Package: flowViz

Version: 1.44.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowViz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowViz_1.44.0.tar.gz

StartedAt: 2018-10-16 21:26:08 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:28:07 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 118.5 seconds

RetCode: 0

Status:  OK

CheckDir: flowViz.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowViz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowViz_1.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/flowViz.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.44.0’
* 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:
  ‘flowCore:::findTimeChannel’ ‘flowCore:::prepareSet’
  ‘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
flowPlot,flowFrame: warning in log(xd, b = 10): partial argument match
  of 'b' to 'base'
flowPlot,flowFrame: warning in log(yd, b = 10): partial argument match
  of 'b' to 'base'
.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’
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’
Undefined global functions or variables:
  as.formula contourLines densCols extends fd filterResult parms
  rainbow rl strict
Consider adding
  importFrom("grDevices", "contourLines", "densCols", "rainbow")
  importFrom("methods", "extends")
  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:149-151: 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 or elapsed time > 5s
                  user system elapsed
xyplot          10.748  0.359  11.211
splom            9.986  0.448  10.524
densityplot      9.137  0.554   9.736
lattice-methods  6.947  0.994   7.980
ecdfplot         4.998  1.117   6.142
timeLinePlot     5.551  0.219   5.821
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/flowViz.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowViz
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowViz’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘filters.Rmd’ 
** testing if installed package can be loaded
* DONE (flowViz)

name	user	system	elapsed
contour-methods	1.136	0.088	1.233
densityplot	9.137	0.554	9.736
ecdfplot	4.998	1.117	6.142
flowPlot	0.881	0.082	0.969
flowViz-package	0.001	0.000	0.001
flowViz.par.get	1.545	0.097	1.658
lattice-methods	6.947	0.994	7.980
splom	9.986	0.448	10.524
timeLinePlot	5.551	0.219	5.821
xyplot	10.748	0.359	11.211