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CHECK report for universalmotif on tokay1

This page was generated on 2019-04-13 11:29:55 -0400 (Sat, 13 Apr 2019).

Package 1613/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
universalmotif 1.0.22
Benjamin Jean-Marie Tremblay
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/universalmotif
Branch: RELEASE_3_8
Last Commit: 34a663f
Last Changed Date: 2019-03-06 10:32:14 -0400 (Wed, 06 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
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: universalmotif
Version: 1.0.22
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:universalmotif.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings universalmotif_1.0.22.tar.gz
StartedAt: 2019-04-13 06:07:48 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:12:19 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 270.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: universalmotif.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:universalmotif.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings universalmotif_1.0.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.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 'universalmotif/DESCRIPTION' ... OK
* this is package 'universalmotif' version '1.0.22'
* 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 'universalmotif' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rownames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'ncol' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rowSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rowMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.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 ... NOTE
Unexported object imported by a ':::' call: 'TFBSTools:::schneider_correction'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
motif_tree: no visible binding for global variable 'group'
motif_tree: no visible binding for global variable 'icscore'
convert_motifs,universalmotif: no visible binding for global variable
  '2'
Undefined global functions or variables:
  2 group icscore
* 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 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/universalmotif/libs/i386/universalmotif.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
Examples with CPU or elapsed time > 5s
               user system elapsed
convert_motifs 8.92   0.65    9.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
convert_motifs 8.46   0.36    8.81
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.Rcheck/00check.log'
for details.



Installation output

universalmotif.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/universalmotif_1.0.22.tar.gz && rm -rf universalmotif.buildbin-libdir && mkdir universalmotif.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=universalmotif.buildbin-libdir universalmotif_1.0.22.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL universalmotif_1.0.22.zip && rm universalmotif_1.0.22.tar.gz universalmotif_1.0.22.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
100  408k  100  408k    0     0  10.1M      0 --:--:-- --:--:-- --:--:-- 11.0M

install for i386

* installing *source* package 'universalmotif' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c add_multifreq_helper.cpp -o add_multifreq_helper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c motif_pvalue_helper.cpp -o motif_pvalue_helper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c motif_simil_helper.cpp -o motif_simil_helper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c scan_sequences_helper.cpp -o scan_sequences_helper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c trim_motifs_helper.cpp -o trim_motifs_helper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c universalmotif_helper.cpp -o universalmotif_helper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o universalmotif.dll tmp.def RcppExports.o add_multifreq_helper.o motif_pvalue_helper.o motif_simil_helper.o scan_sequences_helper.o trim_motifs_helper.o universalmotif_helper.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.dll; fi
[[: not found
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.buildbin-libdir/universalmotif/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'convert_motifs' with signature 'motifs="MotifList"': no definition for class "MotifList"
in method for 'convert_motifs' with signature 'motifs="TFFMFirst"': no definition for class "TFFMFirst"
in method for 'convert_motifs' with signature 'motifs="PFMatrix"': no definition for class "PFMatrix"
in method for 'convert_motifs' with signature 'motifs="PWMatrix"': no definition for class "PWMatrix"
in method for 'convert_motifs' with signature 'motifs="ICMatrix"': no definition for class "ICMatrix"
in method for 'convert_motifs' with signature 'motifs="XMatrixList"': no definition for class "XMatrixList"
in method for 'convert_motifs' with signature 'motifs="pwm"': no definition for class "pwm"
in method for 'convert_motifs' with signature 'motifs="pcm"': no definition for class "pcm"
in method for 'convert_motifs' with signature 'motifs="pfm"': no definition for class "pfm"
in method for 'convert_motifs' with signature 'motifs="PWM"': no definition for class "PWM"
in method for 'convert_motifs' with signature 'motifs="Motif"': no definition for class "Motif"
** help
Loading required namespace: universalmotif
*** installing help indices
  converting help for package 'universalmotif'
    finding HTML links ... done
    ArabidopsisMotif                        html  
    ArabidopsisPromoters                    html  
    finding level-2 HTML links ... done

