BioC 3.3: CHECK report for Chicago on morelia

Package: Chicago

Version: 0.99.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Chicago_0.99.7.tar.gz

StartedAt: 2016-04-21 00:07:59 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 00:10:51 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 171.5 seconds

RetCode: 0

Status:  OK

CheckDir: Chicago.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Chicago_0.99.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Chicago.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Chicago/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Chicago’ version ‘0.99.7’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Chicago’ can be installed ... [6s/7s] 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
.addTLB: no visible global function definition for ‘quantile’
.binning: no visible binding for global variable ‘dist’
.estimateDispersion: no visible binding for global variable ‘dist’
.getAvgFragLength: no visible binding for global variable ‘end’
.getNoOfHypotheses: no visible binding for global variable ‘end’
.getSampleScalingFactors: no visible global function definition for
  ‘median’
.getWeights: no visible binding for global variable ‘end’
.normaliseFragmentSets: no visible global function definition for
  ‘median’
.normaliseFragmentSets: no visible global function definition for
  ‘predict’
.normaliseFragmentSets: no visible global function definition for
  ‘loess’
.normaliseFragmentSets: no visible global function definition for ‘pdf’
.normaliseFragmentSets: no visible global function definition for ‘par’
.normaliseFragmentSets: no visible global function definition for
  ‘lines’
.normaliseFragmentSets: no visible global function definition for
  ‘dev.off’
.normaliseFragmentSets: no visible global function definition for
  ‘pgamma’
.plotNumberOL: no visible binding for global variable ‘dist’
.plotNumberOL: no visible binding for global variable ‘sd’
.plotNumberOL: no visible global function definition for ‘pdf’
.plotNumberOL: no visible global function definition for ‘barplot’
.plotNumberOL: no visible global function definition for ‘arrows’
.plotNumberOL: no visible global function definition for ‘dev.off’
.splitCHiC: no visible global function definition for ‘read.table’
.splitCHiC: no visible binding for global variable ‘dist’
estimateDistFun: no visible global function definition for ‘lm’
estimateDistFun: no visible global function definition for ‘pdf’
estimateDistFun: no visible global function definition for ‘legend’
estimateDistFun: no visible global function definition for ‘dev.off’
estimateTechnicalNoise: no visible global function definition for ‘pdf’
estimateTechnicalNoise: no visible global function definition for ‘par’
estimateTechnicalNoise: no visible global function definition for
  ‘boxplot’
estimateTechnicalNoise: no visible global function definition for
  ‘dev.off’
exportResults: no visible global function definition for ‘write.table’
getPvals: no visible global function definition for ‘ppois’
getPvals: no visible global function definition for ‘pnbinom’
normaliseOtherEnds: no visible global function definition for ‘pdf’
normaliseOtherEnds: no visible global function definition for ‘legend’
normaliseOtherEnds: no visible global function definition for ‘dev.off’
peakEnrichment4Features: no visible global function definition for
  ‘plot’
peakEnrichment4Features: no visible global function definition for
  ‘density’
peakEnrichment4Features: no visible global function definition for
  ‘lines’
plotBaits: no visible global function definition for ‘pdf’
plotBaits: no visible global function definition for ‘par’
plotBaits: no visible global function definition for ‘plot’
plotBaits: no visible global function definition for ‘abline’
plotBaits: no visible global function definition for ‘lines’
plotBaits: no visible global function definition for ‘dev.off’
plotDistFun: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline arrows barplot boxplot density dev.off dist end legend lines
  lm loess median par pdf pgamma plot pnbinom ppois predict quantile
  read.table sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "arrows", "barplot", "boxplot",
             "legend", "lines", "par", "plot")
  importFrom("stats", "density", "dist", "end", "lm", "loess", "median",
             "pgamma", "pnbinom", "ppois", "predict", "quantile", "sd")
  importFrom("utils", "read.table", "write.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/71s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
normaliseOtherEnds 12.534  2.215  49.747
exportResults      12.146  0.274  12.702
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/5s]
 [4s/6s] 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-3.3-bioc/meat/Chicago.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
cdUnitTest	0.053	0.006	0.059
chicagoData	0.001	0.000	0.002
chicagoPipeline	0.087	0.012	0.099
copyCD	0.006	0.001	0.006
defaultSettings	0.001	0.001	0.002
estimateBrownianComponent	0.185	0.012	0.198
estimateDistFun	0.033	0.002	0.035
estimateTechnicalNoise	0.085	0.004	0.089
exportResults	12.146	0.274	12.702
getPvals	0.056	0.001	0.086
getScores	0.067	0.003	0.071
getSkOnly	0.161	0.006	0.167
mergeSamples	0.149	0.008	0.158
modifySettings	0.022	0.002	0.023
normaliseBaits	0.122	0.002	0.124
normaliseOtherEnds	12.534	2.215	49.747
overlapFragWithFeatures	0.123	0.003	0.126
peakEnrichment4Features	3.004	0.535	3.563
plotBaits	0.389	0.019	0.420
plotDistFun	0.010	0.008	0.315
readAndMerge	0.146	0.002	0.149
readSample	0.096	0.002	0.100
setExperiment	0.014	0.001	0.015