BioC 3.1: CHECK report for flowViz on morelia

Package: flowViz

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowViz_1.32.0.tar.gz

StartedAt: 2015-10-09 01:57:44 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:59:53 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 129.0 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 --no-vignettes --timings flowViz_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/flowViz.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.32.0’
* 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 ... [6s/6s] 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:::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 : .local: warning in log(xd, b = 10): partial
  argument match of 'b' to 'base'
flowPlot,flowFrame : .local: warning in log(yd, b = 10): partial
  argument match of 'b' to 'base'
.densityplot.flowSet: no visible global function definition for
  ‘lattice.getOption’
.xyplot.flowSet: no visible global function definition for ‘bwplot’
panel.xyplot.flowframe: no visible global function definition for
  ‘lpoints’
panel.xyplot.flowframe.old: no visible global function definition for
  ‘lpoints’
glpoints,filter-flowFrame-missing : .local: no visible binding for
  global variable ‘parms’
glpoints,filter-flowFrame-missing : .local: no visible binding for
  global variable ‘strict’
gpoints,quadGate-flowFrame-character : .local: no visible binding for
  global variable ‘filterResult’
gpolygon,ellipsoidGate-character : .local: no visible binding for
  global variable ‘fd’
parallel,flowFrame-missing : .local: no visible global function
  definition for ‘parallelplot’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/64s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
xyplot                 11.825  0.912  13.223
densityplot            10.039  0.620  10.760
splom                   9.802  0.679  10.626
latticeMethods-flowSet  7.840  1.390   9.249
ecdfplot                6.151  1.268   7.441
timeLinePlot-methods    5.541  0.347   5.915
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/flowViz.Rcheck/00check.log’
for details.

* installing *source* package ‘flowViz’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowViz)

name	user	system	elapsed
contour-methods	1.316	0.112	1.432
densityplot	10.039	0.620	10.760
ecdfplot	6.151	1.268	7.441
flowPlot	0.876	0.075	0.956
flowViz-package	0	0	0
flowViz.par.get	1.563	0.120	1.691
latticeMethods-flowSet	7.840	1.390	9.249
splom	9.802	0.679	10.626
timeLinePlot-methods	5.541	0.347	5.915
xyplot	11.825	0.912	13.223