    JASPAR2018_CORE_DBSCORES                html  
    JASPAR2018_CORE_DBSCORES_NORM           html  
    add_multifreq                           html  
    compare_motifs                          html  
    convert_motifs                          html  
    convert_type                            html  
    create_motif                            html  
    create_sequences                        html  
    enrich_motifs                           html  
    examplemotif                            html  
    examplemotif2                           html  
    filter_motifs                           html  
    merge_motifs                            html  
    motif_pvalue                            html  
    motif_rc                                html  
    motif_tree                              html  
    read_cisbp                              html  
    read_homer                              html  
    read_jaspar                             html  
    read_matrix                             html  
    read_meme                               html  
    read_motifs                             html  
    read_transfac                           html  
    read_uniprobe                           html  
    reexports                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rownames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'ncol' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rowSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'colMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpueihoe/R.INSTALL1a943f6c83/universalmotif/man/reexports.Rd:25: file link 'rowMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
    run_meme                                html  
    sample_sites                            html  
    scan_sequences                          html  
    shuffle_motifs                          html  
    shuffle_sequences                       html  
    switch_alph                             html  
    trim_motifs                             html  
    universalmotif-class                    html  
    universalmotif-pkg                      html  
    utilities                               html  
    view_motifs                             html  
    write_homer                             html  
    write_jaspar                            html  
    write_matrix                            html  
    write_meme                              html  
    write_motifs                            html  
    write_transfac                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'universalmotif' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c add_multifreq_helper.cpp -o add_multifreq_helper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c motif_pvalue_helper.cpp -o motif_pvalue_helper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c motif_simil_helper.cpp -o motif_simil_helper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c scan_sequences_helper.cpp -o scan_sequences_helper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c trim_motifs_helper.cpp -o trim_motifs_helper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c universalmotif_helper.cpp -o universalmotif_helper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o universalmotif.dll tmp.def RcppExports.o add_multifreq_helper.o motif_pvalue_helper.o motif_simil_helper.o scan_sequences_helper.o trim_motifs_helper.o universalmotif_helper.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.dll; fi
[[: not found
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/universalmotif.buildbin-libdir/universalmotif/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'universalmotif' as universalmotif_1.0.22.zip
* DONE (universalmotif)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'universalmotif' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

universalmotif.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(universalmotif)
> 
> test_check("universalmotif")
== testthat results  ===========================================================
OK: 139 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.37    0.28    6.84 

universalmotif.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(universalmotif)
> 
> test_check("universalmotif")
== testthat results  ===========================================================
OK: 139 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.87    0.23    5.65 

Example timings

universalmotif.Rcheck/examples_i386/universalmotif-Ex.timings

nameusersystemelapsed
add_multifreq0.180.000.94
compare_motifs0.020.000.01
convert_motifs8.920.659.68
convert_type0.010.000.02
create_motif0.330.050.37
create_sequences0.000.010.02
enrich_motifs1.140.311.45
filter_motifs3.490.443.92
merge_motifs000
motif_pvalue2.120.162.28
motif_rc0.020.000.02
motif_tree0.090.000.09
read_cisbp0.020.000.03
read_homer0.000.000.02
read_jaspar000
read_matrix0.010.000.08
read_meme0.020.000.07
read_transfac0.010.000.07
read_uniprobe0.160.000.23
run_meme000
sample_sites0.020.000.02
scan_sequences000
shuffle_sequences0.060.000.06
switch_alph000
trim_motifs0.010.000.02
universalmotif-class0.020.000.01
utilities0.030.000.03
view_motifs000
write_homer0.020.000.02
write_jaspar0.010.000.01
write_matrix000
write_meme0.020.000.02
write_transfac0.010.000.01

universalmotif.Rcheck/examples_x64/universalmotif-Ex.timings

nameusersystemelapsed
add_multifreq0.110.000.36
compare_motifs000
convert_motifs8.460.368.81
convert_type0.010.000.01
create_motif0.350.030.38
create_sequences0.030.020.05
enrich_motifs0.360.030.39
filter_motifs4.320.054.37
merge_motifs000
motif_pvalue1.570.001.56
motif_rc000
motif_tree0.060.010.08
read_cisbp000
read_homer000
read_jaspar000
read_matrix0.020.000.02
read_meme000
read_transfac0.010.000.01
read_uniprobe0.130.000.13
run_meme000
sample_sites0.010.000.01
scan_sequences000
shuffle_sequences0.060.020.08
switch_alph000
trim_motifs0.000.010.02
universalmotif-class0.020.000.01
utilities0.050.000.05
view_motifs000
write_homer000
write_jaspar000
write_matrix0.020.001.00
write_meme0.030.000.03
write_transfac000