_max_post_m' was declared here
  665 |       int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m;
      |                                                       ^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4162:32: warning: 'l_min_post_m' may be used uninitialized [-Wmaybe-uninitialized]
 4162 |   (*min_l)[d1]  = MIN2((*min_l)[d1], d2);
      |                                ^
ViennaRNA/2Dpfold.c:665:40: note: 'l_min_post_m' was declared here
  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 [-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 [-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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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;
      |                                        ^~~~
ViennaRNA/boltzmann_sampling.c: In function 'backtrack':
ViennaRNA/boltzmann_sampling.c:1434:25: warning: 'type' may be used uninitialized [-Wmaybe-uninitialized]
 1434 |               q_temp *= exp_E_IntLoop(u1,
      |                         ^~~~~~~~~~~~~~~~~
 1435 |                                       u2,
      |                                       ~~~
 1436 |                                       type,
      |                                       ~~~~~
 1437 |                                       type_2,
      |                                       ~~~~~~~
 1438 |                                       S1[i + 1],
      |                                       ~~~~~~~~~~
 1439 |                                       S1[j - 1],
      |                                       ~~~~~~~~~~
 1440 |                                       S1[k - 1],
      |                                       ~~~~~~~~~~
 1441 |                                       S1[l + 1],
      |                                       ~~~~~~~~~~
 1442 |                                       pf_params);
      |                                       ~~~~~~~~~~
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 function 'pbacktrack_circ',
    inlined from 'vrna_pbacktrack5_resume_cb' at ViennaRNA/boltzmann_sampling.c:238:11:
ViennaRNA/boltzmann_sampling.c:1786:32: warning: 'type' may be used uninitialized [-Wmaybe-uninitialized]
 1786 |                     q_temp  *= exp_E_IntLoop(ln2 + ln3,
      |                                ^~~~~~~~~~~~~~~~~~~~~~~~
 1787 |                                              ln1,
      |                                              ~~~~
 1788 |                                              type2,
      |                                              ~~~~~~
 1789 |                                              type,
      |                                              ~~~~~
 1790 |                                              S1[l + 1],
      |                                              ~~~~~~~~~~
 1791 |                                              S1[k - 1],
      |                                              ~~~~~~~~~~
 1792 |                                              S1[i - 1],
      |                                              ~~~~~~~~~~
 1793 |                                              S1[j + 1],
      |                                              ~~~~~~~~~~
 1794 |                                              pf_params);
      |                                              ~~~~~~~~~~
ViennaRNA/boltzmann_sampling.c: In function 'vrna_pbacktrack5_resume_cb':
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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/dist_vars.c -o ViennaRNA/dist_vars.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 [-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:594:49: note: 'p_c2_S' was declared here
  594 |   double      temp, Z, rev_d, E, Z2, **p_c_S, **p_c2_S, int_scale;
      |                                                 ^~~~~~
ViennaRNA/part_func_up.c: In function 'Up_plot':
ViennaRNA/part_func_up.c:1615:10: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized]
 1615 |   return ret;
      |          ^~~
ViennaRNA/part_func_up.c:1587:11: note: 'ret' was declared here
 1587 |   int     ret;
      |           ^~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/special_const.c -o ViennaRNA/special_const.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/bs_wrappers.c -o ViennaRNA/bs_wrappers.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/dp_matrices.c -o ViennaRNA/dp_matrices.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 [-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;
      |             ^~~~~~~~~
In function 'plot_max_CXS',
    inlined from 'Lduplexfold_CXS' at ViennaRNA/c_plex.c:804:5:
ViennaRNA/c_plex.c:948:72: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized]
  948 |     char  *s3               = (char *)vrna_alloc(sizeof(char) * (end_t - begin_t + 2));
      |                                                                  ~~~~~~^~~~~~~~~
ViennaRNA/c_plex.c: In function 'Lduplexfold_CXS':
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 [-Wmaybe-uninitialized]
  780 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/c_plex.c:519:13: note: 'min_j_colonne' was declared here
  519 |   int       min_j_colonne;
      |             ^~~~~~~~~~~~~
ViennaRNA/c_plex.c: In function 'Lduplexfold_C':
ViennaRNA/c_plex.c:1602:55: warning: 'max_pos' may be used uninitialized [-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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/mfe_window.c -o ViennaRNA/mfe_window.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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;
      |                            ^~
ViennaRNA/subopt.c: At top level:
ViennaRNA/subopt.c:429:1: warning: 'print_stack' defined but not used [-Wunused-function]
  429 | print_stack(LIST *list)
