Package: motifmatchr

Version: 1.6.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:motifmatchr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings motifmatchr_1.6.0.tar.gz

StartedAt: 2019-10-16 03:19:44 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:24:47 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 303.0 seconds

RetCode: 0

Status:  OK

CheckDir: motifmatchr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:motifmatchr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings motifmatchr_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/motifmatchr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifmatchr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifmatchr’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘motifmatchr’ can be installed ... OK
* 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
* 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 is not available
* 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 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 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/motifmatchr.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL motifmatchr
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘motifmatchr’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c r_interface.cpp -o r_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c MOODS/scanner.cpp -o MOODS/scanner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp: In member function ‘std::vector MOODS::scan::MotifH::expected_scores(const std::vector&)’:
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 MOODS::scan::MotifH::check_hit(const string&, const std::vector&, 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]];
                    ~~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c MOODS/motif_0.cpp -o MOODS/motif_0.o
MOODS/motif_0.cpp: In function ‘std::vector MOODS::scan::expected_differences(const score_matrix&, const std::vector&)’:
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&, 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 MOODS::scan::compute_lookahead_order(const std::vector&, 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)
                                    ~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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&, 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 >&, const std::vector >&, const std::vector&, 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&, 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)
                               ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp: In function ‘std::vector > MOODS::scan::scan_best_hits_dna(const string&, const std::vector > >&, 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::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]];
                            ~~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I. -I./MOODS/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c MOODS/match_types.cpp -o MOODS/match_types.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o motifmatchr.so ./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 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-motifmatchr/00new/motifmatchr/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 18.220   0.667  18.889 

name	user	system	elapsed
example_motifs	0.005	0.000	0.006
matchMotifs	0.882	0.013	0.894
motifCounts	0.701	0.027	0.729
motifMatches	0.431	0.027	0.459
motifScores	0.472	0.000	0.472
pwmType	0.010	0.001	0.010