| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:34 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the XNAString package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2075/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XNAString 1.2.2 (landing page) Marianna Plucinska
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: XNAString |
| Version: 1.2.2 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XNAString.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings XNAString_1.2.2.tar.gz |
| StartedAt: 2022-04-13 04:50:59 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 05:01:40 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 640.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: XNAString.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XNAString.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings XNAString_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/XNAString.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'XNAString/DESCRIPTION' ... OK
* this is package 'XNAString' version '1.2.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'XNAString' can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
libs 8.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XNAString/libs/i386/XNAString.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.14-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 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XNAVmatchPattern 6.79 0.31 7.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XNAVmatchPattern 6.05 0.22 6.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.14-bioc/meat/XNAString.Rcheck/00check.log'
for details.
XNAString.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/XNAString_1.2.2.tar.gz && rm -rf XNAString.buildbin-libdir && mkdir XNAString.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XNAString.buildbin-libdir XNAString_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL XNAString_1.2.2.zip && rm XNAString_1.2.2.tar.gz XNAString_1.2.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
9 1699k 9 169k 0 0 451k 0 0:00:03 --:--:-- 0:00:03 450k
76 1699k 76 1293k 0 0 937k 0 0:00:01 0:00:01 --:--:-- 937k
100 1699k 100 1699k 0 0 1060k 0 0:00:01 0:00:01 --:--:-- 1060k
install for i386
* installing *source* package 'XNAString' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
exec_fun_zip_add_min:
^~~~~~~~~~~~~~~~~~~~
ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable 'features' [-Wunused-variable]
unsigned int features = vrna_cpu_simd_capabilities();
^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
size_t n, offset, *lengths, num_strings, mem_strings, total_length;
^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
PRIVATE char scale2[] = "....,....5....,....6....,....7....,....8";
^~~~~~
ViennaRNA/utils/utils.c:59:15: warning: 'scale1' defined but not used [-Wunused-variable]
PRIVATE char scale1[] = "....,....1....,....2....,....3....,....4";
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
method = shape_method;
^
ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer
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
if (method == 'D') {
^~
ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer
} 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]
const char warning[] = "SHAPE method parameters not recognized! Using default parameters!";
^~~~~~~
ViennaRNA/constraints/SHAPE.c: In function 'vrna_constraints_add_SHAPE':
ViennaRNA/constraints/SHAPE.c:209:11: warning: 'p2' may be used uninitialized in this function [-Wmaybe-uninitialized]
(void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/constraints/SHAPE.c:209:11: warning: 'p1' may be used uninitialized in this function [-Wmaybe-uninitialized]
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
size_t k, old_size, next_entry, entry;
^~~~~
ViennaRNA/constraints/hc_depot.inc:229:16: warning: unused variable 'old_size' [-Wunused-variable]
size_t k, old_size, next_entry, entry;
^~~~~~~~
ViennaRNA/constraints/hc_depot.inc:229:13: warning: unused variable 'k' [-Wunused-variable]
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]
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]
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]
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]
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]
int p;
^
ViennaRNA/constraints/hard.c:436:49: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, strand, actual_i, *sn, *ss, *se;
^~
ViennaRNA/constraints/hard.c:436:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
unsigned int n, strand, actual_i, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c: In function 'vrna_hc_add_bp_strand':
ViennaRNA/constraints/hard.c:476:48: warning: unused variable 'l' [-Wunused-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:45: warning: unused variable 'k' [-Wunused-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:31: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^~
ViennaRNA/constraints/hard.c:476:26: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^~
ViennaRNA/constraints/hard.c:476:21: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^~
ViennaRNA/constraints/hard.c:476:17: warning: unused variable 'n' [-Wunused-variable]
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]
int k, l, ret;
^
ViennaRNA/constraints/hard.c:533:17: warning: unused variable 'k' [-Wunused-variable]
int k, l, ret;
^
ViennaRNA/constraints/hard.c:532:26: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
^~
ViennaRNA/constraints/hard.c:532:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
^
ViennaRNA/constraints/hard.c: In function 'vrna_hc_free':
ViennaRNA/constraints/hard.c:588:20: warning: unused variable 'i' [-Wunused-variable]
unsigned int i;
^
ViennaRNA/constraints/hard.c: In function 'default_hc_up':
ViennaRNA/constraints/hard.c:841:20: warning: unused variable 'depot' [-Wunused-variable]
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]
int *idx, ij;
^~
ViennaRNA/constraints/hard.c:1010:109: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~
ViennaRNA/constraints/hard.c:1010:99: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~
ViennaRNA/constraints/hard.c:1010:88: warning: unused variable 't_end' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~~~~
ViennaRNA/constraints/hard.c:1010:79: warning: unused variable 't_start' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~~~~~~
