BioC 3.1: CHECK report for flowViz on petty

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: 2015-10-08 23:03:18 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:06:35 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 197.6 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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [9s/9s] 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 ... [98s/100s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
xyplot                 18.193  0.530  19.016
densityplot            16.111  0.724  17.059
splom                  15.646  0.789  16.940
latticeMethods-flowSet 14.076  1.884  15.971
ecdfplot                9.828  1.796  11.691
timeLinePlot-methods    7.676  0.366   8.103
* 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	2.535	0.165	2.860
densityplot	16.111	0.724	17.059
ecdfplot	9.828	1.796	11.691
flowPlot	1.481	0.129	1.621
flowViz-package	0.001	0.001	0.001
flowViz.par.get	2.470	0.151	2.632
latticeMethods-flowSet	14.076	1.884	15.971
splom	15.646	0.789	16.940
timeLinePlot-methods	7.676	0.366	8.103
xyplot	18.193	0.530	19.016