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CHECK report for flowViz on malbec1

This page was generated on 2021-05-06 12:27:36 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the flowViz package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 639/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowViz 1.54.0  (landing page)
Mike Jiang , Jake Wagner
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowViz
Branch: RELEASE_3_12
Last Commit: f80fd24
Last Changed Date: 2020-10-27 10:29:52 -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    WARNINGS    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: flowViz
Version: 1.54.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowViz.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowViz_1.54.0.tar.gz
StartedAt: 2021-05-06 01:38:42 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:41:06 -0400 (Thu, 06 May 2021)
EllapsedTime: 144.5 seconds
RetCode: 0
Status:   OK  
CheckDir: flowViz.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:flowViz.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings flowViz_1.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/flowViz.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 ‘flowViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowViz’ version ‘1.54.0’
* 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 ‘flowViz’ 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:
  ‘flowCore’ ‘lattice’
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
Unexported objects imported by ':::' calls:
  ‘lattice:::hist.constructor’ ‘lattice:::updateList’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.process_overlay_flowSet : <anonymous>: no visible global function
  definition for ‘extends’
.xyplot.flowSet: no visible global function definition for ‘as.formula’
panel.densityplot.flowset.stack: no visible binding for global variable
  ‘rl’
panel.xyplot.flowframe: no visible global function definition for
  ‘densCols’
panel.xyplot.flowframe.old: no visible global function definition for
  ‘densCols’
prepanel.densityplot.flowset.stack: no visible global function
  definition for ‘extends’
contour,flowFrame: no visible global function definition for
  ‘contourLines’
densityplot,formula-ncdfFlowList: no visible global function definition
  for ‘selectMethod’
densityplot,formula-view: no visible global function definition for
  ‘Data’
flowPlot,flowFrame: no visible global function definition for ‘rainbow’
glpoints,filter-flowFrame-missing: no visible binding for global
  variable ‘parms’
glpoints,filter-flowFrame-missing: no visible binding for global
  variable ‘strict’
gpoints,quadGate-flowFrame-character: no visible binding for global
  variable ‘filterResult’
gpolygon,ellipsoidGate-character: no visible binding for global
  variable ‘fd’
histogram,formula-ncdfFlowList: no visible global function definition
  for ‘selectMethod’
xyplot,formula-gateView: no visible global function definition for
  ‘action’
xyplot,formula-gateView: no visible global function definition for
  ‘Data’
xyplot,formula-gateView: no visible global function definition for
  ‘parent’
xyplot,formula-ncdfFlowList: no visible global function definition for
  ‘selectMethod’
xyplot,formula-view: no visible global function definition for ‘Data’
xyplot,view-missing: no visible global function definition for ‘Data’
Undefined global functions or variables:
  Data action as.formula contourLines densCols extends fd filterResult
  parent parms rainbow rl selectMethod strict
Consider adding
  importFrom("grDevices", "contourLines", "densCols", "rainbow")
  importFrom("methods", "extends", "selectMethod")
  importFrom("stats", "as.formula")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: glines-methods.Rd:150-152: Dropping empty section ‘Methods’
prepare_Rd: timeLinePlot.Rd:72-74: Dropping empty section ‘Methods’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/densityplot_vs_histogram.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
xyplot          12.728  0.112  12.878
densityplot     11.840  0.128  11.988
splom           11.304  0.112  11.461
lattice-methods  6.592  0.176   6.789
timeLinePlot     6.532  0.052   6.602
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘data.table’
* 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: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/flowViz.Rcheck/00check.log’
for details.



Installation output

flowViz.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL flowViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘flowViz’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘densityplot’ with signature ‘x="formula",data="view"’: no definition for class “view”
in method for ‘densityplot’ with signature ‘x="formula",data="ncdfFlowSet"’: no definition for class “ncdfFlowSet”
in method for ‘densityplot’ with signature ‘x="formula",data="ncdfFlowList"’: no definition for class “ncdfFlowList”
in method for ‘histogram’ with signature ‘x="formula",data="ncdfFlowSet"’: no definition for class “ncdfFlowSet”
in method for ‘histogram’ with signature ‘x="formula",data="ncdfFlowList"’: no definition for class “ncdfFlowList”
in method for ‘glines’ with signature ‘x="norm2Filter",data="ANY"’: no definition for class “norm2Filter”
in method for ‘glines’ with signature ‘x="norm2Filter",data="logicalFilterResult"’: no definition for class “norm2Filter”
in method for ‘glines’ with signature ‘x="norm2Filter",data="flowFrame"’: no definition for class “norm2Filter”
in method for ‘glpoints’ with signature ‘x="norm2Filter",data="flowFrame",channels="character"’: no definition for class “norm2Filter”
in method for ‘glpolygon’ with signature ‘x="norm2Filter",data="ANY"’: no definition for class “norm2Filter”
in method for ‘glpolygon’ with signature ‘x="norm2Filter",data="logicalFilterResult"’: no definition for class “norm2Filter”
in method for ‘glpolygon’ with signature ‘x="norm2Filter",data="flowFrame"’: no definition for class “norm2Filter”
in method for ‘gpoints’ with signature ‘x="norm2Filter",data="flowFrame",channels="character"’: no definition for class “norm2Filter”
in method for ‘gpolygon’ with signature ‘x="norm2Filter",data="ANY"’: no definition for class “norm2Filter”
in method for ‘gpolygon’ with signature ‘x="norm2Filter",data="logicalFilterResult"’: no definition for class “norm2Filter”
in method for ‘gpolygon’ with signature ‘x="norm2Filter",data="flowFrame"’: no definition for class “norm2Filter”
in method for ‘xyplot’ with signature ‘x="formula",data="view"’: no definition for class “view”
in method for ‘xyplot’ with signature ‘x="view",data="missing"’: no definition for class “view”
in method for ‘xyplot’ with signature ‘x="formula",data="gateView"’: no definition for class “gateView”
in method for ‘xyplot’ with signature ‘x="formula",data="ncdfFlowSet"’: no definition for class “ncdfFlowSet”
in method for ‘xyplot’ with signature ‘x="formula",data="ncdfFlowList"’: no definition for class “ncdfFlowList”
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘filters.Rmd’ 
** 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 (flowViz)

Tests output

flowViz.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowViz)
Loading required package: flowCore
Loading required package: lattice
> 
> test_check("flowViz")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  8.080   0.300   8.954 

Example timings

flowViz.Rcheck/flowViz-Ex.timings

nameusersystemelapsed
contour-methods1.6000.0441.648
densityplot11.840 0.12811.988
ecdfplot4.0960.0524.152
flowPlot0.9160.0320.951
flowViz-package000
flowViz.par.get2.2880.0282.379
lattice-methods6.5920.1766.789
splom11.304 0.11211.461
timeLinePlot6.5320.0526.602
xyplot12.728 0.11212.878