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CHECK report for FourCSeq on merida1

This page was generated on 2019-04-16 11:57:55 -0400 (Tue, 16 Apr 2019).

Package 558/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FourCSeq 1.16.0
Felix A. Klein
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/FourCSeq
Branch: RELEASE_3_8
Last Commit: 2484619
Last Changed Date: 2018-10-30 11:41:55 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FourCSeq
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2019-04-16 00:00:54 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:08:35 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 461.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: FourCSeq.Rcheck
Warnings: 1

Command output

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### Running 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/FourCSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.0’
* 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-3.8-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 : <anonymous>: 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
plotScatter     43.887  2.904  47.103
getZScores      32.355  8.358  40.886
plotDifferences  7.409  0.189   7.604
plotZScores      5.354  0.115   5.499
* 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-3.8-bioc/meat/FourCSeq.Rcheck/00check.log’
for details.



Installation output

FourCSeq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FourCSeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘FourCSeq’ ...
** 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
* DONE (FourCSeq)

Tests output


Example timings

FourCSeq.Rcheck/FourCSeq-Ex.timings

nameusersystemelapsed
FourC0.5500.0630.614
addFragments0.9740.0140.992
addViewpointFrags1.6110.0051.626
combineFragEnds0.2020.0240.228
countFragmentOverlaps1.8270.1692.011
countFragmentOverlapsSecondCutter000
fc0.1290.0110.140
fcf0.2110.0220.233
findViewpointFragments0.6690.0030.681
getAllResults3.8990.1254.037
getDifferences4.3250.1084.449
getDistAroundVp0.3610.0290.392
getNormalizationFactors0.3280.0160.346
getReferenceSeq0.1580.0080.166
getZScores32.355 8.35840.886
normalizeRPM0.2010.0360.238
plotDifferences7.4090.1897.604
plotFits0.5920.0290.634
plotNormalizationFactors2.8130.0632.888
plotScatter43.887 2.90447.103
plotZScores5.3540.1155.499
smoothCounts0.2610.0390.303
smoothHitPerCent2.0460.3282.391
writeTrackFiles0.9450.0791.032