Package: FourCSeq

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FourCSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FourCSeq_1.18.0.tar.gz

StartedAt: 2019-10-16 02:54:46 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:06:31 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 705.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FourCSeq.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FourCSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FourCSeq_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/FourCSeq.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 ‘FourCSeq’ can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/FourCSeq.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 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'
FourC: no visible global function definition for 'formula'
FourC: no visible global function definition for 'new'
addFragments: no visible global function definition for 'metadata'
addFragments: no visible global function definition for
  'subsetByOverlaps'
addFragments: no visible global function definition for 'DataFrame'
addPeaks: no visible global function definition for 'metadata'
addPeaks: no visible global function definition for 'DataFrame'
addViewpointFrags: no visible global function definition for 'metadata'
addViewpointFrags: no visible global function definition for
  'DataFrame'
countFragmentOverlaps: no visible global function definition for
  'metadata'
countFragmentOverlaps: no visible global function definition for
  'DataFrame'
countFragmentOverlaps: no visible global function definition for
  'SimpleList'
countFragmentOverlapsSecondCutter: no visible global function
  definition for 'metadata'
countFragmentOverlapsSecondCutter: no visible global function
  definition for 'DataFrame'
countFragmentOverlapsSecondCutter: no visible global function
  definition for 'SimpleList'
distFitMonotone: no visible global function definition for 'predict'
distFitMonotoneSymmetric: no visible global function definition for
  'predict'
findViewpointFragments: no visible global function definition for
  'metadata'
findViewpointFragments : : no visible global function
  definition for 'Rle'
findViewpointFragments: no visible global function definition for
  'subjectHits'
findViewpointFragments: no visible global function definition for
  'write.table'
getDifferences: no visible global function definition for 'relevel'
getDifferences: no visible global function definition for 'formula'
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'
getReferenceSeq: no visible global function definition for 'metadata'
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 binding for global variable 'mad'
getZScores: no visible binding for global variable 'median'
getZScores: no visible global function definition for 'DataFrame'
getZScores: no visible binding for global variable 'pnorm'
getZScores: no visible binding for global variable 'p.adjust'
getZScores: no visible global function definition for 'metadata'
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 'metadata'
plotDifferences: no visible global function definition for 'ggplot'
plotDifferences: no visible global function definition for
  'subsetByOverlaps'
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'
plotFits: no visible global function definition for 'metadata'
plotFits: no visible global function definition for 'par'
plotFits: no visible global function definition for 'plot'
plotFits: no visible global function definition for 'axis'
plotFits: no visible global function definition for 'mtext'
plotFits: no visible global function definition for 'points'
plotNormalizationFactors: no visible global function definition for
  'plot'
plotNormalizationFactors: no visible global function definition for
  'points'
plotNormalizationFactors: no visible global function definition for
  'legend'
plotNormalizationFactors: no visible global function definition for
  'abline'
plotSmoothScatter: no visible binding for global variable 'blues9'
plotSmoothScatter: no visible global function definition for 'axis'
plotVp: no visible global function definition for 'ggplot'
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'
plotZScores: no visible global function definition for 'metadata'
plotZScores: no visible global function definition for 'ggplot'
plotZScores: no visible global function definition for
  'subsetByOverlaps'
saveGR: no visible global function definition for 'metadata'
saveGR: no visible global function definition for 'seqlengths'
saveGR: no visible global function definition for 'write.table'
smoothCounts: no visible global function definition for 'SimpleList'
smoothHitPerCent: no visible global function definition for
  'SimpleList'
writeTrackFiles: no visible global function definition for 'metadata'
writeTrackFiles: no visible global function definition for
  'keepSeqlevels'
updateObject,FourC: no visible global function definition for
  'callNextMethod'
Undefined global functions or variables:
  DataFrame IRanges Rle Seqinfo SimpleList abline aes axis blues9
  callNextMethod change count differentialInteraction element_blank fit
  fitDown fitUp formula geom_path geom_point ggplot keepSeqlevels labs
  legend mad median metadata mid mtext new p.adjust par peak plot pnorm
  points predict rel relevel scale_fill_gradient2 scale_y_continuous
  seqlengths seqlevels seqlevels<- subjectHits subsetByOverlaps theme
  theme_bw theme_set write.table
Consider adding
  importFrom("grDevices", "blues9")
  importFrom("graphics", "abline", "axis", "legend", "mtext", "par",
             "plot", "points")
  importFrom("methods", "callNextMethod", "new")
  importFrom("stats", "formula", "mad", "median", "p.adjust", "pnorm",
             "predict", "relevel")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
getZScores      54.249 17.283  71.543
plotScatter     49.704  5.005  54.811
plotDifferences 13.153  0.214  13.369
plotZScores      8.618  0.233   8.856
getAllResults    7.207  0.389   7.597
getDifferences   5.519  0.216   5.736
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/FourCSeq.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 FourCSeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘FourCSeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
** 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 (FourCSeq)

name	user	system	elapsed
FourC	1.791	0.087	1.878
addFragments	1.505	0.157	1.663
addViewpointFrags	1.166	0.088	1.254
combineFragEnds	0.244	0.028	0.271
countFragmentOverlaps	2.480	0.026	2.522
countFragmentOverlapsSecondCutter	0	0	0
fc	0.137	0.014	0.151
fcf	0.225	0.038	0.264
findViewpointFragments	0.859	0.012	0.872
getAllResults	7.207	0.389	7.597
getDifferences	5.519	0.216	5.736
getDistAroundVp	0.659	0.057	0.716
getNormalizationFactors	0.395	0.034	0.429
getReferenceSeq	0.279	0.002	0.282
getZScores	54.249	17.283	71.543
normalizeRPM	0.275	0.049	0.324
plotDifferences	13.153	0.214	13.369
plotFits	0.717	0.060	0.785
plotNormalizationFactors	4.389	0.125	4.517
plotScatter	49.704	5.005	54.811
plotZScores	8.618	0.233	8.856
smoothCounts	0.294	0.069	0.364
smoothHitPerCent	1.427	0.607	2.034
writeTrackFiles	0.973	0.110	1.083