Back to Multiple platform build/check report for BioC 3.11
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

CHECK report for FourCSeq on malbec2

This page was generated on 2020-10-17 11:54:46 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE FourCSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 637/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FourCSeq 1.22.1
Mike Smith
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/FourCSeq
Branch: RELEASE_3_11
Last Commit: d10b2c9
Last Changed Date: 2020-08-10 08:17:54 -0400 (Mon, 10 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: FourCSeq
Version: 1.22.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:FourCSeq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings FourCSeq_1.22.1.tar.gz
StartedAt: 2020-10-17 01:25:54 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:35:26 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 571.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: FourCSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:FourCSeq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings FourCSeq_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/FourCSeq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.1’
* package encoding: UTF-8
* 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:
  Warning: Package 'FourCSeq' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/FourCSeq.Rcheck/00install.out’ for details.
* 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 ... NOTE
Package in Depends field not imported from: 'ggplot2'
  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'
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'
getDifferences: no visible global function definition for 'is'
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 'axis'
plotFits: no visible global function definition for 'mtext'
plotFits: no visible global function definition for 'points'
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'
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'
Undefined global functions or variables:
  DataFrame IRanges Rle Seqinfo SimpleList abline aes axis blues9
  change count differentialInteraction element_blank fit fitDown fitUp
  formula geom_path geom_point ggplot is keepSeqlevels labs legend mad
  median metadata mid mtext p.adjust par peak pnorm points predict rel
  relevel scale_fill_gradient2 scale_y_continuous seqlengths seqlevels
  seqlevels<- subjectHits subsetByOverlaps theme theme_bw theme_set
Consider adding
  importFrom("grDevices", "blues9")
  importFrom("graphics", "abline", "axis", "legend", "mtext", "par",
             "points")
  importFrom("methods", "is")
  importFrom("stats", "formula", "mad", "median", "p.adjust", "pnorm",
             "predict", "relevel")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotScatter     49.323  0.528  49.859
getZScores      26.757  0.164  26.920
plotDifferences  7.270  0.015   7.286
getDifferences   6.557  0.000   6.557
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/FourCSeq.Rcheck/00check.log’
for details.



Installation output

FourCSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL FourCSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘FourCSeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'FourCSeq' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'FourCSeq' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (FourCSeq)

Tests output


Example timings

FourCSeq.Rcheck/FourCSeq-Ex.timings

nameusersystemelapsed
FourC0.7930.0200.813
addFragments2.2450.0322.425
addViewpointFrags1.2390.1121.482
combineFragEnds0.2460.0280.274
countFragmentOverlaps2.1490.0162.184
countFragmentOverlapsSecondCutter0.0000.0000.001
fc0.0990.0000.099
fcf0.1740.0040.178
findViewpointFragments0.9740.0000.975
getAllResults4.2700.0204.291
getDifferences6.5570.0006.557
getDistAroundVp0.7900.0310.821
getNormalizationFactors0.2810.0000.282
getReferenceSeq0.3250.0000.324
getZScores26.757 0.16426.920
normalizeRPM0.2310.0000.231
plotDifferences7.2700.0157.286
plotFits1.4540.0161.471
plotNormalizationFactors3.8960.0083.905
plotScatter49.323 0.52849.859
plotZScores4.7550.0244.779
smoothCounts0.2680.0040.272
smoothHitPerCent1.1340.0121.146
writeTrackFiles1.1940.0081.202