BioC 3.3: CHECK report for BiSeq on oaxaca

Package: BiSeq

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiSeq_1.12.0.tar.gz

StartedAt: 2016-10-12 23:43:21 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:48:08 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 287.7 seconds

RetCode: 0

Status:  OK

CheckDir: BiSeq.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 BiSeq_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/BiSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiSeq’ version ‘1.12.0’
* 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 ‘BiSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Formula’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘Formula’
  All declared Imports should be used.
Package in Depends field not imported from: ‘Formula’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.betaRegression : inv.link: no visible global function definition for
  ‘pnorm’
.betaRegression : beta.regr: no visible global function definition for
  ‘as.formula’
.categorialColors: no visible global function definition for ‘colors’
.estLocCor: no visible global function definition for ‘combn’
.logisticRegression : inv.link: no visible global function definition
  for ‘pnorm’
.logisticRegression : logistic.regr: no visible global function
  definition for ‘lm’
.logisticRegression : logistic.regr: no visible global function
  definition for ‘as.formula’
.makeVariogram: no visible global function definition for ‘qnorm’
.plotBindingSites: no visible global function definition for
  ‘txtProgressBar’
.plotBindingSites: no visible global function definition for
  ‘setTxtProgressBar’
.plotBindingSites : <anonymous>: no visible global function definition
  for ‘ksmooth’
.plotBindingSites: no visible global function definition for ‘rainbow’
.plotBindingSites: no visible binding for global variable ‘plot’
.plotBindingSites: no visible global function definition for ‘lines’
.plotBindingSites: no visible global function definition for ‘rgb’
.plotBindingSites: no visible global function definition for ‘col2rgb’
.plotMeth: no visible global function definition for ‘col2rgb’
.plotMeth: no visible global function definition for ‘rgb’
.plotMeth: no visible binding for global variable ‘plot’
.plotMeth: no visible global function definition for ‘lines’
.plotMeth: no visible global function definition for ‘legend’
.plotMethMap: no visible global function definition for
  ‘colorRampPalette’
.plotMethMap: no visible binding for global variable ‘heatmap’
.plotSmoothMeth: no visible global function definition for ‘rainbow’
.plotSmoothMeth: no visible binding for global variable ‘plot’
.plotSmoothMeth: no visible global function definition for ‘lines’
.predictMeth: no visible global function definition for
  ‘txtProgressBar’
.predictMeth: no visible global function definition for
  ‘setTxtProgressBar’
.testClusters: no visible global function definition for ‘pnorm’
.trimClusters : integrand: no visible global function definition for
  ‘pnorm’
.trimClusters : integrand: no visible global function definition for
  ‘qnorm’
.trimClusters : integrand: no visible global function definition for
  ‘dnorm’
.trimClusters: no visible global function definition for ‘integrate’
.trimClusters: no visible global function definition for ‘pnorm’
.trimClusters: no visible global function definition for ‘qnorm’
.variogram: no visible global function definition for ‘dist’
.variogram: no visible global function definition for ‘txtProgressBar’
.variogram: no visible global function definition for
  ‘setTxtProgressBar’
.writeBED_BSraw: no visible global function definition for ‘colorRamp’
.writeBED_BSraw: no visible global function definition for ‘rgb’
.writeBED_BSrel: no visible global function definition for ‘colorRamp’
.writeBED_BSrel: no visible global function definition for ‘rgb’
betaRegression,formula-character-BSrel-numeric : inv.link: no visible
  global function definition for ‘pnorm’
betaRegression,formula-character-BSrel-numeric : beta.regr: no visible
  global function definition for ‘as.formula’
estLocCor,list: no visible global function definition for ‘combn’
logisticRegression,formula-character-BSrel-numeric : inv.link: no
  visible global function definition for ‘pnorm’
logisticRegression,formula-character-BSrel-numeric : logistic.regr: no
  visible global function definition for ‘lm’
logisticRegression,formula-character-BSrel-numeric : logistic.regr: no
  visible global function definition for ‘as.formula’
makeVariogram,data.frame-logical-numeric-numeric: no visible global
  function definition for ‘qnorm’
plotMethMap,BSrel-GRanges-factor-logical: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-factor-logical: no visible binding for global
  variable ‘heatmap’
plotMethMap,BSrel-GRanges-factor-missing: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-factor-missing: no visible binding for global
  variable ‘heatmap’
plotMethMap,BSrel-GRanges-missing-logical: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-missing-logical: no visible binding for
  global variable ‘heatmap’
plotMethMap,BSrel-GRanges-missing-missing: no visible global function
  definition for ‘colorRampPalette’
plotMethMap,BSrel-GRanges-missing-missing: no visible binding for
  global variable ‘heatmap’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for ‘txtProgressBar’
predictMeth,BSraw-numeric-numeric-numeric: no visible global function
  definition for ‘setTxtProgressBar’
testClusters,list-numeric: no visible global function definition for
  ‘pnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘pnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘qnorm’
trimClusters,list-numeric : integrand: no visible global function
  definition for ‘dnorm’
trimClusters,list-numeric: no visible global function definition for
  ‘integrate’
trimClusters,list-numeric: no visible global function definition for
  ‘pnorm’
trimClusters,list-numeric: no visible global function definition for
  ‘qnorm’
writeBED,BSraw-character-character: no visible global function
  definition for ‘colorRamp’
writeBED,BSraw-character-character: no visible global function
  definition for ‘rgb’
writeBED,BSrel-character-character: no visible global function
  definition for ‘colorRamp’
writeBED,BSrel-character-character: no visible global function
  definition for ‘rgb’
Undefined global functions or variables:
  as.formula col2rgb colorRamp colorRampPalette colors combn dist dnorm
  heatmap integrate ksmooth legend lines lm plot pnorm qnorm rainbow
  rgb setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "col2rgb", "colorRamp", "colorRampPalette",
             "colors", "rainbow", "rgb")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "as.formula", "dist", "dnorm", "heatmap",
             "integrate", "ksmooth", "lm", "pnorm", "qnorm")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
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
globalTest     26.459  0.130  26.706
betaRegression 12.942  0.600  13.784
estLocCor       5.446  0.639   6.139
makeVariogram   4.996  0.440   5.443
* 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-3.3-bioc/meat/BiSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘BiSeq’ ...
** 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 (BiSeq)

