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BioC 3.5: CHECK report for FourCSeq on veracruz2

This page was generated on 2017-08-16 13:32:19 -0400 (Wed, 16 Aug 2017).

Package 479/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FourCSeq 1.10.0
Felix A. Klein
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/FourCSeq
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FourCSeq
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FourCSeq_1.10.0.tar.gz
StartedAt: 2017-08-16 02:55:37 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:03:34 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 477.4 seconds
RetCode: 0
Status:  OK 
CheckDir: FourCSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FourCSeq_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/FourCSeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.10.0’
* 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 ... 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'
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getZScores      47.283  7.914  56.626
plotScatter     40.479  2.134  43.818
plotDifferences 11.372  0.081  11.770
plotZScores      5.729  0.120   5.990
* 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-3.5-bioc/meat/FourCSeq.Rcheck/00check.log’
for details.


FourCSeq.Rcheck/00install.out:

* installing *source* package ‘FourCSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (FourCSeq)

FourCSeq.Rcheck/FourCSeq-Ex.timings:

nameusersystemelapsed
FourC0.6980.0050.731
addFragments1.6980.0061.750
addViewpointFrags0.9940.0041.027
combineFragEnds0.1670.0150.184
countFragmentOverlaps2.9880.0603.153
countFragmentOverlapsSecondCutter0.0010.0010.000
fc0.0970.0080.105
fcf0.1860.0200.220
findViewpointFragments0.5540.0060.575
getAllResults4.1360.0644.316
getDifferences4.2710.0344.408
getDistAroundVp0.1610.0110.173
getNormalizationFactors0.2410.0160.257
getReferenceSeq0.0730.0010.073
getZScores47.283 7.91456.626
normalizeRPM0.1840.0280.219
plotDifferences11.372 0.08111.770
plotFits0.5230.0300.564
plotNormalizationFactors2.3410.0282.415
plotScatter40.479 2.13443.818
plotZScores5.7290.1205.990
smoothCounts0.1830.0300.222
smoothHitPerCent1.6350.3302.055
writeTrackFiles0.8380.0490.923