Package: plateCore

Version: 1.36.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.36.0.tar.gz

StartedAt: 2018-04-12 01:50:29 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:52:41 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 132.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: plateCore.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/plateCore.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plateCore/DESCRIPTION’ ... OK
* this is package ‘plateCore’ version ‘1.36.0’
* 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 ‘plateCore’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘flowViz’ ‘latticeExtra’
  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
panel.xyplot.flowPlate: warning in filterBoundary(filter =
  filter[[nm]], parameters = c(channel.x.name, channel.y.name), frame =
  frames[[nm]]): partial argument match of 'filter' to 'filter.object'
fixAutoFl,flowPlate: no visible binding for global variable
  ‘Sample.Type’
fpbind,flowPlate-flowPlate : <anonymous>: no visible binding for global
  variable ‘name’
gutterPlot,flowPlate: no visible global function definition for ‘plot’
mfiPlot,flowPlate: no visible global function definition for ‘plot’
plotPlate,flowPlate: no visible global function definition for ‘plot’
setControlGates,flowPlate: no visible binding for global variable
  ‘Sample.Type’
setControlGates,flowPlate: no visible binding for global variable
  ‘Channel’
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable ‘Well.Id’
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable ‘plateName’
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable ‘name’
Undefined global functions or variables:
  Channel Sample.Type Well.Id name plateName plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'flowPlate,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/plateCore.Rcheck/00check.log’
for details.

* installing *source* package ‘plateCore’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in package ‘flowStats’ for request: ‘%on%’ when loading ‘plateCore’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘flowStats’ for request: ‘%on%’ when loading ‘plateCore’
* DONE (plateCore)

name	user	system	elapsed
Subset-methods	1.640	0.036	1.679
applyControlGates-methods	4.788	0.020	4.812
compensate-methods	2.060	0.004	2.066
compensationSet	0.116	0.008	0.128
densityplot-methods	0.844	0.000	0.845
fixAutoFl-methods	2.192	0.004	2.199
flowPlate-class	1.252	0.004	1.258
flowPlate-method	1.260	0.004	1.265
fpbind-methods	2.320	0.000	2.322
getGroups-methods	0.516	0.000	0.515
gutterPlot-methods	0.760	0.008	0.768
mfiPlot-methods	4.720	0.000	4.722
on-methods	3.840	0.016	3.861
panel.densityplot.flowPlate	1.044	0.008	1.055
panel.xyplot.flowPlate	0.644	0.016	0.658
plateCore-package	1.220	0.000	1.222
plateSet-methods	1.072	0.004	1.075
plotPlate-methods	1.236	0.000	1.236
prepanel.densityplot.flowPlate	0.620	0.000	0.624
prepanel.xyplot.flowPlate	0.592	0.004	0.597
setControlGates-methods	1.128	0.004	1.131
summaryStats-methods	4.508	0.012	4.525
wellAnnotation-methods	0.736	0.000	0.735
xyplot-methods	0.532	0.008	0.539