ViennaRNA/constraints/hard.c:1010:74: warning: unused variable 'end' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~~
ViennaRNA/constraints/hard.c:1010:67: warning: unused variable 'start' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~~~~
ViennaRNA/constraints/hard.c:1009:27: warning: unused variable 'type' [-Wunused-variable]
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]
unsigned char constraint, type, t1, t2;
^~
ViennaRNA/constraints/hard.c:1122:35: warning: unused variable 't1' [-Wunused-variable]
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]
unsigned int i, n, u;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/char_stream.c -o ViennaRNA/datastructures/char_stream.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
void *child_v, *child_v2, *v;
^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/stream_output.c -o ViennaRNA/datastructures/stream_output.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
FILE *out;
^~~
ViennaRNA/io/file_formats.c:80:15: warning: unused variable 's' [-Wunused-variable]
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]
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]
int i;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
int E, d;
^
ViennaRNA/landscape/findpath.c:451:31: warning: unused variable 'E' [-Wunused-variable]
int E, d;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/landscape/move.c -o ViennaRNA/landscape/move.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
int i, j;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/io/io_utils.c -o ViennaRNA/io/io_utils.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external.c -o ViennaRNA/loops/external.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal.c -o ViennaRNA/loops/internal.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external_bt.c -o ViennaRNA/loops/external_bt.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin_pf.c -o ViennaRNA/loops/hairpin_pf.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal_bt.c -o ViennaRNA/loops/internal_bt.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch_pf.c -o ViennaRNA/loops/multibranch_pf.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin.c -o ViennaRNA/loops/hairpin.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch.c -o ViennaRNA/loops/multibranch.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external_pf.c -o ViennaRNA/loops/external_pf.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin_bt.c -o ViennaRNA/loops/hairpin_bt.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal_pf.c -o ViennaRNA/loops/internal_pf.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch_bt.c -o ViennaRNA/loops/multibranch_bt.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/params/default.c -o ViennaRNA/params/default.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
char *cp;
^~
At top level:
ViennaRNA/params/io.c:967:1: warning: 'rd_6dim' defined but not used [-Wunused-function]
rd_6dim(char **content,
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/params/params.c -o ViennaRNA/params/params.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/search/BoyerMoore.c -o ViennaRNA/search/BoyerMoore.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/2Dfold.c -o ViennaRNA/2Dfold.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
if (n > 1600)
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
int length, energy, bonus, bonus_cnt, s;
^~~~~~~~~
ViennaRNA/snofold.c:360:23: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
int length, energy, bonus, bonus_cnt, s;
^~~~~
ViennaRNA/snofold.c: In function 'alifill_arrays':
ViennaRNA/snofold.c:587:7: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
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]
int ml, ss, cij, traced, i1, j1, p, q;
^~
ViennaRNA/snofold.c:747:30: warning: variable 'i1' set but not used [-Wunused-but-set-variable]
int ml, ss, cij, traced, i1, j1, p, q;
^~
ViennaRNA/snofold.c:734:7: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
int bonus, n_seq, *type;
^~~~~
ViennaRNA/snofold.c: In function 'backtrack':
ViennaRNA/snofold.c:1097:30: warning: variable 'j1' set but not used [-Wunused-but-set-variable]
int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;
^~
ViennaRNA/snofold.c:1097:26: warning: variable 'i1' set but not used [-Wunused-but-set-variable]
int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;
^~
At top level:
ViennaRNA/snofold.c:153:15: warning: 'alpha' defined but not used [-Wunused-variable]
PRIVATE char alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
^~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/2Dpfold.c -o ViennaRNA/2Dpfold.o
ViennaRNA/2Dpfold.c: In function 'pf2D_linear':
ViennaRNA/2Dpfold.c:4163:17: warning: 'l_max_post' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*max_l)[d1] = MAX2((*max_l)[d1], d2);
ViennaRNA/2Dpfold.c:967:49: note: 'l_max_post' was declared here
int k_min_post, k_max_post, *l_min_post, *l_max_post;
^~~~~~~~~~
ViennaRNA/2Dpfold.c:4162:17: warning: 'l_min_post' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*min_l)[d1] = MIN2((*min_l)[d1], d2);
ViennaRNA/2Dpfold.c:967:36: note: 'l_min_post' was declared here
int k_min_post, k_max_post, *l_min_post, *l_max_post;
^~~~~~~~~~
ViennaRNA/2Dpfold.c:668:58: warning: 'l_max_post_m1' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k_min_post_m1, k_max_post_m1, *l_min_post_m1, *l_max_post_m1;
^~~~~~~~~~~~~
ViennaRNA/2Dpfold.c:668:42: warning: 'l_min_post_m1' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k_min_post_m1, k_max_post_m1, *l_min_post_m1, *l_max_post_m1;
^~~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4163:17: warning: 'l_max_post_m' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*max_l)[d1] = MAX2((*max_l)[d1], d2);
ViennaRNA/2Dpfold.c:665:55: note: 'l_max_post_m' was declared here
int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m;
^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4162:17: warning: 'l_min_post_m' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*min_l)[d1] = MIN2((*min_l)[d1], d2);
ViennaRNA/2Dpfold.c:665:40: note: 'l_min_post_m' was declared here
int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m;
^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4163:17: warning: 'l_max_post_b' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*max_l)[d1] = MAX2((*max_l)[d1], d2);
