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CHECK report for universalmotif on tokay2

This page was generated on 2019-04-09 12:43:02 -0400 (Tue, 09 Apr 2019).

Package 1665/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
universalmotif 1.1.66
Benjamin Jean-Marie Tremblay
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/universalmotif
Branch: master
Last Commit: 658826b
Last Changed Date: 2019-04-08 09:22:42 -0400 (Mon, 08 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: universalmotif
Version: 1.1.66
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:universalmotif.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings universalmotif_1.1.66.tar.gz
StartedAt: 2019-04-09 06:33:23 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:40:33 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 429.7 seconds
RetCode: 1
Status:  ERROR  
CheckDir: universalmotif.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:universalmotif.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings universalmotif_1.1.66.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/universalmotif.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.1.66'
* 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 'universalmotif' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/universalmotif/man/get_bkg.Rd:53: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/universalmotif/man/motif_pvalue.Rd:69: file link 'qnorm' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/universalmotif/man/reexports.Rd:25: file link 'rowMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/universalmotif/man/scan_sequences.Rd:75: file link 'mask' in package 'Biostrings' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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
convert_to_tfbstools_tffmfirst: no visible binding for global variable
  '2'
motif_peaks: no visible binding for global variable 'x'
motif_peaks: no visible binding for global variable 'y'
motif_tree: no visible binding for global variable 'group'
motif_tree: no visible binding for global variable 'icscore'
Undefined global functions or variables:
  2 group icscore x y
* 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-3.9-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)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/universalmotif/libs/x64/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
motif_peaks    16.39   1.12   17.63
convert_motifs  9.47   0.80   10.60
filter_motifs   4.66   0.39    5.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
convert_motifs 11.92   0.37   12.29
motif_peaks     9.85   0.09    9.96
add_multifreq   1.07   0.02    9.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(universalmotif)
  > 
  > test_check("universalmotif")
  == testthat results  ===========================================================
  OK: 211 SKIPPED: 1 FAILED: 0
** running tests for arch 'x64' ...
  Running 'spelling.R'
  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 ERROR, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/universalmotif_1.1.66.tar.gz && rm -rf universalmotif.buildbin-libdir && mkdir universalmotif.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=universalmotif.buildbin-libdir universalmotif_1.1.66.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL universalmotif_1.1.66.zip && rm universalmotif_1.1.66.tar.gz universalmotif_1.1.66.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  427k  100  427k    0     0  1394k      0 --:--:-- --:--:-- --:--:-- 1428k

install for i386

* installing *source* package 'universalmotif' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c motif_peaks_helper.cpp -o motif_peaks_helper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c shuffle_sequences_helper.cpp -o shuffle_sequences_helper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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_peaks_helper.o motif_pvalue_helper.o motif_simil_helper.o scan_sequences_helper.o shuffle_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˜1.9-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-3.9-bioc/meat/universalmotif.buildbin-libdir/00LOCK-universalmotif/00new/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
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
*** 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  
    get_bkg                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/universalmotif/man/get_bkg.Rd:53: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
    merge_motifs                            html  
    motif_peaks                             html  
    motif_pvalue                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/universalmotif/man/motif_pvalue.Rd:69: file link 'qnorm' in package 'stats' does not exist and so has been treated as a topic
    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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/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  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2h9Dzx/R.INSTALL1ba42ddb781f/universalmotif/man/scan_sequences.Rd:75: file link 'mask' in package 'Biostrings' does not exist and so has been treated as a topic
    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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'universalmotif' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c motif_peaks_helper.cpp -o motif_peaks_helper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c shuffle_sequences_helper.cpp -o shuffle_sequences_helper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-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_peaks_helper.o motif_pvalue_helper.o motif_simil_helper.o scan_sequences_helper.o shuffle_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˜1.9-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-3.9-bioc/meat/universalmotif.buildbin-libdir/universalmotif/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'universalmotif' as universalmotif_1.1.66.zip
* DONE (universalmotif)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'universalmotif' successfully unpacked and MD5 sums checked

Tests output

universalmotif.Rcheck/tests_i386/spelling.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.20    0.03    0.21 

universalmotif.Rcheck/tests_x64/spelling.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.12    0.10    0.21 

universalmotif.Rcheck/tests_i386/testthat.Rout.fail


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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: 211 SKIPPED: 1 FAILED: 0

universalmotif.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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: 211 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  16.53    0.39   19.50 

Example timings

universalmotif.Rcheck/examples_i386/universalmotif-Ex.timings

nameusersystemelapsed
add_multifreq0.790.041.99
compare_motifs0.020.000.01
convert_motifs 9.47 0.8010.60
convert_type000
create_motif0.370.020.39
create_sequences0.020.000.01
enrich_motifs0.370.071.91
filter_motifs4.660.395.05
get_bkg0.830.040.86
merge_motifs000
motif_peaks16.39 1.1217.63
motif_pvalue0.030.000.03
motif_rc000
motif_tree0.080.000.08
read_cisbp0.000.000.06
read_homer0.000.000.11
read_jaspar0.020.000.01
read_matrix0.010.000.19
read_meme0.000.000.35
read_transfac0.000.000.15
read_uniprobe0.020.000.51
run_meme000
sample_sites0.010.000.02
scan_sequences0.290.070.36
shuffle_sequences0.010.000.01
switch_alph000
trim_motifs0.020.000.02
universalmotif-class0.010.000.02
utilities0.030.000.03
view_motifs000
write_homer000
write_jaspar0.020.000.02
write_matrix0.000.000.12
write_meme0.030.000.03
write_transfac0.000.020.02

universalmotif.Rcheck/examples_x64/universalmotif-Ex.timings

nameusersystemelapsed
add_multifreq1.070.029.56
compare_motifs0.020.000.02
convert_motifs11.92 0.3712.29
convert_type0.020.000.02
create_motif0.480.050.53
create_sequences0.020.000.02
enrich_motifs0.140.010.15
filter_motifs3.700.133.83
get_bkg0.830.000.82
merge_motifs000
motif_peaks9.850.099.96
motif_pvalue0.020.000.01
motif_rc000
motif_tree0.060.000.06
read_cisbp000
read_homer000
read_jaspar0.020.000.02
read_matrix000
read_meme0.010.000.02
read_transfac000
read_uniprobe0.000.020.01
run_meme000
sample_sites0.020.000.02
scan_sequences0.300.040.34
shuffle_sequences0.010.000.02
switch_alph000
trim_motifs0.020.000.01
universalmotif-class0.030.000.03
utilities0.010.000.02
view_motifs000
write_homer000
write_jaspar0.020.000.01
write_matrix0.000.000.21
write_meme0.030.000.03
write_transfac0.020.000.01