Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:06:56 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

INSTALL results for motifmatchr on tokay2


To the developers/maintainers of the motifmatchr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifmatchr.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.

raw results

Package 1203/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifmatchr 1.16.0  (landing page)
Alicia Schep
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/motifmatchr
git_branch: RELEASE_3_14
git_last_commit: c191ebc
git_last_commit_date: 2021-10-26 12:35:43 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: motifmatchr
Version: 1.16.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/motifmatchr_1.16.0.tar.gz && rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifmatchr.buildbin-libdir motifmatchr_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL motifmatchr_1.16.0.zip && rm motifmatchr_1.16.0.tar.gz motifmatchr_1.16.0.zip
StartedAt: 2022-04-12 06:34:09 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:37:01 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 172.5 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/motifmatchr_1.16.0.tar.gz && rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifmatchr.buildbin-libdir motifmatchr_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL motifmatchr_1.16.0.zip && rm motifmatchr_1.16.0.tar.gz motifmatchr_1.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 17 74566   17 13290    0     0   157k      0 --:--:-- --:--:-- --:--:--  158k
100 74566  100 74566    0     0   266k      0 --:--:-- --:--:-- --:--:--  265k

install for i386

* installing *source* package 'motifmatchr' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c r_interface.cpp -o r_interface.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/scanner.cpp -o MOODS/scanner.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp: In member function 'std::vector<double> MOODS::scan::MotifH::expected_scores(const std::vector<double>&)':
MOODS/motif_h.cpp:26:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for (int i = 0; i < cols; ++i){
                     ~~^~~~~~
MOODS/motif_h.cpp:27:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int j = 0; j < rows; ++j){
                         ~~^~~~~~
MOODS/motif_h.cpp: In member function 'virtual std::pair<bool, double> MOODS::scan::MotifH::check_hit(const string&, const std::vector<unsigned char>&, std::size_t, double)':
MOODS/motif_h.cpp:256:25: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses]
             CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
                    ~~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/motif_0.cpp -o MOODS/motif_0.o
MOODS/motif_0.cpp: In function 'std::vector<double> MOODS::scan::expected_differences(const score_matrix&, const std::vector<double>&)':
MOODS/motif_0.cpp:28:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'unsigned int'} [-Wsign-compare]
     for (int i = 0; i < m; ++i)
                     ~~^~~
MOODS/motif_0.cpp:31:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'unsigned int'} [-Wsign-compare]
         for (int j = 0; j < a; ++j)
                         ~~^~~
MOODS/motif_0.cpp:38:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'unsigned int'} [-Wsign-compare]
         for (int j = 0; j < a; ++j)
                         ~~^~~
MOODS/motif_0.cpp: In function 'unsigned int MOODS::scan::window_position(const std::vector<double>&, unsigned int, unsigned int)':
MOODS/motif_0.cpp:64:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int i = 0; i < m - l; ++i)
                         ~~^~~~~~~
MOODS/motif_0.cpp: In function 'std::vector<unsigned int> MOODS::scan::compute_lookahead_order(const std::vector<double>&, unsigned int, unsigned int, unsigned int)':
MOODS/motif_0.cpp:96:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int i = 0; i < window_pos; ++i)
                         ~~^~~~~~~~~~~~
MOODS/motif_0.cpp:100:38: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int i = window_pos+l; i < m; ++i)
                                    ~~^~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&)':
MOODS/moods_tools.cpp:155:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 0; i < n; ++i)
                        ~~^~~
MOODS/moods_tools.cpp:157:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t j = 0; j < a; ++j)
                            ~~^~~
MOODS/moods_tools.cpp:168:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 0; i < n; ++i)
                        ~~^~~
MOODS/moods_tools.cpp:172:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t j = 1; j < a; ++j)
                            ~~^~~
MOODS/moods_tools.cpp:190:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t j = 0; j < a; ++j)
                        ~~^~~
MOODS/moods_tools.cpp:193:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 1; i < n; ++i)
                        ~~^~~
MOODS/moods_tools.cpp:195:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t j = 0; j < a; ++j)
                            ~~^~~
MOODS/moods_tools.cpp: In function 'score_matrix MOODS::tools::log_odds(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<double>&, double, std::size_t)':
MOODS/moods_tools.cpp:320:38: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
         for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){
                                ~~~~~~^~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp:328:46: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
                 for (size_t SCODE = 0; SCODE < 1 << (SHIFT * (q - r - 1)); ++SCODE){
                                        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&, std::size_t)':
MOODS/moods_tools.cpp:454:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 0; i < cols; ++i)
                        ~~^~~~~~
MOODS/moods_tools.cpp:456:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t CODE = 0; CODE < rows; ++CODE)
                               ~~~~~^~~~~~
MOODS/moods_tools.cpp:468:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 0; i < cols; ++i)
                        ~~^~~~~~
MOODS/moods_tools.cpp:472:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t CODE = 1; CODE < rows; ++CODE)
                               ~~~~~^~~~~~
MOODS/moods_tools.cpp:489:32: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
     for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){
                           ~~~~~^~~~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp:500:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 1; i < cols; ++i)
                        ~~^~~~~~
MOODS/moods_tools.cpp:503:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
         for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
                               ~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp: In function 'std::vector<std::vector<MOODS::match> > MOODS::scan::scan_best_hits_dna(const string&, const std::vector<std::vector<std::vector<double> > >&, std::size_t, int, unsigned int, std::size_t, std::size_t)':
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
         bool done = 0;
              ^~~~
MOODS/moods_scan.cpp: In function 'std::vector<MOODS::match> MOODS::scan::naive_scan_dna(const string&, score_matrix, double, std::size_t)':
MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
                     CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
                            ~~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/match_types.cpp -o MOODS/match_types.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o motifmatchr.dll tmp.def ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -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/motifmatchr.buildbin-libdir/00LOCK-motifmatchr/00new/motifmatchr/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'motifmatchr'
    finding HTML links ... done
    example_motifs                          html  
    matchMotifs                             html  
    motifCounts                             html  
    motifMatches                            html  
    motifScores                             html  
    motifmatchr                             html  
    motifmatchr_deprecated                  html  
    pwmType                                 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 'motifmatchr' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c r_interface.cpp -o r_interface.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/scanner.cpp -o MOODS/scanner.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp: In member function 'std::vector<double> MOODS::scan::MotifH::expected_scores(const std::vector<double>&)':
MOODS/motif_h.cpp:26:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for (int i = 0; i < cols; ++i){
                     ~~^~~~~~
MOODS/motif_h.cpp:27:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int j = 0; j < rows; ++j){
                         ~~^~~~~~
MOODS/motif_h.cpp: In member function 'virtual std::pair<bool, double> MOODS::scan::MotifH::check_hit(const string&, const std::vector<unsigned char>&, std::size_t, double)':
MOODS/motif_h.cpp:256:25: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses]
             CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
                    ~~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/motif_0.cpp -o MOODS/motif_0.o
MOODS/motif_0.cpp: In function 'std::vector<double> MOODS::scan::expected_differences(const score_matrix&, const std::vector<double>&)':
MOODS/motif_0.cpp:28:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for (int i = 0; i < m; ++i)
                     ~~^~~
MOODS/motif_0.cpp:31:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long long unsigned int'} [-Wsign-compare]
         for (int j = 0; j < a; ++j)
                         ~~^~~
MOODS/motif_0.cpp:38:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long long unsigned int'} [-Wsign-compare]
         for (int j = 0; j < a; ++j)
                         ~~^~~
MOODS/motif_0.cpp: In function 'unsigned int MOODS::scan::window_position(const std::vector<double>&, unsigned int, unsigned int)':
MOODS/motif_0.cpp:64:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int i = 0; i < m - l; ++i)
                         ~~^~~~~~~
MOODS/motif_0.cpp: In function 'std::vector<unsigned int> MOODS::scan::compute_lookahead_order(const std::vector<double>&, unsigned int, unsigned int, unsigned int)':
MOODS/motif_0.cpp:96:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int i = 0; i < window_pos; ++i)
                         ~~^~~~~~~~~~~~
MOODS/motif_0.cpp:100:38: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int i = window_pos+l; i < m; ++i)
                                    ~~^~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&)':
MOODS/moods_tools.cpp:155:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 0; i < n; ++i)
                        ~~^~~
MOODS/moods_tools.cpp:157:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t j = 0; j < a; ++j)
                            ~~^~~
MOODS/moods_tools.cpp:168:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 0; i < n; ++i)
                        ~~^~~
MOODS/moods_tools.cpp:172:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t j = 1; j < a; ++j)
                            ~~^~~
MOODS/moods_tools.cpp:190:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t j = 0; j < a; ++j)
                        ~~^~~
MOODS/moods_tools.cpp:193:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 1; i < n; ++i)
                        ~~^~~
MOODS/moods_tools.cpp:195:30: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t j = 0; j < a; ++j)
                            ~~^~~
MOODS/moods_tools.cpp: In function 'score_matrix MOODS::tools::log_odds(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<double>&, double, std::size_t)':
MOODS/moods_tools.cpp:320:38: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){
                                ~~~~~~^~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp:328:46: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
                 for (size_t SCODE = 0; SCODE < 1 << (SHIFT * (q - r - 1)); ++SCODE){
                                        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&, std::size_t)':
MOODS/moods_tools.cpp:454:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 0; i < cols; ++i)
                        ~~^~~~~~
MOODS/moods_tools.cpp:456:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t CODE = 0; CODE < rows; ++CODE)
                               ~~~~~^~~~~~
MOODS/moods_tools.cpp:468:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 0; i < cols; ++i)
                        ~~^~~~~~
MOODS/moods_tools.cpp:472:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
         for (size_t CODE = 1; CODE < rows; ++CODE)
                               ~~~~~^~~~~~
MOODS/moods_tools.cpp:489:32: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
     for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){
                           ~~~~~^~~~~~~~~~~~~~~~~~~~
MOODS/moods_tools.cpp:500:26: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'long int' [-Wsign-compare]
     for (size_t i = 1; i < cols; ++i)
                        ~~^~~~~~
MOODS/moods_tools.cpp:503:36: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
                               ~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp: In function 'std::vector<std::vector<MOODS::match> > MOODS::scan::scan_best_hits_dna(const string&, const std::vector<std::vector<std::vector<double> > >&, std::size_t, int, unsigned int, std::size_t, std::size_t)':
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
         bool done = 0;
              ^~~~
MOODS/moods_scan.cpp: In function 'std::vector<MOODS::match> MOODS::scan::naive_scan_dna(const string&, score_matrix, double, std::size_t)':
MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
                     CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
                            ~~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I. -I./MOODS/ -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/match_types.cpp -o MOODS/match_types.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o motifmatchr.dll tmp.def ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -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/motifmatchr.buildbin-libdir/motifmatchr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifmatchr' as motifmatchr_1.16.0.zip
* DONE (motifmatchr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'motifmatchr' successfully unpacked and MD5 sums checked