ViennaRNA/2Dpfold.c:446:57: note: 'l_max_post_b' was declared here
int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b;
^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4162:17: warning: 'l_min_post_b' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*min_l)[d1] = MIN2((*min_l)[d1], d2);
ViennaRNA/2Dpfold.c:446:42: note: 'l_min_post_b' was declared here
int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b;
^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
FLT_OR_DBL r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale;
^~~
ViennaRNA/boltzmann_sampling.c:428:61: warning: variable 'q' set but not used [-Wunused-but-set-variable]
FLT_OR_DBL r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale;
^
ViennaRNA/boltzmann_sampling.c:427:50: warning: unused variable 'u' [-Wunused-variable]
int ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext;
^
ViennaRNA/boltzmann_sampling.c:427:47: warning: unused variable 'k' [-Wunused-variable]
int ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext;
^
ViennaRNA/boltzmann_sampling.c: In function 'backtrack_qm':
ViennaRNA/boltzmann_sampling.c:826:40: warning: variable 'span' set but not used [-Wunused-but-set-variable]
int k, u, cnt, span, turn, is_unpaired, *my_iindx, *jindx, *hc_up_ml, ret;
^~~~
In file included from ../src/ViennaRNA/loops/all.h:33,
from ViennaRNA/boltzmann_sampling.c:21:
ViennaRNA/boltzmann_sampling.c: In function 'backtrack':
../src/ViennaRNA/loops/internal.h:587:69: warning: 'type' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((noGUclosure) && ((type2 == 3) || (type2 == 4) || (type == 3) || (type == 4)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/boltzmann_sampling.c:1253:49: note: 'type' was declared here
unsigned int **a2s, s, n_seq, n, type, type_2, *types, u1_local, u2_local;
^~~~
In file included from ../src/ViennaRNA/loops/all.h:33,
from ViennaRNA/boltzmann_sampling.c:21:
ViennaRNA/boltzmann_sampling.c: In function 'vrna_pbacktrack5_resume_cb':
../src/ViennaRNA/loops/internal.h:587:38: warning: 'type' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((noGUclosure) && ((type2 == 3) || (type2 == 4) || (type == 3) || (type == 4)))
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/boltzmann_sampling.c:1651:29: note: 'type' was declared here
unsigned int type, type2, *tt, s, n_seq, **a2s, u1_local,
^~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/dist_vars.c -o ViennaRNA/dist_vars.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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:594:49: warning: 'p_c2_S' may be used uninitialized in this function [-Wmaybe-uninitialized]
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 in this function [-Wmaybe-uninitialized]
return ret;
^~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/special_const.c -o ViennaRNA/special_const.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/bs_wrappers.c -o ViennaRNA/bs_wrappers.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/dp_matrices.c -o ViennaRNA/dp_matrices.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
int max;
^~~
ViennaRNA/c_plex.c:864:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/c_plex.c: In function 'duplexfold_C':
ViennaRNA/c_plex.c:982:19: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
int i, j, l1, Emin = INF, i_min = 0, j_min = 0;
^~
ViennaRNA/c_plex.c: In function 'find_max_C':
ViennaRNA/c_plex.c:1528:13: warning: variable 'max' set but not used [-Wunused-but-set-variable]
int max;
^~~
ViennaRNA/c_plex.c:1526:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/c_plex.c: In function 'Lduplexfold_CXS':
ViennaRNA/c_plex.c:948:72: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
char *s3 = (char *)vrna_alloc(sizeof(char) * (end_t - begin_t + 2));
~~~~~~^~~~~~~~~
ViennaRNA/c_plex.c:516:13: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
ViennaRNA/c_plex.c:947:54: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
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
int max_pos_j;
^~~~~~~~~
ViennaRNA/c_plex.c:780:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/c_plex.c: In function 'Lduplexfold_C':
ViennaRNA/c_plex.c:1602:55: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
int end_t = MIN2(n1 - 10, max_pos + 1);
^
ViennaRNA/c_plex.c:1235:7: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_window.c -o ViennaRNA/mfe_window.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
int length, i, j, s;
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
unsigned int *so, *ss, *se;
^~
At top level:
ViennaRNA/subopt.c:429:1: warning: 'print_stack' defined but not used [-Wunused-function]
print_stack(LIST *list)
^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/equilibrium_probs.c -o ViennaRNA/equilibrium_probs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_window_wrappers.c -o ViennaRNA/mfe_window_wrappers.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/pf_fold.c -o ViennaRNA/pf_fold.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
unsigned int *sn, *so, *ss;
^~
ViennaRNA/eval.c:245:23: warning: variable 'so' set but not used [-Wunused-but-set-variable]
unsigned int *sn, *so, *ss;
^~
ViennaRNA/eval.c: In function 'en_corr_of_loop_gquad':
ViennaRNA/eval.c:697:18: warning: variable 'sequence' set but not used [-Wunused-but-set-variable]
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]
char *string;
^~~~~~
ViennaRNA/eval.c:880:28: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
unsigned int *sn, *so, *ss;
^~
ViennaRNA/eval.c:880:23: warning: variable 'so' set but not used [-Wunused-but-set-variable]
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]
char *sequence = vc->cons_seq;
^~~~~~~~
ViennaRNA/eval.c:1963:42: warning: 'elem_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
(elem_i - r - 1 + s - elem_j - 1 - up_mis) * P->MLbase;
~~~~~~~~~~~~~~~~~~~^~~~~~~~
ViennaRNA/eval.c:1963:30: warning: 'elem_i' may be used uninitialized in this function [-Wmaybe-uninitialized]
(elem_i - r - 1 + s - elem_j - 1 - up_mis) * P->MLbase;
~~~~~~~^~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_wrappers.c -o ViennaRNA/mfe_wrappers.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
int jdiff = j_pos + j - 11;
^~~~~
ViennaRNA/plex.c:996:7: warning: variable 'endy' set but not used [-Wunused-but-set-variable]
int endy;
^~~~
ViennaRNA/plex.c:994:7: warning: variable 'endx' set but not used [-Wunused-but-set-variable]