      | ^~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/equilibrium_probs.c -o ViennaRNA/equilibrium_probs.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/mfe_window_wrappers.c -o ViennaRNA/mfe_window_wrappers.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/pf_fold.c -o ViennaRNA/pf_fold.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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;
      |                  ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/mfe_wrappers.c -o ViennaRNA/mfe_wrappers.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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;
      |         ^~
In file included from ViennaRNA/plex.c:43:
../src/ViennaRNA/utils/basic.h: In function 'fduplexfold':
../src/ViennaRNA/utils/basic.h:121:42: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized]
  121 | #define MAX2(A, B)      ((A) > (B) ? (A) : (B))
      |                                          ^
ViennaRNA/plex.c:2781:13: note: 'max_pos_j' was declared here
 2781 |   int       max_pos_j;
      |             ^~~~~~~~~
In function 'fbacktrack',
    inlined from 'fduplexfold' at ViennaRNA/plex.c:3029:11:
ViennaRNA/plex.c:3101:20: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized]
 3101 |   type    = pair[S1[i]][S2[j]];
      |                    ^
ViennaRNA/plex.c: In function 'fduplexfold':
ViennaRNA/plex.c:2780:13: note: 'max_pos' was declared here
 2780 |   int       max_pos;                                    /* get position of the best hit */
      |             ^~~~~~~
ViennaRNA/plex.c: In function 'fduplexfold_XS':
ViennaRNA/plex.c:1009:10: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized]
 1009 |     j_min--;
      |     ~~~~~^~
ViennaRNA/plex.c:608:13: note: 'max_pos_j' was declared here
  608 |   int       max_pos_j;
      |             ^~~~~~~~~
In function 'fbacktrack_XS',
    inlined from 'fduplexfold_XS' at ViennaRNA/plex.c:975:11:
ViennaRNA/plex.c:1110:20: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized]
 1110 |   type    = pair[S1[i]][S2[j]];
      |                    ^
ViennaRNA/plex.c: In function 'fduplexfold_XS':
ViennaRNA/plex.c:607:13: note: 'max_pos' was declared here
  607 |   int       max_pos;                  /* get position of the best hit */
      |             ^~~~~~~
ViennaRNA/plex.c: In function 'Lduplexfold_XS':
ViennaRNA/plex.c:2298:27: warning: 'min_j_colonne' may be used uninitialized [-Wmaybe-uninitialized]
 2298 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/plex.c:1918:13: note: 'min_j_colonne' was declared here
 1918 |   int       min_j_colonne;
      |             ^~~~~~~~~~~~~
ViennaRNA/plex.c: In function 'Lduplexfold':
ViennaRNA/plex.c:3999:27: warning: 'min_j_colonne' may be used uninitialized [-Wmaybe-uninitialized]
 3999 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/plex.c:3698:13: note: 'min_j_colonne' was declared here
 3698 |   int       min_j_colonne;
      |             ^~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/eval_wrappers.c -o ViennaRNA/eval_wrappers.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/mm.c -o ViennaRNA/mm.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/plex_functions.c -o ViennaRNA/plex_functions.o
In function 'backtrack_XS',
    inlined from 'duplexfold_XS' at ViennaRNA/plex_functions.c:201:15,
    inlined from 'PKLduplexfold_XS' at ViennaRNA/plex_functions.c:349:3:
ViennaRNA/plex_functions.c:303:12: warning: 'type2' may be used uninitialized [-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: In function 'PKLduplexfold_XS':
ViennaRNA/plex_functions.c:253:21: note: 'type2' was declared here
  253 |   int   p, q, type, type2, E, traced, i0, j0;
      |                     ^~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/units.c -o ViennaRNA/units.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 [-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 [-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 [-Wmaybe-uninitialized]
  777 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/ali_plex.c:458:9: note: 'min_j_colonne' was declared here
  458 |   int   min_j_colonne;
      |         ^~~~~~~~~~~~~
ViennaRNA/ali_plex.c: In function 'aliLduplexfold_XS':
ViennaRNA/ali_plex.c:1770:45: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized]
 1770 |     int   end_q   = MIN2(n2 - 10, max_pos_j + alignment_length - 1);
      |                                             ^
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 [-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 [-Wmaybe-uninitialized]
 1601 |     position_j[i + delta] = min_j_colonne;
      |     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/ali_plex.c:1263:9: note: 'min_j_colonne' was declared here
 1263 |   int   min_j_colonne;
      |         ^~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/combinatorics.c -o ViennaRNA/combinatorics.o
ViennaRNA/combinatorics.c: In function 'vrna_rotational_symmetry_db_pos':
ViennaRNA/combinatorics.c:489:7: warning: 'shifts' may be used uninitialized [-Wmaybe-uninitialized]
  489 |       free(shifts);
      |       ^~~~~~~~~~~~
ViennaRNA/combinatorics.c:381:22: note: 'shifts' declared here
  381 |       unsigned int  *shifts, s, r, i, j, ii, jj, string_permutations;
      |                      ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/fold.c -o ViennaRNA/fold.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/model.c -o ViennaRNA/model.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/commands.c -o ViennaRNA/commands.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ViennaRNA/unstructured_domains.c -o ViennaRNA/unstructured_domains.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c predict_mfe.cpp -o predict_mfe.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
C:\rtools43\x86_64-w64-mingw32.static.posix\bin\nm.exe: Warning: '.' is a directory
g++ -shared -s -static-libgcc -o XNAString.dll tmp.def ./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 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-XNAString/00new/XNAString/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XNAString)

