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CHECK report for motifmatchr on tokay1

This page was generated on 2019-04-13 11:27:55 -0400 (Sat, 13 Apr 2019).

Package 996/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifmatchr 1.4.0
Alicia Schep
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/motifmatchr
Branch: RELEASE_3_8
Last Commit: 3761e63
Last Changed Date: 2018-10-30 11:42:05 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifmatchr
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifmatchr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings motifmatchr_1.4.0.tar.gz
StartedAt: 2019-04-13 03:58:29 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:05:00 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 390.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: motifmatchr.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifmatchr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings motifmatchr_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifmatchr.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'motifmatchr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'motifmatchr' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/example_motifs.Rd:11: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:52: file link 'PFMatrix' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:53: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:53: file link 'PWMatrix' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:54: file link 'PWMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:56: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:57: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:57: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:62: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:63: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:64: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:66: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:89: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:90: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifmatchr.Rcheck/00install.out' for details.
* 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 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 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 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-3.8-bioc/R/library/motifmatchr/libs/i386/motifmatchr.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifmatchr.Rcheck/00check.log'
for details.

Installation output

motifmatchr.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/motifmatchr_1.4.0.tar.gz && rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifmatchr.buildbin-libdir motifmatchr_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL motifmatchr_1.4.0.zip && rm motifmatchr_1.4.0.tar.gz motifmatchr_1.4.0.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
100 75448  100 75448    0     0  1181k      0 --:--:-- --:--:-- --:--:-- 1248k

install for i386

* installing *source* package 'motifmatchr' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c r_interface.cpp -o r_interface.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MOODS/scanner.cpp -o MOODS/scanner.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < cols; ++i){
                       ^
MOODS/motif_h.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-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:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < m; ++i)
                       ^
MOODS/motif_0.cpp:31:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j < a; ++j)
                           ^
MOODS/motif_0.cpp:38:27: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < window_pos; ++i)
                           ^
MOODS/motif_0.cpp:100:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = window_pos+l; i < m; ++i)
                                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 0; i < n; ++i)
                          ^
MOODS/moods_tools.cpp:157:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t j = 0; j < a; ++j)
                              ^
MOODS/moods_tools.cpp:168:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 0; i < n; ++i)
                          ^
MOODS/moods_tools.cpp:172:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t j = 1; j < a; ++j)
                              ^
MOODS/moods_tools.cpp:190:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t j = 0; j < a; ++j)
                          ^
MOODS/moods_tools.cpp:193:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 1; i < n; ++i)
                          ^
MOODS/moods_tools.cpp:195:30: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){
                                      ^
MOODS/moods_tools.cpp:328:46: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 0; i < cols; ++i)
                          ^
MOODS/moods_tools.cpp:456:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t CODE = 0; CODE < rows; ++CODE)
                                    ^
MOODS/moods_tools.cpp:468:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 0; i < cols; ++i)
                          ^
MOODS/moods_tools.cpp:472:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t CODE = 1; CODE < rows; ++CODE)
                                    ^
MOODS/moods_tools.cpp:489:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){
                                ^
MOODS/moods_tools.cpp:500:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 1; i < cols; ++i)
                          ^
MOODS/moods_tools.cpp:503:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
                                    ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MOODS/match_types.cpp -o MOODS/match_types.o
C:/Rtools/mingw_32/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˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/motifmatchr.buildbin-libdir/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  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/example_motifs.Rd:11: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
    matchMotifs                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:52: file link 'PFMatrix' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:53: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:53: file link 'PWMatrix' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:54: file link 'PWMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:56: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:57: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:57: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:62: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:63: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:64: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:66: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:89: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpyA2WZU/R.INSTALL1fec21c09ba/motifmatchr/man/matchMotifs.Rd:90: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    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
In R CMD INSTALL

install for x64

* installing *source* package 'motifmatchr' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c r_interface.cpp -o r_interface.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MOODS/scanner.cpp -o MOODS/scanner.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < cols; ++i){
                       ^
MOODS/motif_h.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-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:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < m; ++i)
                       ^
MOODS/motif_0.cpp:31:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j < a; ++j)
                           ^
MOODS/motif_0.cpp:38:27: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < window_pos; ++i)
                           ^
MOODS/motif_0.cpp:100:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = window_pos+l; i < m; ++i)
                                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 0; i < n; ++i)
                          ^
MOODS/moods_tools.cpp:157:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t j = 0; j < a; ++j)
                              ^
MOODS/moods_tools.cpp:168:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 0; i < n; ++i)
                          ^
MOODS/moods_tools.cpp:172:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t j = 1; j < a; ++j)
                              ^
MOODS/moods_tools.cpp:190:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t j = 0; j < a; ++j)
                          ^
MOODS/moods_tools.cpp:193:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 1; i < n; ++i)
                          ^
MOODS/moods_tools.cpp:195:30: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){
                                      ^
MOODS/moods_tools.cpp:328:46: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 0; i < cols; ++i)
                          ^
MOODS/moods_tools.cpp:456:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t CODE = 0; CODE < rows; ++CODE)
                                    ^
MOODS/moods_tools.cpp:468:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 0; i < cols; ++i)
                          ^
MOODS/moods_tools.cpp:472:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t CODE = 1; CODE < rows; ++CODE)
                                    ^
MOODS/moods_tools.cpp:489:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){
                                ^
MOODS/moods_tools.cpp:500:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i = 1; i < cols; ++i)
                          ^
MOODS/moods_tools.cpp:503:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
                                    ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MOODS/match_types.cpp -o MOODS/match_types.o
C:/Rtools/mingw_64/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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/motifmatchr.buildbin-libdir/motifmatchr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifmatchr' as motifmatchr_1.4.0.zip
* DONE (motifmatchr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'motifmatchr' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

motifmatchr.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(motifmatchr)

> 
> test_check("motifmatchr")
== testthat results  ===========================================================
OK: 50 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  12.06    1.06   13.12

motifmatchr.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(motifmatchr)

> 
> test_check("motifmatchr")
== testthat results  ===========================================================
OK: 50 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.07    0.81   17.87

Example timings

motifmatchr.Rcheck/examples_i386/motifmatchr-Ex.timings

nameusersystemelapsed
example_motifs000
matchMotifs0.510.110.63
motifCounts0.530.360.89
motifMatches0.280.250.53
motifScores0.360.090.45
pwmType0.000.020.01

motifmatchr.Rcheck/examples_x64/motifmatchr-Ex.timings

nameusersystemelapsed
example_motifs0.020.000.02
matchMotifs1.840.071.91
motifCounts0.750.090.84
motifMatches0.520.090.61
motifScores0.480.050.53
pwmType000