int endx;
^~~~
ViennaRNA/plex.c:613:13: warning: variable 'maxPenalty' set but not used [-Wunused-but-set-variable]
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]
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]
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]
int max;
^~~
ViennaRNA/plex.c:2379:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/plex.c:2434:15: warning: unused variable 'l1' [-Wunused-variable]
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]
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]
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]
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]
int max;
^~~
ViennaRNA/plex.c:4073:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/plex.c:4117:15: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/plex.c:4239:15: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/plex.c: In function 'plot_max':
ViennaRNA/plex.c:4287:13: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/plex.c:4306:9: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/plex.c: In function 'fduplexfold':
ViennaRNA/plex.c:3034:10: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
j_min--;
~~~~~^~
ViennaRNA/plex.c:3031:10: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
i_min++;
~~~~~^~
ViennaRNA/plex.c: In function 'fduplexfold_XS':
ViennaRNA/plex.c:1009:10: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
j_min--;
~~~~~^~
ViennaRNA/plex.c:1110:20: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
type = pair[S1[i]][S2[j]];
^
ViennaRNA/plex.c:607:13: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
ViennaRNA/plex.c: In function 'Lduplexfold_XS':
ViennaRNA/plex.c:2532:45: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
int end_q = MIN2(n2 - 10, max_pos_j + alignment_length2 - 1);
^
ViennaRNA/plex.c:1917:13: note: 'max_pos_j' was declared here
int max_pos_j;
^~~~~~~~~
ViennaRNA/plex.c:2530:43: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
int end_t = MIN2(n1 - 10, max_pos + 1);
^
ViennaRNA/plex.c:1916:13: note: 'max_pos' was declared here
int max_pos;
^~~~~~~
ViennaRNA/plex.c:2298:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/plex.c: In function 'Lduplexfold':
ViennaRNA/plex.c:3999:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/plex.c:4272:43: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
int end_t = MIN2(n1 - 10, max_pos + 1);
^
ViennaRNA/plex.c:3695:13: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/eval_wrappers.c -o ViennaRNA/eval_wrappers.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mm.c -o ViennaRNA/mm.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/plex_functions.c -o ViennaRNA/plex_functions.o
ViennaRNA/plex_functions.c: In function 'PKLduplexfold_XS':
ViennaRNA/plex_functions.c:303:12: warning: 'type2' may be used uninitialized in this function [-Wmaybe-uninitialized]
E -= vrna_E_ext_stem(type2, ((k < i) ? SS1[k + 1] : -1), ((l > j - 1) ? SS1[l - 1] : -1), P);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/plex_functions.c:253:21: note: 'type2' was declared here
int p, q, type, type2, E, traced, i0, j0;
^~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/units.c -o ViennaRNA/units.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
int max;
^~~
ViennaRNA/ali_plex.c:848:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/ali_plex.c:891:15: warning: unused variable 'l1' [-Wunused-variable]
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]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/ali_plex.c: In function 'aliLduplexfold':
ViennaRNA/ali_plex.c:928:43: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
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
int max_pos_j;
^~~~~~~~~
ViennaRNA/ali_plex.c:925:38: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
int begin_t = MAX2(11, max_pos - alignment_length + 1);
^
ViennaRNA/ali_plex.c:455:9: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
ViennaRNA/ali_plex.c:777:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/ali_plex.c: In function 'aliLduplexfold_XS':
ViennaRNA/ali_plex.c:1774:45: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
j_flag = (begin_q == max_pos_j - 1 ? 1 : 0);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
ViennaRNA/ali_plex.c:1261:9: note: 'max_pos_j' was declared here
int max_pos_j;
^~~~~~~~~
ViennaRNA/ali_plex.c:1767:38: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
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
int max_pos; /* get position of the best hit */
^~~~~~~
ViennaRNA/ali_plex.c:1601:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/combinatorics.c -o ViennaRNA/combinatorics.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/fold.c -o ViennaRNA/fold.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/model.c -o ViennaRNA/model.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/commands.c -o ViennaRNA/commands.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
char *seq, *seq2;
^~~~
ViennaRNA/fold_compound.c:613:18: warning: unused variable 'seq' [-Wunused-variable]
char *seq, *seq2;
^~~
ViennaRNA/fold_compound.c:612:17: warning: variable 'cp' set but not used [-Wunused-but-set-variable]
int cp;
^~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
for (size_t i = 1, p = 0; i < obj->length; i++) {
^
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/unstructured_domains.c -o ViennaRNA/unstructured_domains.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c predict_mfe.cpp -o predict_mfe.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
C:\rtools40\mingw32\bin\nm.exe: Warning: '.' is a directory
C:/rtools40/mingw32/bin/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/XNAString.buildbin-libdir/00LOCK-XNAString/00new/XNAString/libs/i386
** 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
converting help for package 'XNAString'
finding HTML links ... done
XNAMatchPDict html
finding level-2 HTML links ... done
XNAMatchPattern html
XNAPairwiseAlignment html
XNAString2XNAStringSet html
XNAStringFromHelm html
XNAStringToHelm html
XNAVmatchPattern html
alphabetFrequency html
backbone html
base html
changeBase html
compl_dictionary html
complementary_bases html
concatDict html
conjugate3 html
conjugate5 html
default_backbone html
default_sugar html
dictionary html
dinucleotideFrequency html
dt2Set html
duplexStructure html
duplex_structure html
helm2String html
instanceOf html
