Package: ggcyto

Version: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2020-01-09 04:36:52 -0500 (Thu, 09 Jan 2020)

EndedAt: 2020-01-09 04:42:17 -0500 (Thu, 09 Jan 2020)

EllapsedTime: 325.0 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_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ggcyto.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.15.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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:::gh_pop_is_negated’
  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 : <anonymous>: no visible binding for global variable ‘axis’
as.ggplot : <anonymous>: no visible binding for global variable ‘name’
as.ggplot: no visible binding for global variable ‘density’
autoplot.GatingHierarchy : <anonymous>: 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 : <anonymous>: 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 (user + system) or elapsed time > 5s
                            user system elapsed
autoplot                  37.741 16.102  22.928
plus-.ggcyto_GatingLayout 21.241 11.617   9.720
ggcyto.flowSet            12.801  3.599  11.481
ggcyto                    10.667  1.687   8.780
geom_stats                 7.469  2.255   4.012
replace_data               5.601  2.689   2.149
ggcyto_flowSet_add         5.932  2.234   3.957
geom_overlay               4.980  2.724   3.086
labs_cyto                  4.485  2.994   2.138
geom_gate                  5.762  1.713   4.685
ggcyto_par_set             4.309  2.662   2.265
marginalFilter             4.347  2.344   3.107
scale_x_logicle            3.237  1.805   2.005
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
> library(vdiffr)
> 
> test_check("ggcyto")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 7 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
116.594  41.891  88.770 

name	user	system	elapsed
as.ggplot	1.632	0.384	1.657
autoplot	37.741	16.102	22.928
axis_x_inverse_trans	2.462	0.793	2.317
compute_stats	1.357	0.441	1.346
flowCore_asinht_trans	0.007	0.006	0.004
fortify.ellipsoidGate	0.030	0.022	0.015
fortify.filterList	0.066	0.043	0.047
fortify.flowSet	2.354	0.370	0.452
fortify.polygonGate	0.011	0.007	0.006
fortify.rectangleGate	0.029	0.018	0.018
fortify_fs	0.992	0.358	1.021
geom_gate	5.762	1.713	4.685
geom_hvline	0.531	0.010	0.552
geom_overlay	4.980	2.724	3.086
geom_stats	7.469	2.255	4.012
getFlowFrame	0.881	0.169	1.060
ggcyto.GatingSet	3.706	0.870	1.694
ggcyto	10.667	1.687	8.780
ggcyto.flowSet	12.801	3.599	11.481
ggcyto_GatingSet_add	2.924	1.811	1.834
ggcyto_arrange	0.000	0.001	0.001
ggcyto_flowSet_add	5.932	2.234	3.957
ggcyto_par_default	0.017	0.001	0.018
ggcyto_par_set	4.309	2.662	2.265
is.ggcyto	0.831	0.229	0.902
is.ggcyto_flowSet	1.206	0.624	0.898
is.ggcyto_par	0.011	0.008	0.004
labs_cyto	4.485	2.994	2.138
marginalFilter	4.347	2.344	3.107
merge.quad.gates	0.205	0.006	0.212
plus-.ggcyto_GatingLayout	21.241	11.617	9.720
replace_data	5.601	2.689	2.149
scale_x_flowCore_fasinh	2.504	1.413	1.678
scale_x_flowjo_biexp	3.563	0.899	1.618
scale_x_flowjo_fasinh	2.779	1.392	1.556
scale_x_logicle	3.237	1.805	2.005
stat_position	0.812	0.141	0.941