Package: alsace

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings alsace_1.14.0.tar.gz

StartedAt: 2018-04-12 00:16:39 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:17:40 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 60.9 seconds

RetCode: 0

Status:  OK

CheckDir: alsace.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings alsace_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/alsace.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alsace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alsace’ version ‘1.14.0’
* 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 ‘alsace’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘lattice’ 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
correctPeaks : <anonymous> : <anonymous>: no visible global function
  definition for ‘predict’
doALS: no visible global function definition for ‘capture.output’
findpeaks: no visible global function definition for ‘embed’
fitpeaks : fitpk: no visible global function definition for ‘dnorm’
getAllPeaks: no visible global function definition for ‘median’
getPeakTable: no visible global function definition for ‘par’
getPeakTable: no visible global function definition for
  ‘colorRampPalette’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘hclust’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘dist’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘cutree’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘aggregate’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.abline’
matchCprofiles : <anonymous>: no visible global function definition for
  ‘cor’
matchCprofiles: no visible global function definition for ‘median’
matchCprofiles: no visible global function definition for ‘cutree’
matchCprofiles: no visible global function definition for ‘hclust’
matchCprofiles: no visible global function definition for ‘as.dist’
mergeTimeWindows : <anonymous>: no visible global function definition
  for ‘cor’
mergeTimeWindows: no visible global function definition for ‘cor’
mergeTimeWindows: no visible global function definition for ‘cutree’
mergeTimeWindows: no visible global function definition for ‘hclust’
mergeTimeWindows: no visible global function definition for ‘as.dist’
mergeTimeWindows: no visible global function definition for ‘aggregate’
plot.ALS: no visible global function definition for ‘matplot’
plot.ALS: no visible global function definition for ‘abline’
preprocess : <anonymous>: no visible global function definition for
  ‘approx’
preprocess : <anonymous>: no visible global function definition for
  ‘smooth.spline’
showALSresult: no visible global function definition for
  ‘terrain.colors’
showALSresult: no visible global function definition for ‘par’
showALSresult: no visible global function definition for ‘layout’
showALSresult: no visible global function definition for ‘matplot’
showALSresult: no visible global function definition for ‘title’
showALSresult: no visible global function definition for ‘image’
showALSresult: no visible global function definition for ‘box’
showALSresult: no visible global function definition for ‘contour’
showALSresult: no visible global function definition for ‘plot’
showALSresult: no visible global function definition for ‘text’
showALSresult: no visible global function definition for ‘rect’
showALSresult: no visible global function definition for ‘axTicks’
suggestCompCombis : cC.aux: no visible global function definition for
  ‘cor’
suggestCompCombis: no visible global function definition for ‘as.dist’
suggestCompCombis: no visible global function definition for ‘hclust’
suggestCompCombis: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  abline aggregate approx as.dist axTicks box capture.output
  colorRampPalette contour cor cutree dist dnorm embed hclust image
  layout matplot median panel.abline panel.stripplot par plot predict
  rect smooth.spline stripplot terrain.colors text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "abline", "axTicks", "box", "contour", "image",
             "layout", "matplot", "par", "plot", "rect", "text", "title")
  importFrom("stats", "aggregate", "approx", "as.dist", "cor", "cutree",
             "dist", "dnorm", "embed", "hclust", "median", "predict",
             "smooth.spline")
  importFrom("utils", "capture.output")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
components   10.387  0.112  10.657
correctPeaks  6.607  0.191   6.891
* 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-3.6-bioc/meat/alsace.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
components	10.387	0.112	10.657
correctPeaks	6.607	0.191	6.891
correctRT	3.349	0.111	3.520
doALS	3.846	0.082	3.986
filterPeaks	0.068	0.002	0.072
fitpeaks	3.656	0.077	3.815
getAllPeaks	0.036	0.002	0.039
getPeakTable	3.485	0.098	3.647
opa	1.418	0.042	1.483
preprocess	0.139	0.005	0.151
showALSresult	0.064	0.004	0.070
tea	0.099	0.005	0.110
teaMerged	4.597	0.121	4.798
windows	0.199	0.010	0.211