listOflists2Dt html
mfeStructure html
mimir2XnaDict html
name html
objects html
parseRnaHelmComponent html
replaceBase html
reverseComplement html
reverseComplementFun html
secondary_structure html
seqAlphabetFrequency html
seqDinucleotideFrequency html
seqVectorAlphabetFrequency html
seqVectorDinucleotideFrequency html
set2Dt html
set2List html
siRNA_HELM html
sugar html
target html
typedListCheck html
uniqueChars html
xnaObj2Dt html
xna_dictionary html
xnastringClass html
xnastringClassUnions html
xnastringElementsNumber html
xnastringSetClass html
** 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
install for x64
* installing *source* package 'XNAString' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
exec_fun_zip_add_min:
^~~~~~~~~~~~~~~~~~~~
ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable 'features' [-Wunused-variable]
unsigned int features = vrna_cpu_simd_capabilities();
^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
size_t n, offset, *lengths, num_strings, mem_strings, total_length;
^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
PRIVATE char scale2[] = "....,....5....,....6....,....7....,....8";
^~~~~~
ViennaRNA/utils/utils.c:59:15: warning: 'scale1' defined but not used [-Wunused-variable]
PRIVATE char scale1[] = "....,....1....,....2....,....3....,....4";
^~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
method = shape_method;
^
ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer
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
if (method == 'D') {
^~
ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer
} 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]
const char warning[] = "SHAPE method parameters not recognized! Using default parameters!";
^~~~~~~
ViennaRNA/constraints/SHAPE.c: In function 'vrna_constraints_add_SHAPE':
ViennaRNA/constraints/SHAPE.c:209:11: warning: 'p2' may be used uninitialized in this function [-Wmaybe-uninitialized]
(void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/constraints/SHAPE.c:209:11: warning: 'p1' may be used uninitialized in this function [-Wmaybe-uninitialized]
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
size_t k, old_size, next_entry, entry;
^~~~~
ViennaRNA/constraints/hc_depot.inc:229:16: warning: unused variable 'old_size' [-Wunused-variable]
size_t k, old_size, next_entry, entry;
^~~~~~~~
ViennaRNA/constraints/hc_depot.inc:229:13: warning: unused variable 'k' [-Wunused-variable]
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]
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]
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]
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]
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]
int p;
^
ViennaRNA/constraints/hard.c:436:49: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, strand, actual_i, *sn, *ss, *se;
^~
ViennaRNA/constraints/hard.c:436:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
unsigned int n, strand, actual_i, *sn, *ss, *se;
^
ViennaRNA/constraints/hard.c: In function 'vrna_hc_add_bp_strand':
ViennaRNA/constraints/hard.c:476:48: warning: unused variable 'l' [-Wunused-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:45: warning: unused variable 'k' [-Wunused-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^
ViennaRNA/constraints/hard.c:476:31: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^~
ViennaRNA/constraints/hard.c:476:26: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^~
ViennaRNA/constraints/hard.c:476:21: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, n_i, n_j, k, l;
^~
ViennaRNA/constraints/hard.c:476:17: warning: unused variable 'n' [-Wunused-variable]
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]
int k, l, ret;
^
ViennaRNA/constraints/hard.c:533:17: warning: unused variable 'k' [-Wunused-variable]
int k, l, ret;
^
ViennaRNA/constraints/hard.c:532:26: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
^~
ViennaRNA/constraints/hard.c:532:17: warning: variable 'n' set but not used [-Wunused-but-set-variable]
unsigned int n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
^
ViennaRNA/constraints/hard.c: In function 'vrna_hc_free':
ViennaRNA/constraints/hard.c:588:20: warning: unused variable 'i' [-Wunused-variable]
unsigned int i;
^
ViennaRNA/constraints/hard.c: In function 'default_hc_up':
ViennaRNA/constraints/hard.c:841:20: warning: unused variable 'depot' [-Wunused-variable]
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]
int *idx, ij;
^~
ViennaRNA/constraints/hard.c:1010:109: warning: variable 'se' set but not used [-Wunused-but-set-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~
ViennaRNA/constraints/hard.c:1010:99: warning: variable 'sn' set but not used [-Wunused-but-set-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~
ViennaRNA/constraints/hard.c:1010:88: warning: unused variable 't_end' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~~~~
ViennaRNA/constraints/hard.c:1010:79: warning: unused variable 't_start' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~~~~~~
ViennaRNA/constraints/hard.c:1010:74: warning: unused variable 'end' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~~
ViennaRNA/constraints/hard.c:1010:67: warning: unused variable 'start' [-Wunused-variable]
unsigned int i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
^~~~~
ViennaRNA/constraints/hard.c:1009:27: warning: unused variable 'type' [-Wunused-variable]
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]
unsigned char constraint, type, t1, t2;
^~
ViennaRNA/constraints/hard.c:1122:35: warning: unused variable 't1' [-Wunused-variable]
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]
unsigned int i, n, u;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/char_stream.c -o ViennaRNA/datastructures/char_stream.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
void *child_v, *child_v2, *v;
^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/datastructures/stream_output.c -o ViennaRNA/datastructures/stream_output.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
FILE *out;
^~~
ViennaRNA/io/file_formats.c:80:15: warning: unused variable 's' [-Wunused-variable]
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]
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]
int i;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
int E, d;
^
ViennaRNA/landscape/findpath.c:451:31: warning: unused variable 'E' [-Wunused-variable]
