Package: plateCore

Version: 1.41.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:plateCore.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings plateCore_1.41.1.tar.gz

StartedAt: 2019-03-18 03:37:17 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 03:40:16 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 179.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: plateCore.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:plateCore.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings plateCore_1.41.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/plateCore.Rcheck’
* using R Under development (unstable) (2019-01-21 r75999)
* 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 ‘1.41.1’
* 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 ... WARNING
Found the following significant warnings:
    The prototype for class “flowPlate” has undefined slot(s): 'plateConfig'
See ‘/home/biocbuild/bbs-3.9-bioc/meat/plateCore.Rcheck/00install.out’ for details.
* 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
applyControlGates-methods 7.414  0.056   7.664
mfiPlot-methods           6.935  0.020   7.027
summaryStats-methods      6.568  0.004   6.591
on-methods                5.463  0.016   5.496
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/plateCore.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL plateCore
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* installing to library ‘/home/biocbuild/bbs-3.9-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’
Warning in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses,  :
  The prototype for class “flowPlate” has undefined slot(s): 'plateConfig'
** 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	2.057	0.021	2.130
applyControlGates-methods	7.414	0.056	7.664
compensate-methods	2.423	0.004	2.445
compensationSet	0.212	0.000	0.214
densityplot-methods	1.029	0.016	1.070
fixAutoFl-methods	3.161	0.011	3.181
flowPlate-class	1.641	0.004	1.646
flowPlate-method	1.675	0.004	1.682
fpbind-methods	3.341	0.007	3.358
getGroups-methods	0.687	0.008	0.696
gutterPlot-methods	0.925	0.004	0.931
mfiPlot-methods	6.935	0.020	7.027
on-methods	5.463	0.016	5.496
panel.densityplot.flowPlate	1.195	0.004	1.203
panel.xyplot.flowPlate	0.893	0.004	0.899
plateCore-package	1.653	0.004	1.659
plateSet-methods	1.433	0.004	1.440
plotPlate-methods	1.685	0.004	1.692
prepanel.densityplot.flowPlate	0.986	0.032	1.018
prepanel.xyplot.flowPlate	0.930	0.012	0.944
setControlGates-methods	2.180	0.012	2.196
summaryStats-methods	6.568	0.004	6.591
wellAnnotation-methods	0.739	0.008	0.748
xyplot-methods	0.882	0.004	0.887