BioC 3.0: CHECK report for FourCSeq on oaxaca

Package: FourCSeq

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch FourCSeq_1.0.0.tar.gz

StartedAt: 2015-04-09 23:35:07 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:45:30 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 622.8 seconds

RetCode: 0

Status:  OK

CheckDir: FourCSeq.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 --no-multiarch FourCSeq_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/FourCSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FourCSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FourCSeq’ version ‘1.0.0’
* 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 ‘FourCSeq’ can be installed ... [43s/44s] 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:
  ‘DESeq2’ ‘GenomicRanges’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘ggplot2’ ‘methods’
  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
FourC: no visible global function definition for ‘SimpleList’
addFragments: no visible global function definition for ‘DataFrame’
addPeaks: no visible global function definition for ‘DataFrame’
addViewpointFrags: no visible global function definition for
  ‘DataFrame’
countFragmentOverlaps: no visible global function definition for
  ‘DataFrame’
countFragmentOverlaps: no visible global function definition for
  ‘SimpleList’
countFragmentOverlapsSecondCutter: no visible global function
  definition for ‘DataFrame’
countFragmentOverlapsSecondCutter: no visible global function
  definition for ‘SimpleList’
findViewpointFragments : <anonymous>: no visible global function
  definition for ‘Rle’
getDistAroundVp: no visible global function definition for ‘DataFrame’
getFragments: no visible global function definition for ‘Rle’
getFragments: no visible global function definition for ‘IRanges’
getFragments: no visible global function definition for ‘seqlengths’
getSites: no visible global function definition for ‘seqlevels<-’
getSites: no visible global function definition for ‘seqlevels’
getSites: no visible global function definition for ‘Seqinfo’
getSites: no visible global function definition for ‘Rle’
getZScores: no visible global function definition for ‘DataFrame’
getZScores: no visible global function definition for ‘SimpleList’
plotDifferences: no visible global function definition for ‘theme_bw’
plotDifferences: no visible global function definition for ‘rel’
plotDifferences: no visible global function definition for ‘theme_set’
plotDifferences: no visible global function definition for ‘aes’
plotDifferences: no visible binding for global variable ‘change’
plotDifferences: no visible global function definition for
  ‘scale_fill_gradient2’
plotDifferences: no visible global function definition for ‘theme’
plotDifferences: no visible global function definition for
  ‘element_blank’
plotDifferences: no visible binding for global variable ‘mid’
plotDifferences: no visible global function definition for ‘labs’
plotDifferences: no visible global function definition for ‘geom_path’
plotDifferences: no visible global function definition for ‘geom_point’
plotDifferences: no visible global function definition for
  ‘scale_y_continuous’
plotDifferences: no visible binding for global variable ‘peak’
plotDifferences: no visible binding for global variable
  ‘differentialInteraction’
plotVp: no visible global function definition for ‘aes’
plotVp: no visible binding for global variable ‘mid’
plotVp: no visible binding for global variable ‘count’
plotVp: no visible global function definition for ‘labs’
plotVp: no visible global function definition for ‘geom_path’
plotVp: no visible binding for global variable ‘fit’
plotVp: no visible binding for global variable ‘fitUp’
plotVp: no visible binding for global variable ‘fitDown’
plotVp: no visible global function definition for ‘geom_point’
plotVp: no visible global function definition for ‘scale_y_continuous’
plotVp: no visible binding for global variable ‘peak’
plotVp: no visible binding for global variable
  ‘differentialInteraction’
plotZScores: no visible global function definition for ‘theme_bw’
plotZScores: no visible global function definition for ‘rel’
plotZScores: no visible global function definition for ‘theme_set’
saveGR: no visible global function definition for ‘seqlengths’
smoothCounts: no visible global function definition for ‘SimpleList’
smoothHitPerCent: no visible global function definition for
  ‘SimpleList’
writeTrackFiles: no visible global function definition for
  ‘keepSeqlevels’
* 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 ... [161s/166s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getZScores      72.108 10.105  82.686
plotDifferences 11.364  0.075  11.742
plotZScores      7.545  0.055   7.782
plotScatter      6.118  0.320   9.553
getAllResults    6.090  0.078   6.182
getDifferences   5.081  0.041   5.140
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/FourCSeq.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
FourC	0.310	0.011	0.321
addFragments	1.392	0.009	1.403
addViewpointFrags	0.977	0.010	0.989
combineFragEnds	1.014	0.021	1.036
countFragmentOverlaps	3.309	0.050	3.363
countFragmentOverlapsSecondCutter	0.000	0.000	0.001
fc	0.135	0.012	0.147
fcf	0.231	0.018	0.250
findViewpointFragments	0.928	0.007	0.935
getAllResults	6.090	0.078	6.182
getDifferences	5.081	0.041	5.140
getDistAroundVp	0.215	0.015	0.230
getNormalizationFactors	0.297	0.017	0.316
getReferenceSeq	0.128	0.002	0.131
getZScores	72.108	10.105	82.686
normalizeRPM	0.211	0.043	0.254
plotDifferences	11.364	0.075	11.742
plotFits	0.635	0.035	0.732
plotNormalizationFactors	4.222	0.068	4.674
plotScatter	6.118	0.320	9.553
plotZScores	7.545	0.055	7.782
smoothCounts	0.272	0.051	0.325
smoothHitPerCent	3.801	0.319	4.225
writeTrackFiles	1.272	0.078	1.477