name	user	system	elapsed
BSraw-class	0.208	0.019	0.229
BSrel-class	0.124	0.008	0.132
DMRs	0.059	0.003	0.063
annotateGRanges	0.230	0.011	0.257
betaRegression	12.942	0.600	13.784
betaResults	0.006	0.001	0.007
betaResultsNull	0.006	0.002	0.007
binomLikelihoodSmooth	0.006	0.000	0.007
clusterSites	0.378	0.176	0.617
clusterSitesToGR	0.465	0.234	0.677
compareTwoSamples	2.688	1.927	4.360
covBoxplots	0.110	0.016	0.126
covStatistics	0.054	0.010	0.064
estLocCor	5.446	0.639	6.139
filterByCov	0.124	0.011	0.135
filterBySharedRegions	0.126	0.016	0.143
findDMRs	0.544	0.013	0.557
globalTest	26.459	0.130	26.706
limitCov	0.378	0.172	0.679
logisticRegression	1.703	0.085	1.790
makeVariogram	4.996	0.440	5.443
plotBindingSites	2.075	0.051	2.130
plotMeth	0.212	0.020	0.234
plotMethMap	0.233	0.022	0.256
plotSmoothMeth	0.129	0.011	0.142
predictMeth	1.022	0.609	1.506
predictedMeth	0.019	0.012	0.031
promoters	0.063	0.013	0.077
rawToRel	0.067	0.016	0.084
readBismark	0.078	0.010	0.088
rrbs	0.051	0.011	0.062
smoothVariogram	0.023	0.005	0.028
summarizeRegions	1.404	0.406	1.952
testClusters	0.092	0.009	0.105
trimClusters	0.565	0.045	0.611
vario	0.003	0.002	0.004
writeBED	0.203	0.014	0.218