Package: universalmotif

Version: 1.1.66

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings universalmotif_1.1.66.tar.gz

StartedAt: 2019-04-09 04:18:38 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:21:57 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 199.0 seconds

RetCode: 0

Status:  OK

CheckDir: universalmotif.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings universalmotif_1.1.66.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/universalmotif.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘universalmotif’ 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 ... 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
convert_motifs 11.007  0.446  11.518
motif_peaks     7.411  0.365   7.872
filter_motifs   7.270  0.266   7.592
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/universalmotif.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL universalmotif
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘universalmotif’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c add_multifreq_helper.cpp -o add_multifreq_helper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c motif_peaks_helper.cpp -o motif_peaks_helper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c motif_pvalue_helper.cpp -o motif_pvalue_helper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c motif_simil_helper.cpp -o motif_simil_helper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c scan_sequences_helper.cpp -o scan_sequences_helper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c shuffle_sequences_helper.cpp -o shuffle_sequences_helper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c trim_motifs_helper.cpp -o trim_motifs_helper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c universalmotif_helper.cpp -o universalmotif_helper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o universalmotif.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/universalmotif/libs
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (universalmotif)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  0.288   0.078   0.336 

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 212 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 16.478   0.884  17.466 

name	user	system	elapsed
add_multifreq	0.853	0.016	0.875
compare_motifs	0.006	0.001	0.007
convert_motifs	11.007	0.446	11.518
convert_type	0.011	0.001	0.011
create_motif	0.540	0.011	0.556
create_sequences	0.013	0.001	0.014
enrich_motifs	0.209	0.011	0.224
filter_motifs	7.270	0.266	7.592
get_bkg	1.244	0.018	1.269
merge_motifs	0.168	0.005	0.173
motif_peaks	7.411	0.365	7.872
motif_pvalue	0.016	0.001	0.017
motif_rc	0.004	0.000	0.005
motif_tree	0.049	0.001	0.049
read_cisbp	0.003	0.000	0.004
read_homer	0.004	0.000	0.005
read_jaspar	0.005	0.000	0.005
read_matrix	0.004	0.000	0.004
read_meme	0.017	0.001	0.017
read_transfac	0.009	0.001	0.009
read_uniprobe	0.007	0.000	0.007
run_meme	0.000	0.000	0.001
sample_sites	0.03	0.00	0.03
scan_sequences	0.241	0.008	0.249
shuffle_sequences	0.009	0.001	0.010
switch_alph	0.002	0.000	0.002
trim_motifs	0.006	0.000	0.006
universalmotif-class	0.016	0.002	0.018
utilities	0.017	0.001	0.017
view_motifs	0	0	0
write_homer	0.005	0.000	0.005
write_jaspar	0.021	0.001	0.021
write_matrix	0.003	0.000	0.003
write_meme	0.029	0.001	0.032
write_transfac	0.008	0.001	0.008