Package: ggcyto

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggcyto_1.12.0.tar.gz

StartedAt: 2019-10-16 03:14:57 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:20:29 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 331.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ggcyto.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggcyto_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ggcyto.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggcyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggcyto’ version ‘1.12.0’
* 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 ‘ggcyto’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
':::' call which should be '::': ‘flowWorkspace:::isNegated’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’
  ‘flowWorkspace:::fix_y_axis’ ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’
  ‘ggplot2:::as_gg_data_frame’ ‘ggplot2:::check_aesthetics’
  ‘ggplot2:::hex_binwidth’ ‘ggplot2:::is.waive’
  ‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_labels’
  ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’
  ‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_add_defaults’
  ‘ggplot2:::scales_list’ ‘ggplot2:::update_theme’
  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
.fs2dt: no visible binding for global variable ‘name’
add_ggcyto: no visible binding for global variable ‘name’
add_ggcyto: no visible global function definition for ‘modifyList’
add_ggcyto: no visible binding for global variable ‘axis’
add_ggcyto: no visible binding for global variable ‘desc’
add_par: no visible global function definition for ‘modifyList’
as.ggplot: no visible binding for global variable ‘axis’
as.ggplot: no visible binding for global variable ‘name’
as.ggplot : : no visible binding for global variable ‘axis’
as.ggplot : : no visible binding for global variable ‘name’
as.ggplot: no visible binding for global variable ‘density’
autoplot.GatingHierarchy : : no visible global function
  definition for ‘gray’
autoplot.GatingSetList: no visible global function definition for
  ‘getS3method’
autoplot.ncdfFlowList: no visible global function definition for
  ‘getS3method’
density_fr_all : : no visible global function definition for
  ‘gray’
fortify.GatingSetList: no visible global function definition for
  ‘getS3method’
fortify.ncdfFlowList: no visible global function definition for
  ‘getS3method’
fortify_fs.GatingSetList: no visible global function definition for
  ‘getS3method’
getFlowFrame.GatingSetList: no visible global function definition for
  ‘getS3method’
getFlowFrame.ncdfFlowList: no visible global function definition for
  ‘getS3method’
ggcyto.GatingSetList: no visible global function definition for
  ‘getS3method’
ggcyto.flowSet: no visible binding for global variable ‘name’
ggcyto.flowSet: no visible binding for global variable ‘axis’
ggcyto.ncdfFlowList: no visible global function definition for
  ‘getS3method’
ggcyto_arrange: no visible binding for global variable ‘name’
Undefined global functions or variables:
  axis density desc getS3method gray modifyList name
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis")
  importFrom("stats", "density")
  importFrom("utils", "getS3method", "modifyList")
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 'ggcyto'
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 ... WARNING
Undocumented arguments in documentation object 'fortify.filterList'
  ‘data’ ‘nPoints’

Undocumented arguments in documentation object 'fortify.polygonGate'
  ‘nPoints’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
autoplot                  34.387 12.293  20.246
plus-.ggcyto_GatingLayout 15.581  4.795   9.370
ggcyto.flowSet            15.511  2.017  13.770
ggcyto                     9.528  1.173   9.782
geom_gate                  6.929  1.693   4.797
geom_overlay               5.539  1.486   3.056
ggcyto_flowSet_add         5.656  0.880   4.707
labs_cyto                  4.785  1.621   2.311
marginalFilter             4.249  1.808   3.447
geom_stats                 4.317  1.701   4.015
replace_data               4.447  1.452   2.273
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ggcyto.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ggcyto
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ggcyto’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggcyto)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ggcyto)
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: flowWorkspace
> library(vdiffr)
> 
> test_check("ggcyto")
loading R object...
loading tree object...
Done
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 7 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
108.926  33.200  90.119 

name	user	system	elapsed
as.ggplot	1.975	0.724	1.567
autoplot	34.387	12.293	20.246
axis_x_inverse_trans	3.900	0.657	2.094
compute_stats	1.360	0.339	1.476
flowCore_asinht_trans	0.006	0.004	0.004
fortify.ellipsoidGate	0.014	0.005	0.013
fortify.filterList	0.044	0.014	0.043
fortify.flowSet	0.679	0.331	0.708
fortify.polygonGate	0.005	0.000	0.006
fortify.rectangleGate	0.018	0.003	0.017
fortify_fs	0.904	0.235	0.986
geom_gate	6.929	1.693	4.797
geom_hvline	0.559	0.021	0.589
geom_overlay	5.539	1.486	3.056
geom_stats	4.317	1.701	4.015
getFlowFrame	0.886	0.184	1.100
ggcyto.GatingSet	3.405	0.513	1.639
ggcyto	9.528	1.173	9.782
ggcyto.flowSet	15.511	2.017	13.770
ggcyto_GatingSet_add	3.986	0.848	2.112
ggcyto_arrange	0.000	0.000	0.001
ggcyto_flowSet_add	5.656	0.880	4.707
ggcyto_par_default	0.008	0.001	0.009
ggcyto_par_set	2.915	1.410	2.195
is.ggcyto	0.883	0.183	0.987
is.ggcyto_flowSet	1.089	0.375	0.936
is.ggcyto_par	0.007	0.004	0.003
labs_cyto	4.785	1.621	2.311
marginalFilter	4.249	1.808	3.447
merge.quad.gates	0.198	0.003	0.203
plus-.ggcyto_GatingLayout	15.581	4.795	9.370
replace_data	4.447	1.452	2.273
scale_x_flowCore_fasinh	2.310	0.804	1.958
scale_x_flowJo_biexp	1.992	0.503	1.753
scale_x_flowJo_fasinh	3.213	0.446	1.764
scale_x_logicle	3.450	0.363	2.073
stat_position	0.808	0.115	0.929