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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifmatchr.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings motifmatchr_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/motifmatchr.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'motifmatchr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'motifmatchr' version '1.28.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'motifmatchr' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/motifmatchr/libs/x64/motifmatchr.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/motifmatchr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL motifmatchr
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'motifmatchr' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c r_interface.cpp -o r_interface.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/scanner.cpp -o MOODS/scanner.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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]
   26 |     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]
   27 |         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 std::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]
  256 |             CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
      |                    ~~~~~^~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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]
   28 |     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]
   31 |         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]
   38 |         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]
   64 |         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]
   96 |         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]
  100 |         for (int i = window_pos+l; i < m; ++i)
      |                                    ~~^~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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]
  155 |     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]
  157 |         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]
  168 |     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]
  172 |         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]
  190 |     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]
  193 |     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]
  195 |         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]
  320 |         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]
  328 |                 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]
  454 |     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]
  456 |         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]
  468 |     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]
  472 |         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]
  489 |     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]
  500 |     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]
  503 |         for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
      |                               ~~~~~^~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/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 std::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]
   97 |         bool done = 0;
      |              ^~~~
MOODS/moods_scan.cpp: In function 'std::vector<MOODS::match> MOODS::scan::naive_scan_dna(const std::string&, score_matrix, double, std::size_t)':
MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
  252 |                     CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
      |                            ~~~~~^~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MOODS/match_types.cpp -o MOODS/match_types.o
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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-motifmatchr/00new/motifmatchr/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (motifmatchr)

R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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Type 'contributors()' for more information and
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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(motifmatchr)

> 
> test_check("motifmatchr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
> 
> proc.time()
   user  system elapsed 
  20.60    1.21   23.64