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CHECK report for flowPlots on malbec1

This page was generated on 2021-05-06 12:27:35 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the flowPlots package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 629/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowPlots 1.38.0  (landing page)
N. Hawkins
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowPlots
Branch: RELEASE_3_12
Last Commit: 52a3878
Last Changed Date: 2020-10-27 10:40:39 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: flowPlots
Version: 1.38.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowPlots.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowPlots_1.38.0.tar.gz
StartedAt: 2021-05-06 01:37:22 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:37:54 -0400 (Thu, 06 May 2021)
EllapsedTime: 32.0 seconds
RetCode: 0
Status:   OK  
CheckDir: flowPlots.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowPlots.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowPlots_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/flowPlots.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPlots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowPlots’ version ‘1.38.0’
* 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 ‘flowPlots’ can be installed ... OK
* 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: ‘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
GroupListBoxplot: no visible global function definition for ‘boxplot’
GroupListBoxplot: no visible global function definition for ‘points’
GroupListBoxplot: no visible global function definition for ‘axis’
GroupListBoxplot: no visible global function definition for ‘mtext’
GroupListBoxplot: no visible global function definition for ‘box’
GroupListBoxplot: no visible global function definition for ‘legend’
GroupListBoxplot: no visible global function definition for ‘title’
GroupListBoxplot: no visible global function definition for ‘text’
computePFDGroupStatsList: no visible global function definition for
  ‘sd’
get2GroupPValues: no visible global function definition for
  ‘wilcox.test’
getMultiGroupPValues: no visible global function definition for
  ‘kruskal.test’
readStackedData,character: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  axis box boxplot kruskal.test legend mtext points read.csv sd text
  title wilcox.test
Consider adding
  importFrom("graphics", "axis", "box", "boxplot", "legend", "mtext",
             "points", "text", "title")
  importFrom("stats", "kruskal.test", "sd", "wilcox.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/flowPlots.Rcheck/00check.log’
for details.



Installation output

flowPlots.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL flowPlots
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘flowPlots’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowPlots)

Tests output


Example timings

flowPlots.Rcheck/flowPlots-Ex.timings

nameusersystemelapsed
GroupListBoxplot0.1400.0040.142
StackedData-class4.9040.0044.911
adultsNeonates0.0000.0000.001
computeMarginalData-methods1.0160.0001.014
computeMarkers-methods000
computePFDData-methods0.8040.0160.820
computePFDGroupStatsList0.1840.0080.260
computePFDPartsData-methods1.5840.0081.601
computeProfileData-methods1.5160.0041.539
legendPFDStatsGroupNames0.0640.0000.063
makeBarplotData0.0120.0000.012
makeDataList0.0520.0040.058
makeTernaryData0.0560.0040.060
marginalDF0.0000.0000.001
marginalData-methods0.0000.0040.002
markerMatrix0.0000.0000.001
markers-methods0.0000.0040.002
pfdDF0.0000.0000.001
pfdData-methods0.0040.0000.002
pfdPartsData-methods0.0040.0000.002
pfdPartsList0.0000.0000.001
profileDF0.0040.0000.001
profileData-methods0.0000.0000.002
readStackedData-methods0.0480.0000.068
stackedData-methods0.0640.0000.065