Marianna Plucinska
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/XNAString |
| git_branch: devel |
| git_last_commit: 1a0e1a0 |
| git_last_commit_date: 2024-04-30 11:34:34 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 2232/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XNAString 1.13.0 (landing page) Marianna Plucinska
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
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. |
| Package: XNAString |
| Version: 1.13.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:XNAString.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings XNAString_1.13.0.tar.gz |
| StartedAt: 2024-07-16 05:29:11 -0400 (Tue, 16 Jul 2024) |
| EndedAt: 2024-07-16 05:37:34 -0400 (Tue, 16 Jul 2024) |
| EllapsedTime: 502.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: XNAString.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:XNAString.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings XNAString_1.13.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/XNAString.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* 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 '1.13.0'
* 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) 13.2.0'
* 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 code 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 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XNAString/libs/x64/XNAString.dll':
Found '_exit', possibly from '_exit' (C)
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 10.65 0.23 10.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
'C:/Users/biocbuild/bbs-3.20-bioc/meat/XNAString.Rcheck/00check.log'
for details.
XNAString.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL XNAString
###
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'XNAString' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/2Dfold.c -o ViennaRNA/2Dfold.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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:649:11: warning: 'l_min_post_b' may be used uninitialized [-Wmaybe-uninitialized]
649 | adjustArrayBoundaries(&matrices->Q_B[ij],
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
650 | &matrices->k_min_Q_B[ij],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
651 | &matrices->k_max_Q_B[ij],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
652 | &matrices->l_min_Q_B[ij],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
653 | &matrices->l_max_Q_B[ij],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
654 | k_min_post_b,
| ~~~~~~~~~~~~~
655 | k_max_post_b,
| ~~~~~~~~~~~~~
656 | l_min_post_b,
| ~~~~~~~~~~~~~
657 | l_max_post_b
| ~~~~~~~~~~~~
658 | );
| ~
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;
| ^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:649:11: warning: 'l_max_post_b' may be used uninitialized [-Wmaybe-uninitialized]
649 | adjustArrayBoundaries(&matrices->Q_B[ij],
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
650 | &matrices->k_min_Q_B[ij],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
651 | &matrices->k_max_Q_B[ij],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
652 | &matrices->l_min_Q_B[ij],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
653 | &matrices->l_max_Q_B[ij],
| ~~~~~~~~~~~~~~~~~~~~~~~~~
654 | k_min_post_b,
| ~~~~~~~~~~~~~
655 | k_max_post_b,
| ~~~~~~~~~~~~~
656 | l_min_post_b,
| ~~~~~~~~~~~~~
657 | l_max_post_b
| ~~~~~~~~~~~~
658 | );
| ~
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;
| ^~~~~~~~~~~~
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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 '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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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: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;
| ^~~~~~~~~~~~~
In function 'plot_max_CXS',
inlined from 'Lduplexfold_CXS' at ViennaRNA/c_plex.c:804:5:
ViennaRNA/c_plex.c:944:47: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized]
944 | int begin_t = MAX2(9, max_pos - alignment_length);
| ^
ViennaRNA/c_plex.c:180:33: note: in definition of macro 'MAX2'
180 | #define MAX2(A, B) ((A) > (B) ? (A) : (B))
| ^
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 */
| ^~~~~~~
In function 'plot_max_CXS',
inlined from 'Lduplexfold_CXS' at ViennaRNA/c_plex.c:804:5:
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:179:33: note: in definition of macro 'MIN2'
179 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
ViennaRNA/c_plex.c: In function 'Lduplexfold_CXS':
