Package: motifStack

Version: 1.22.4

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings motifStack_1.22.4.tar.gz

StartedAt: 2018-04-12 01:16:19 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:19:46 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 207.0 seconds

RetCode: 0

Status:  OK

CheckDir: motifStack.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings motifStack_1.22.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/motifStack.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.22.4’
* 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 ‘motifStack’ 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 ... NOTE
motifCircos: no visible global function definition for ‘par’
motifCircos: no visible global function definition for ‘plot.default’
motifCircos: no visible binding for global variable ‘strwidth’
motifCircos : plotBgArc: no visible global function definition for
  ‘polygon’
motifCircos: no visible global function definition for ‘text’
motifCircos: no visible global function definition for ‘segments’
motifCircos: no visible global function definition for ‘points’
motifCircos: no visible global function definition for ‘lines’
motifCircos: no visible global function definition for ‘symbols’
motifCircos: no visible global function definition for ‘strwidth’
motifCircos: no visible global function definition for ‘box’
motifCloud: no visible global function definition for ‘par’
motifCloud: no visible global function definition for ‘plot.new’
motifCloud: no visible global function definition for ‘strheight’
motifCloud: no visible global function definition for ‘plot.window’
motifCloud: no visible global function definition for ‘plot.default’
motifCloud : plotUnrootedTree: no visible global function definition
  for ‘segments’
motifCloud : plotUnrootedTree: no visible global function definition
  for ‘strheight’
motifCloud: no visible global function definition for ‘segments’
motifCloud: no visible global function definition for ‘legend’
motifPiles: no visible global function definition for ‘par’
motifPiles: no visible global function definition for ‘plot.default’
motifPiles: no visible binding for global variable ‘strwidth’
motifPiles: no visible global function definition for ‘strwidth’
motifPiles: no visible global function definition for ‘points’
motifPiles: no visible global function definition for ‘segments’
motifPiles: no visible global function definition for ‘abline’
motifPiles: no visible global function definition for ‘rect’
motifPiles: no visible global function definition for ‘text’
motifStack: no visible global function definition for ‘plot’
plotAffinityLogo: no visible binding for global variable ‘plot.new’
plotAffinityLogo: no visible global function definition for ‘plot.new’
plotAffinityLogo: no visible global function definition for ‘text’
plotMotifLogo: no visible global function definition for ‘plot.new’
plotMotifLogo: no visible global function definition for ‘text’
plotMotifLogo: no visible global function definition for ‘mtext’
plotMotifLogoStack: no visible global function definition for ‘par’
plotMotifLogoStack: no visible global function definition for ‘plot’
plotMotifLogoStackWithTree: no visible global function definition for
  ‘par’
plotMotifLogoStackWithTree: no visible global function definition for
  ‘layout’
plotMotifLogoStackWithTree: no visible global function definition for
  ‘plot.new’
plotMotifLogoStackWithTree: no visible global function definition for
  ‘plot’
plotMotifOverMotif: no visible global function definition for
  ‘plot.new’
plotMotifStackWithPhylog: no visible global function definition for
  ‘par’
plotMotifStackWithPhylog: no visible global function definition for
  ‘plot.default’
plotMotifStackWithPhylog: no visible binding for global variable
  ‘strwidth’
plotMotifStackWithPhylog: no visible global function definition for
  ‘strwidth’
plotMotifStackWithPhylog: no visible global function definition for
  ‘text’
plotMotifStackWithPhylog: no visible global function definition for
  ‘segments’
plotMotifStackWithPhylog: no visible global function definition for
  ‘points’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘par’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘plot.default’
plotMotifStackWithRadialPhylog: no visible binding for global variable
  ‘strwidth’
plotMotifStackWithRadialPhylog : plotBgArc: no visible global function
  definition for ‘polygon’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘text’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘segments’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘points’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘lines’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘symbols’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘strwidth’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘box’
plotXaxis: no visible global function definition for ‘axis’
plotYaxis: no visible global function definition for ‘axis’
plotYaxis: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline axis box layout legend lines mtext par plot plot.default
  plot.new plot.window points polygon rect segments strheight strwidth
  symbols text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "layout", "legend",
             "lines", "mtext", "par", "plot", "plot.default", "plot.new",
             "plot.window", "points", "polygon", "rect", "segments",
             "strheight", "strwidth", "symbols", "text")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.6-bioc/meat/motifStack.Rcheck/00check.log’
for details.

* installing *source* package ‘motifStack’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifStack)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

> require("motifStack") || stop("unable to load Package:motifStack")
Loading required package: motifStack
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: MotIV
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'MotIV'

The following object is masked from 'package:stats':

    filter

Loading required package: ade4

Attaching package: 'ade4'

The following object is masked from 'package:BiocGenerics':

    score

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] TRUE
> #require("MotifDb") || stop("unalble to load Package::motifDb")
> BiocGenerics:::testPackage("motifStack")
Read 76 items
Read 72 items
Read 32 items
Read 28 items
Read 28 items
Read 44 items
Read 28 items
Read 36 items
Read 32 items
Read 44 items
Read 44 items
Read 32 items
Read 44 items
Read 60 items
Read 60 items
Read 55 items
Read 45 items
Read 35 items


RUNIT TEST PROTOCOL -- Thu Apr 12 01:19:41 2018 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
motifStack RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 13.012   0.168  13.188 

name	user	system	elapsed
DNAmotifAlignment	0.656	0.000	0.656
browseMotifs	2.248	0.032	2.293
colorset	0	0	0
getRankedUniqueMotifs	0.004	0.000	0.001
highlightCol	0.000	0.000	0.001
importMatrix	0.520	0.000	0.518
mergeMotifs	0.196	0.000	0.195
motifCircos	0.008	0.000	0.005
motifCloud	0.004	0.000	0.003
motifPiles	0.004	0.000	0.004
motifSignature	0.004	0.000	0.003
motifStack	0.000	0.000	0.001
ouNode-class	0.000	0.000	0.002
pcm-class	1.036	0.296	1.869
pcm-methods	0.008	0.000	0.008
pfm-class	0.788	0.316	1.155
pfm-methods	0.008	0.000	0.010
pfm2pwm	0.156	0.008	0.164
plotAffinityLogo	1.160	0.296	1.495
plotMotifLogo	0.524	0.312	0.889
plotMotifLogoA	0.888	0.288	1.217
plotMotifLogoStack	0.528	0.272	0.844
plotMotifLogoStackWithTree	1.484	0.536	2.096
plotMotifOverMotif	0.568	0.244	0.854
plotMotifStackWithPhylog	0.000	0.000	0.003
plotMotifStackWithRadialPhylog	0.000	0.000	0.003
psam-class	1.096	0.288	1.428
psam-methods	0.012	0.004	0.013
readPCM	0.008	0.000	0.009
reorderUPGMAtree	0.004	0.000	0.002