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CHECK report for FourCSeq on tokay2

This page was generated on 2020-10-17 11:56:36 -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: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FourCSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings FourCSeq_1.22.1.tar.gz
StartedAt: 2020-10-17 04:10:51 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:26:01 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 910.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: FourCSeq.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FourCSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings FourCSeq_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/FourCSeq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'FourCSeq' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'FourCSeq' is deprecated and will be removed from Bioconductor
See 'C:/Users/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotScatter     72.08   2.54   75.22
getZScores      41.59   2.60   44.19
plotDifferences  7.12   0.00    7.13
getDifferences   5.17   0.22    5.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotScatter     67.66   2.28   69.97
getZScores      37.39   2.92   40.33
plotDifferences  9.69   0.03    9.72
getAllResults    5.89   0.06    5.95
plotZScores      5.83   0.04    5.86
getDifferences   5.85   0.00    5.85
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/FourCSeq.Rcheck/00check.log'
for details.



Installation output

FourCSeq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/FourCSeq_1.22.1.tar.gz && rm -rf FourCSeq.buildbin-libdir && mkdir FourCSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FourCSeq.buildbin-libdir FourCSeq_1.22.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL FourCSeq_1.22.1.zip && rm FourCSeq_1.22.1.tar.gz FourCSeq_1.22.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 18 2038k   18  368k    0     0   629k      0  0:00:03 --:--:--  0:00:03  636k
100 2038k  100 2038k    0     0  2527k      0 --:--:-- --:--:-- --:--:-- 2548k

install for i386

* installing *source* package 'FourCSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FourCSeq'
    finding HTML links ... done
    FourC                                   html  
    addFragments                            html  
    addPeaks                                html  
    addViewpointFrags                       html  
    combineFragEnds                         html  
    countFragmentOverlaps                   html  
    countFragmentOverlapsSecondCutter       html  
    distFitMonotone                         html  
    distFitMonotoneSymmetric                html  
    fc                                      html  
    fcf                                     html  
    findViewpointFragments                  html  
    getAllResults                           html  
    getDifferences                          html  
    getDistAroundVp                         html  
    getNormalizationFactors                 html  
    getReferenceSeq                         html  
    getZScores                              html  
    normalizeRPM                            html  
    plotDifferences                         html  
    plotFits                                html  
    plotNormalizationFactors                html  
    plotScatter                             html  
    plotZScores                             html  
    smoothCounts                            html  
    smoothHitPerCent                        html  
    writeTrackFiles                         html  
** 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

install for x64

* installing *source* package 'FourCSeq' ...
** testing if installed package can be loaded
Warning: Package 'FourCSeq' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'FourCSeq' as FourCSeq_1.22.1.zip
* DONE (FourCSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'FourCSeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

FourCSeq.Rcheck/examples_i386/FourCSeq-Ex.timings

nameusersystemelapsed
FourC0.720.270.98
addFragments1.130.081.20
addViewpointFrags1.240.001.23
combineFragEnds0.290.000.30
countFragmentOverlaps2.880.002.88
countFragmentOverlapsSecondCutter000
fc0.110.010.12
fcf0.230.020.25
findViewpointFragments0.830.391.22
getAllResults4.270.704.97
getDifferences5.170.225.39
getDistAroundVp0.610.020.62
getNormalizationFactors0.340.010.36
getReferenceSeq0.30.00.3
getZScores41.59 2.6044.19
normalizeRPM0.300.010.31
plotDifferences7.120.007.13
plotFits2.160.022.20
plotNormalizationFactors3.090.003.09
plotScatter72.08 2.5475.22
plotZScores4.250.074.31
smoothCounts0.250.010.27
smoothHitPerCent1.00.51.5
writeTrackFiles0.840.130.97

FourCSeq.Rcheck/examples_x64/FourCSeq-Ex.timings

nameusersystemelapsed
FourC0.540.050.59
addFragments1.500.031.53
addViewpointFrags1.030.031.06
combineFragEnds0.190.000.19
countFragmentOverlaps2.110.002.11
countFragmentOverlapsSecondCutter000
fc0.110.000.11
fcf0.190.000.19
findViewpointFragments0.970.000.97
getAllResults5.890.065.95
getDifferences5.850.005.85
getDistAroundVp0.980.000.98
getNormalizationFactors0.440.020.46
getReferenceSeq0.480.000.48
getZScores37.39 2.9240.33
normalizeRPM0.240.000.23
plotDifferences9.690.039.72
plotFits2.230.002.24
plotNormalizationFactors3.920.063.98
plotScatter67.66 2.2869.97
plotZScores5.830.045.86
smoothCounts0.290.000.30
smoothHitPerCent1.630.351.98
writeTrackFiles1.250.101.34