ViennaRNA/c_plex.c:517:13: note: 'max_pos_j' was declared here
517 | int max_pos_j;
| ^~~~~~~~~
In function 'plot_max_C',
inlined from 'Lduplexfold_C' at ViennaRNA/c_plex.c:1477:5:
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:179:33: note: in definition of macro 'MIN2'
179 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
ViennaRNA/c_plex.c: In function 'Lduplexfold_C':
ViennaRNA/c_plex.c:1235:7: note: 'max_pos' was declared here
1235 | int max_pos; /* get position of the best hit */
| ^~~~~~~
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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 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 */
| ^~~~~~~
In file included from ViennaRNA/plex.c:43:
In function 'fbacktrack',
inlined from 'fduplexfold' at ViennaRNA/plex.c:3029:11:
../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:3090:9: note: in expansion of macro 'MAX2'
3090 | j0 = MAX2(j - 1, 11);
| ^~~~
ViennaRNA/plex.c: In function 'fduplexfold':
ViennaRNA/plex.c:2781:13: note: 'max_pos_j' was declared here
2781 | int max_pos_j;
| ^~~~~~~~~
In function 'fbacktrack_XS',
inlined from 'fduplexfold_XS' at ViennaRNA/plex.c:975:11:
ViennaRNA/plex.c:1074:16: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized]
1074 | i0 = MIN2(i + 1, n3 - 10);
../src/ViennaRNA/utils/basic.h:116:27: note: in definition of macro 'MIN2'
116 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
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 */
| ^~~~~~~
In function 'fbacktrack_XS',
inlined from 'fduplexfold_XS' at ViennaRNA/plex.c:975:11:
../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:1075:9: note: in expansion of macro 'MAX2'
1075 | j0 = MAX2(j - 1, 11);
| ^~~~
ViennaRNA/plex.c: In function 'fduplexfold_XS':
ViennaRNA/plex.c:608:13: note: 'max_pos_j' was declared here
608 | int max_pos_j;
| ^~~~~~~~~
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;
| ^~~~~~~~~~~~~
In function 'plot_max_XS',
inlined from 'Lduplexfold_XS' at ViennaRNA/plex.c:2326:5:
ViennaRNA/plex.c:2530:43: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized]
2530 | int end_t = MIN2(n1 - 10, max_pos + 1);
../src/ViennaRNA/utils/basic.h:116:33: note: in definition of macro 'MIN2'
116 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
ViennaRNA/plex.c: In function 'Lduplexfold_XS':
ViennaRNA/plex.c:1916:13: note: 'max_pos' was declared here
1916 | int max_pos;
| ^~~~~~~
In function 'plot_max_XS',
inlined from 'Lduplexfold_XS' at ViennaRNA/plex.c:2326:5:
ViennaRNA/plex.c:2532:45: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized]
2532 | int end_q = MIN2(n2 - 10, max_pos_j + alignment_length2 - 1);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
../src/ViennaRNA/utils/basic.h:116:33: note: in definition of macro 'MIN2'
116 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
ViennaRNA/plex.c: In function 'Lduplexfold_XS':
ViennaRNA/plex.c:1917:13: note: 'max_pos_j' was declared here
1917 | int max_pos_j;
| ^~~~~~~~~
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;
| ^~~~~~~~~~~~~
In function 'plot_max',
inlined from 'Lduplexfold' at ViennaRNA/plex.c:4024:5:
ViennaRNA/plex.c:4272:43: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized]
4272 | int end_t = MIN2(n1 - 10, max_pos + 1);
../src/ViennaRNA/utils/basic.h:116:33: note: in definition of macro 'MIN2'
116 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
ViennaRNA/plex.c: In function 'Lduplexfold':
ViennaRNA/plex.c:3695:13: note: 'max_pos' was declared here
3695 | int max_pos; /* get position of the best hit */
| ^~~~~~~
In function 'plot_max',
inlined from 'Lduplexfold' at ViennaRNA/plex.c:4024:5:
ViennaRNA/plex.c:4298:47: warning: 'max_pos_j' may be used uninitialized [-Wmaybe-uninitialized]
4298 | int end_q = MIN2(n2 - 10, max_pos_j + alignment_length2 - 1);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
../src/ViennaRNA/utils/basic.h:116:33: note: in definition of macro 'MIN2'
116 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
ViennaRNA/plex.c: In function 'Lduplexfold':
ViennaRNA/plex.c:3696:13: note: 'max_pos_j' was declared here
3696 | int max_pos_j;
| ^~~~~~~~~
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mm.c -o ViennaRNA/mm.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/units.c -o ViennaRNA/units.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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: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;
| ^~~~~~~~~~~~~
In file included from ViennaRNA/ali_plex.c:43:
In function 'aliplot_max',
inlined from 'aliLduplexfold' at ViennaRNA/ali_plex.c:799:3:
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);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~
../src/ViennaRNA/utils/basic.h:121:33: note: in definition of macro 'MAX2'
121 | #define MAX2(A, B) ((A) > (B) ? (A) : (B))
| ^
ViennaRNA/ali_plex.c: In function 'aliLduplexfold':
ViennaRNA/ali_plex.c:455:9: note: 'max_pos' was declared here
455 | int max_pos; /* get position of the best hit */
| ^~~~~~~
In function 'aliplot_max',
inlined from 'aliLduplexfold' at ViennaRNA/ali_plex.c:799:3:
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);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
../src/ViennaRNA/utils/basic.h:116:33: note: in definition of macro 'MIN2'
116 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
ViennaRNA/ali_plex.c: In function 'aliLduplexfold':
ViennaRNA/ali_plex.c:456:9: note: 'max_pos_j' was declared here
456 | int max_pos_j;
| ^~~~~~~~~
ViennaRNA/ali_plex.c: In function 'aliLduplexfold_XS':
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;
| ^~~~~~~~~~~~~
In function 'aliplot_max_XS',
inlined from 'aliLduplexfold_XS' at ViennaRNA/ali_plex.c:1624:3:
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.. */
../src/ViennaRNA/utils/basic.h:121:33: note: in definition of macro 'MAX2'
121 | #define MAX2(A, B) ((A) > (B) ? (A) : (B))
| ^
ViennaRNA/ali_plex.c: In function 'aliLduplexfold_XS':
ViennaRNA/ali_plex.c:1260:9: note: 'max_pos' was declared here
1260 | int max_pos; /* get position of the best hit */
| ^~~~~~~
In function 'aliplot_max_XS',
inlined from 'aliLduplexfold_XS' at ViennaRNA/ali_plex.c:1624:3:
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);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
../src/ViennaRNA/utils/basic.h:116:33: note: in definition of macro 'MIN2'
116 | #define MIN2(A, B) ((A) < (B) ? (A) : (B))
| ^
ViennaRNA/ali_plex.c: In function 'aliLduplexfold_XS':
ViennaRNA/ali_plex.c:1261:9: note: 'max_pos_j' was declared here
1261 | int max_pos_j;
| ^~~~~~~~~
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/fold.c -o ViennaRNA/fold.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/model.c -o ViennaRNA/model.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/commands.c -o ViennaRNA/commands.o
gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
C:\rtools44\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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-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)
XNAString.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 3 | SKIP 0 | PASS 158 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ]
>
> proc.time()
user system elapsed
186.09 11.45 199.48
XNAString.Rcheck/XNAString-Ex.timings
| name | user | system | elapsed | |
| XNAMatchPDict | 2.01 | 0.00 | 2.01 | |
| XNAMatchPattern | 0.42 | 0.00 | 0.42 | |
| XNAPairwiseAlignment | 0.12 | 0.00 | 0.13 | |
| XNAStringFromHelm | 0.17 | 0.02 | 0.19 | |
| XNAStringToHelm | 0.04 | 0.00 | 0.03 | |
| XNAVmatchPattern | 10.65 | 0.23 | 10.89 | |
| alphabetFrequency | 0.14 | 0.00 | 0.14 | |
| backbone | 0.02 | 0.00 | 0.01 | |
| base | 0.01 | 0.00 | 0.02 | |
| compl_dictionary | 0.02 | 0.00 | 0.01 | |
| concatDict | 0 | 0 | 0 | |
| conjugate3 | 0.02 | 0.00 | 0.02 | |
| conjugate5 | 0.01 | 0.02 | 0.03 | |
| default_backbone | 0.02 | 0.00 | 0.01 | |
| default_sugar | 0.01 | 0.00 | 0.02 | |
| dictionary | 0.02 | 0.00 | 0.02 | |
| dinucleotideFrequency | 0.06 | 0.00 | 0.06 | |
| dt2Set | 0.06 | 0.00 | 0.06 | |
| duplexStructure | 0.03 | 0.00 | 0.03 | |
| duplex_structure | 0.00 | 0.01 | 0.02 | |
| helm2String | 0 | 0 | 0 | |
| instanceOf | 0 | 0 | 0 | |
| listOflists2Dt | 0.02 | 0.00 | 0.01 | |
| mfeStructure | 0.02 | 0.00 | 0.02 | |
| mimir2XnaDict | 0 | 0 | 0 | |
| name | 0.15 | 0.00 | 0.15 | |
| objects | 0.05 | 0.00 | 0.05 | |
| parseRnaHelmComponent | 0 | 0 | 0 | |
| reverseComplement | 0.03 | 0.00 | 0.03 | |
| secondary_structure | 0.02 | 0.00 | 0.02 | |
| seqAlphabetFrequency | 0 | 0 | 0 | |
| seqDinucleotideFrequency | 0 | 0 | 0 | |
| seqVectorAlphabetFrequency | 0 | 0 | 0 | |
| seqVectorDinucleotideFrequency | 0 | 0 | 0 | |
| set2Dt | 0.10 | 0.02 | 0.11 | |
| set2List | 0.06 | 0.01 | 0.07 | |
| siRNA_HELM | 0.05 | 0.00 | 0.05 | |
| sugar | 0.00 | 0.03 | 0.03 | |
| target | 0.00 | 0.02 | 0.02 | |
| typedListCheck | 0.00 | 0.06 | 0.06 | |
| uniqueChars | 0 | 0 | 0 | |
| xnastringClass | 0.15 | 0.03 | 0.19 | |
| xnastringElementsNumber | 0.02 | 0.00 | 0.01 | |
| xnastringSetClass | 0.05 | 0.03 | 0.08 | |