int E, d;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/landscape/move.c -o ViennaRNA/landscape/move.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
int i, j;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/io/io_utils.c -o ViennaRNA/io/io_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external.c -o ViennaRNA/loops/external.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal.c -o ViennaRNA/loops/internal.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external_bt.c -o ViennaRNA/loops/external_bt.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin_pf.c -o ViennaRNA/loops/hairpin_pf.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal_bt.c -o ViennaRNA/loops/internal_bt.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch_pf.c -o ViennaRNA/loops/multibranch_pf.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin.c -o ViennaRNA/loops/hairpin.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch.c -o ViennaRNA/loops/multibranch.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/external_pf.c -o ViennaRNA/loops/external_pf.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/hairpin_bt.c -o ViennaRNA/loops/hairpin_bt.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/internal_pf.c -o ViennaRNA/loops/internal_pf.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/loops/multibranch_bt.c -o ViennaRNA/loops/multibranch_bt.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/params/default.c -o ViennaRNA/params/default.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
char *cp;
^~
At top level:
ViennaRNA/params/io.c:967:1: warning: 'rd_6dim' defined but not used [-Wunused-function]
rd_6dim(char **content,
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/params/params.c -o ViennaRNA/params/params.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/search/BoyerMoore.c -o ViennaRNA/search/BoyerMoore.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/2Dfold.c -o ViennaRNA/2Dfold.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/concentrations.c -o ViennaRNA/concentrations.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/gquad.c -o ViennaRNA/gquad.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
if (n > 1600)
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
int length, energy, bonus, bonus_cnt, s;
^~~~~~~~~
ViennaRNA/snofold.c:360:23: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
int length, energy, bonus, bonus_cnt, s;
^~~~~
ViennaRNA/snofold.c: In function 'alifill_arrays':
ViennaRNA/snofold.c:587:7: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
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]
int ml, ss, cij, traced, i1, j1, p, q;
^~
ViennaRNA/snofold.c:747:30: warning: variable 'i1' set but not used [-Wunused-but-set-variable]
int ml, ss, cij, traced, i1, j1, p, q;
^~
ViennaRNA/snofold.c:734:7: warning: variable 'bonus' set but not used [-Wunused-but-set-variable]
int bonus, n_seq, *type;
^~~~~
ViennaRNA/snofold.c: In function 'backtrack':
ViennaRNA/snofold.c:1097:30: warning: variable 'j1' set but not used [-Wunused-but-set-variable]
int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;
^~
ViennaRNA/snofold.c:1097:26: warning: variable 'i1' set but not used [-Wunused-but-set-variable]
int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;
^~
At top level:
ViennaRNA/snofold.c:153:15: warning: 'alpha' defined but not used [-Wunused-variable]
PRIVATE char alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/2Dpfold.c -o ViennaRNA/2Dpfold.o
ViennaRNA/2Dpfold.c: In function 'pf2D_linear':
ViennaRNA/2Dpfold.c:967:49: warning: 'l_max_post' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k_min_post, k_max_post, *l_min_post, *l_max_post;
^~~~~~~~~~
ViennaRNA/2Dpfold.c:967:36: warning: 'l_min_post' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k_min_post, k_max_post, *l_min_post, *l_max_post;
^~~~~~~~~~
ViennaRNA/2Dpfold.c:668:58: warning: 'l_max_post_m1' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k_min_post_m1, k_max_post_m1, *l_min_post_m1, *l_max_post_m1;
^~~~~~~~~~~~~
ViennaRNA/2Dpfold.c:668:42: warning: 'l_min_post_m1' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k_min_post_m1, k_max_post_m1, *l_min_post_m1, *l_max_post_m1;
^~~~~~~~~~~~~
ViennaRNA/2Dpfold.c:665:55: warning: 'l_max_post_m' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m;
^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:665:40: warning: 'l_min_post_m' may be used uninitialized in this function [-Wmaybe-uninitialized]
int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m;
^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4163:32: warning: 'l_max_post_b' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*max_l)[d1] = MAX2((*max_l)[d1], d2);
^
ViennaRNA/2Dpfold.c:446:57: note: 'l_max_post_b' was declared here
int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b;
^~~~~~~~~~~~
ViennaRNA/2Dpfold.c:4162:32: warning: 'l_min_post_b' may be used uninitialized in this function [-Wmaybe-uninitialized]
(*min_l)[d1] = MIN2((*min_l)[d1], d2);
^
ViennaRNA/2Dpfold.c:446:42: note: 'l_min_post_b' was declared here
int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b;
^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/alphabet.c -o ViennaRNA/alphabet.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/grammar.c -o ViennaRNA/grammar.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
FLT_OR_DBL r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale;
^~~
ViennaRNA/boltzmann_sampling.c:428:61: warning: variable 'q' set but not used [-Wunused-but-set-variable]
FLT_OR_DBL r, fbd, fbds, qt, q_temp, qkl, *q, *qb, *q1k, *qln, *scale;
^
ViennaRNA/boltzmann_sampling.c:427:50: warning: unused variable 'u' [-Wunused-variable]
int ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext;
^
ViennaRNA/boltzmann_sampling.c:427:47: warning: unused variable 'k' [-Wunused-variable]
int ret, i, j, ij, n, k, u, type, *my_iindx, hc_decompose, *hc_up_ext;
^
ViennaRNA/boltzmann_sampling.c: In function 'backtrack_qm':
ViennaRNA/boltzmann_sampling.c:826:40: warning: variable 'span' set but not used [-Wunused-but-set-variable]
int k, u, cnt, span, turn, is_unpaired, *my_iindx, *jindx, *hc_up_ml, ret;
^~~~
In file included from ../src/ViennaRNA/loops/all.h:33,
from ViennaRNA/boltzmann_sampling.c:21:
ViennaRNA/boltzmann_sampling.c: In function 'backtrack':
