Package: plateCore

Version: 1.40.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:plateCore.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings plateCore_1.40.1.tar.gz

StartedAt: 2019-04-16 02:07:26 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:09:53 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 147.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: plateCore.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:plateCore.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings plateCore_1.40.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/plateCore.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.40.1’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
mfiPlot-methods           6.364  0.000   6.374
summaryStats-methods      6.260  0.000   6.271
applyControlGates-methods 5.860  0.024   5.923
* 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-3.8-bioc/meat/plateCore.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL plateCore
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘plateCore’ ...
** R
** data
** byte-compile and prepare 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	2.148	0.012	2.181
applyControlGates-methods	5.860	0.024	5.923
compensate-methods	2.352	0.008	2.371
compensationSet	0.112	0.016	0.128
densityplot-methods	0.948	0.008	0.955
fixAutoFl-methods	2.968	0.000	2.971
flowPlate-class	1.584	0.008	1.593
flowPlate-method	1.680	0.000	1.679
fpbind-methods	2.572	0.000	2.575
getGroups-methods	0.812	0.008	0.820
gutterPlot-methods	1.312	0.000	1.314
mfiPlot-methods	6.364	0.000	6.374
on-methods	4.420	0.028	4.460
panel.densityplot.flowPlate	1.040	0.000	1.041
panel.xyplot.flowPlate	1.120	0.004	1.124
plateCore-package	1.388	0.000	1.388
plateSet-methods	1.664	0.008	1.673
plotPlate-methods	1.480	0.008	1.486
prepanel.densityplot.flowPlate	0.764	0.000	0.768
prepanel.xyplot.flowPlate	0.584	0.000	0.587
setControlGates-methods	1.732	0.016	1.752
summaryStats-methods	6.260	0.000	6.271
wellAnnotation-methods	0.680	0.008	0.687
xyplot-methods	0.716	0.008	0.727