Package: seqPattern

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqPattern.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqPattern_1.18.0.tar.gz

StartedAt: 2020-04-15 05:37:32 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:41:18 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 225.5 seconds

RetCode: 0

Status:  OK

CheckDir: seqPattern.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:seqPattern.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqPattern_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/seqPattern.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqPattern/DESCRIPTION’ ... OK
* this is package ‘seqPattern’ version ‘1.18.0’
* 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 ‘seqPattern’ 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
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.pattern.smoothscatter: no visible global function definition for
  ‘mclapply’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘png’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘par’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘colorRampPalette’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘axis’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘box’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘lines’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘text’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘abline’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘dev.off’
.pattern.smoothscatter: no visible global function definition for ‘png’
.pattern.smoothscatter: no visible global function definition for ‘par’
.pattern.smoothscatter: no visible global function definition for
  ‘colorRampPalette’
.pattern.smoothscatter: no visible global function definition for
  ‘axis’
.pattern.smoothscatter: no visible global function definition for ‘box’
.pattern.smoothscatter: no visible global function definition for
  ‘lines’
.pattern.smoothscatter: no visible global function definition for
  ‘text’
.pattern.smoothscatter: no visible global function definition for
  ‘abline’
.pattern.smoothscatter: no visible global function definition for
  ‘dev.off’
.pattern.smoothscatter: no visible global function definition for
  ‘plot’
.plot.motif.heatmap: no visible global function definition for ‘par’
.plot.motif.heatmap: no visible global function definition for ‘image’
.plot.motif.heatmap: no visible global function definition for ‘axis’
.plot.motif.heatmap: no visible global function definition for ‘box’
.plot.motif.heatmap: no visible global function definition for ‘lines’
.plot.motif.heatmap: no visible global function definition for ‘text’
.plot.motif.heatmap: no visible global function definition for ‘abline’
.plot.windowed.average: no visible global function definition for
  ‘rainbow’
.plot.windowed.average: no visible global function definition for
  ‘plot’
.plot.windowed.average : <anonymous>: no visible global function
  definition for ‘lines’
.plot.windowed.average: no visible global function definition for
  ‘legend’
.plot.windowed.average: no visible global function definition for
  ‘abline’
.smoothScatter: no visible global function definition for
  ‘colorRampPalette’
.smoothScatter: no visible binding for global variable ‘blues9’
.smoothScatter: no visible binding for global variable ‘box’
.smoothScatter: no visible global function definition for ‘par’
.smoothScatter: no visible global function definition for ‘xy.coords’
.smoothScatter: no visible global function definition for ‘image’
.smoothScatter: no visible global function definition for ‘points’
plotPatternOccurrenceAverage: no visible global function definition for
  ‘rainbow’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘installed.packages’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘detectCores’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘mclapply’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘png’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘colorRampPalette’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘layout’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘par’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘plot’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘box’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘dev.off’
plotPatternDensityMap,DNAStringSet: no visible global function
  definition for ‘installed.packages’
plotPatternDensityMap,DNAStringSet: no visible global function
  definition for ‘detectCores’
plotPatternOccurrenceAverage,DNAStringSet: no visible global function
  definition for ‘rainbow’
Undefined global functions or variables:
  abline axis blues9 box colorRampPalette detectCores dev.off image
  installed.packages layout legend lines mclapply par plot png points
  rainbow text xy.coords
Consider adding
  importFrom("grDevices", "blues9", "colorRampPalette", "dev.off", "png",
             "rainbow", "xy.coords")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "legend", "lines", "par", "plot", "points", "text")
  importFrom("utils", "installed.packages")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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
plotPatternDensityMap 54.235  0.654  55.161
plotMotifDensityMap   23.885  0.235  24.318
plotMotifScanScores   16.245  0.111  16.477
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/seqPattern.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 seqPattern
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘seqPattern’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (seqPattern)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("seqPattern")
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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

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



RUNIT TEST PROTOCOL -- Wed Apr 15 05:41:08 2020 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
seqPattern RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  5.475   0.357   5.873 

name	user	system	elapsed
getPatternOccurrenceList	1.953	0.048	2.019
motifScanHits	3.920	0.033	3.992
motifScanScores	2.399	0.033	2.453
plotMotifDensityMap	23.885	0.235	24.318
plotMotifOccurrenceAverage	3.832	0.057	3.921
plotMotifScanScores	16.245	0.111	16.477
plotPatternDensityMap	54.235	0.654	55.161
plotPatternOccurrenceAverage	3.245	0.100	3.410