../src/ViennaRNA/loops/internal.h:587:69: warning: 'type' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((noGUclosure) && ((type2 == 3) || (type2 == 4) || (type == 3) || (type == 4)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/boltzmann_sampling.c:1253:49: note: 'type' was declared here
unsigned int **a2s, s, n_seq, n, type, type_2, *types, u1_local, u2_local;
^~~~
In file included from ../src/ViennaRNA/loops/all.h:33,
from ViennaRNA/boltzmann_sampling.c:21:
ViennaRNA/boltzmann_sampling.c: In function 'vrna_pbacktrack5_resume_cb':
../src/ViennaRNA/loops/internal.h:587:38: warning: 'type' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((noGUclosure) && ((type2 == 3) || (type2 == 4) || (type == 3) || (type == 4)))
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/boltzmann_sampling.c:1651:29: note: 'type' was declared here
unsigned int type, type2, *tt, s, n_seq, **a2s, u1_local,
^~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/dist_vars.c -o ViennaRNA/dist_vars.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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 in this function [-Wmaybe-uninitialized]
tt = qint_4[i][j][a][b] * p_c_S[add_i5][add_i3] * p_c2_S[j][b] * scalew * rev_d;
^
ViennaRNA/part_func_up.c: In function 'Up_plot':
ViennaRNA/part_func_up.c:1615:10: warning: 'ret' may be used uninitialized in this function [-Wmaybe-uninitialized]
return ret;
^~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/special_const.c -o ViennaRNA/special_const.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/Lfold.c -o ViennaRNA/Lfold.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/bs_wrappers.c -o ViennaRNA/bs_wrappers.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/dp_matrices.c -o ViennaRNA/dp_matrices.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe.c -o ViennaRNA/mfe.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/MEA.c -o ViennaRNA/MEA.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
int max;
^~~
ViennaRNA/c_plex.c:864:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/c_plex.c: In function 'duplexfold_C':
ViennaRNA/c_plex.c:982:19: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
int i, j, l1, Emin = INF, i_min = 0, j_min = 0;
^~
ViennaRNA/c_plex.c: In function 'find_max_C':
ViennaRNA/c_plex.c:1528:13: warning: variable 'max' set but not used [-Wunused-but-set-variable]
int max;
^~~
ViennaRNA/c_plex.c:1526:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/c_plex.c: In function 'Lduplexfold_CXS':
ViennaRNA/c_plex.c:948:72: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
char *s3 = (char *)vrna_alloc(sizeof(char) * (end_t - begin_t + 2));
~~~~~~^~~~~~~~~
ViennaRNA/c_plex.c:516:13: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
ViennaRNA/c_plex.c:947:54: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
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
int max_pos_j;
^~~~~~~~~
ViennaRNA/c_plex.c:780:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/c_plex.c: In function 'Lduplexfold_C':
ViennaRNA/c_plex.c:1602:55: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
int end_t = MIN2(n1 - 10, max_pos + 1);
^
ViennaRNA/c_plex.c:1235:7: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/duplex.c -o ViennaRNA/duplex.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_window.c -o ViennaRNA/mfe_window.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
int length, i, j, s;
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
unsigned int *so, *ss, *se;
^~
At top level:
ViennaRNA/subopt.c:429:1: warning: 'print_stack' defined but not used [-Wunused-function]
print_stack(LIST *list)
^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ProfileAln.c -o ViennaRNA/ProfileAln.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/centroid.c -o ViennaRNA/centroid.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/equilibrium_probs.c -o ViennaRNA/equilibrium_probs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_window_wrappers.c -o ViennaRNA/mfe_window_wrappers.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/pf_fold.c -o ViennaRNA/pf_fold.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/cofold.c -o ViennaRNA/cofold.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
unsigned int *sn, *so, *ss;
^~
ViennaRNA/eval.c:245:23: warning: variable 'so' set but not used [-Wunused-but-set-variable]
unsigned int *sn, *so, *ss;
^~
ViennaRNA/eval.c: In function 'en_corr_of_loop_gquad':
ViennaRNA/eval.c:697:18: warning: variable 'sequence' set but not used [-Wunused-but-set-variable]
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]
char *string;
^~~~~~
ViennaRNA/eval.c:880:28: warning: variable 'ss' set but not used [-Wunused-but-set-variable]
unsigned int *sn, *so, *ss;
^~
ViennaRNA/eval.c:880:23: warning: variable 'so' set but not used [-Wunused-but-set-variable]
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]
char *sequence = vc->cons_seq;
^~~~~~~~
ViennaRNA/eval.c:1963:42: warning: 'elem_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
(elem_i - r - 1 + s - elem_j - 1 - up_mis) * P->MLbase;
~~~~~~~~~~~~~~~~~~~^~~~~~~~
ViennaRNA/eval.c:1963:30: warning: 'elem_i' may be used uninitialized in this function [-Wmaybe-uninitialized]
(elem_i - r - 1 + s - elem_j - 1 - up_mis) * P->MLbase;
~~~~~~~^~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mfe_wrappers.c -o ViennaRNA/mfe_wrappers.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
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]
int jdiff = j_pos + j - 11;
^~~~~
ViennaRNA/plex.c:996:7: warning: variable 'endy' set but not used [-Wunused-but-set-variable]
int endy;
^~~~
ViennaRNA/plex.c:994:7: warning: variable 'endx' set but not used [-Wunused-but-set-variable]
int endx;
^~~~
ViennaRNA/plex.c:613:13: warning: variable 'maxPenalty' set but not used [-Wunused-but-set-variable]
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]
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]
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]
int max;
^~~
ViennaRNA/plex.c:2379:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/plex.c:2434:15: warning: unused variable 'l1' [-Wunused-variable]
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]
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]
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]
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]
int max;
^~~