Tests output

XNAString.Rcheck/tests/testthat.Rout


R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 158 ]
> 
> proc.time()
   user  system elapsed 
 199.96    9.48  212.01 

Example timings

XNAString.Rcheck/XNAString-Ex.timings

nameusersystemelapsed
XNAMatchPDict1.590.001.59
XNAMatchPattern0.140.000.15
XNAPairwiseAlignment0.150.020.15
XNAStringFromHelm0.310.000.31
XNAStringToHelm0.010.000.02
XNAVmatchPattern13.74 0.1113.84
alphabetFrequency0.150.000.16
backbone0.020.000.02
base0.030.000.03
compl_dictionary0.030.000.03
concatDict000
conjugate30.030.000.03
conjugate50.030.000.04
default_backbone0.040.000.03
default_sugar0.030.000.03
dictionary0.030.000.03
dinucleotideFrequency0.110.000.11
dt2Set0.090.000.09
duplexStructure0.030.000.03
duplex_structure0.030.000.04
helm2String000
instanceOf000
listOflists2Dt000
mfeStructure0.040.000.03
mimir2XnaDict000
name0.170.000.17
objects0.040.000.05
parseRnaHelmComponent000
reverseComplement0.040.000.03
secondary_structure0.010.000.01
seqAlphabetFrequency000
seqDinucleotideFrequency000
seqVectorAlphabetFrequency000
seqVectorDinucleotideFrequency000
set2Dt0.090.010.11
set2List0.080.000.08
siRNA_HELM0.070.000.06
sugar0.000.020.01
target0.020.000.01
typedListCheck0.060.000.07
uniqueChars000
xnastringClass0.190.030.22
xnastringElementsNumber0.010.020.03
xnastringSetClass0.050.030.08