ViennaRNA/plex.c:4073:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/plex.c:4117:15: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/plex.c:4239:15: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/plex.c: In function 'plot_max':
ViennaRNA/plex.c:4287:13: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/plex.c:4306:9: warning: unused variable 'l1' [-Wunused-variable]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/plex.c: In function 'fduplexfold':
ViennaRNA/plex.c:3034:10: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
j_min--;
~~~~~^~
ViennaRNA/plex.c:3031:10: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
i_min++;
~~~~~^~
ViennaRNA/plex.c: In function 'fduplexfold_XS':
ViennaRNA/plex.c:1009:10: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
j_min--;
~~~~~^~
ViennaRNA/plex.c:1110:20: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
type = pair[S1[i]][S2[j]];
^
ViennaRNA/plex.c:607:13: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
ViennaRNA/plex.c: In function 'Lduplexfold_XS':
ViennaRNA/plex.c:2532:45: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
int end_q = MIN2(n2 - 10, max_pos_j + alignment_length2 - 1);
^
ViennaRNA/plex.c:1917:13: note: 'max_pos_j' was declared here
int max_pos_j;
^~~~~~~~~
ViennaRNA/plex.c:2530:43: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
int end_t = MIN2(n1 - 10, max_pos + 1);
^
ViennaRNA/plex.c:1916:13: note: 'max_pos' was declared here
int max_pos;
^~~~~~~
ViennaRNA/plex.c:2298:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/plex.c: In function 'Lduplexfold':
ViennaRNA/plex.c:3999:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/plex.c:4272:43: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
int end_t = MIN2(n1 - 10, max_pos + 1);
^
ViennaRNA/plex.c:3695:13: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/RNAstruct.c -o ViennaRNA/RNAstruct.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/eval_wrappers.c -o ViennaRNA/eval_wrappers.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/mm.c -o ViennaRNA/mm.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/plex_functions.c -o ViennaRNA/plex_functions.o
ViennaRNA/plex_functions.c: In function 'PKLduplexfold_XS':
ViennaRNA/plex_functions.c:303:12: warning: 'type2' may be used uninitialized in this function [-Wmaybe-uninitialized]
E -= vrna_E_ext_stem(type2, ((k < i) ? SS1[k + 1] : -1), ((l > j - 1) ? SS1[l - 1] : -1), P);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/plex_functions.c:253:21: note: 'type2' was declared here
int p, q, type, type2, E, traced, i0, j0;
^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/units.c -o ViennaRNA/units.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
int max;
^~~
ViennaRNA/ali_plex.c:848:13: warning: variable 'max_pos_j' set but not used [-Wunused-but-set-variable]
int max_pos_j;
^~~~~~~~~
ViennaRNA/ali_plex.c:891:15: warning: unused variable 'l1' [-Wunused-variable]
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]
int l1 = strchr(test.structure, '&') - test.structure;
^~
ViennaRNA/ali_plex.c: In function 'aliLduplexfold':
ViennaRNA/ali_plex.c:928:43: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
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
int max_pos_j;
^~~~~~~~~
ViennaRNA/ali_plex.c:925:38: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
int begin_t = MAX2(11, max_pos - alignment_length + 1);
^
ViennaRNA/ali_plex.c:455:9: note: 'max_pos' was declared here
int max_pos; /* get position of the best hit */
^~~~~~~
ViennaRNA/ali_plex.c:777:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
ViennaRNA/ali_plex.c: In function 'aliLduplexfold_XS':
ViennaRNA/ali_plex.c:1774:45: warning: 'max_pos_j' may be used uninitialized in this function [-Wmaybe-uninitialized]
j_flag = (begin_q == max_pos_j - 1 ? 1 : 0);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
ViennaRNA/ali_plex.c:1261:9: note: 'max_pos_j' was declared here
int max_pos_j;
^~~~~~~~~
ViennaRNA/ali_plex.c:1767:38: warning: 'max_pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
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
int max_pos; /* get position of the best hit */
^~~~~~~
ViennaRNA/ali_plex.c:1601:27: warning: 'min_j_colonne' may be used uninitialized in this function [-Wmaybe-uninitialized]
position_j[i + delta] = min_j_colonne;
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/combinatorics.c -o ViennaRNA/combinatorics.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/fold.c -o ViennaRNA/fold.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/model.c -o ViennaRNA/model.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/ribo.c -o ViennaRNA/ribo.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/commands.c -o ViennaRNA/commands.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
char *seq, *seq2;
^~~~
ViennaRNA/fold_compound.c:613:18: warning: unused variable 'seq' [-Wunused-variable]
char *seq, *seq2;
^~~
ViennaRNA/fold_compound.c:612:17: warning: variable 'cp' set but not used [-Wunused-but-set-variable]
int cp;
^~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -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]
for (size_t i = 1, p = 0; i < obj->length; i++) {
^
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ViennaRNA/unstructured_domains.c -o ViennaRNA/unstructured_domains.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c predict_mfe.cpp -o predict_mfe.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
C:\rtools40\mingw64\bin\nm.exe: Warning: '.' is a directory
C:/rtools40/mingw64/bin/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/XNAString.buildbin-libdir/XNAString/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'XNAString' as XNAString_1.2.2.zip
* DONE (XNAString)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'XNAString' successfully unpacked and MD5 sums checked
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XNAString.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 161 ]
>
> proc.time()
user system elapsed
150.87 12.54 190.07
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XNAString.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 161 ]
>
> proc.time()
user system elapsed
119.78 7.10 126.89
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XNAString.Rcheck/examples_i386/XNAString-Ex.timings
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XNAString.Rcheck/examples_x64/XNAString-Ex.timings
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