Package: ggcyto

Version: 1.14.1

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_1.14.1.tar.gz

StartedAt: 2020-04-15 02:42:26 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:46:32 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 246.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ggcyto.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running 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_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ggcyto.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.1’
* 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 ... 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’
  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 or elapsed time > 5s
                            user system elapsed
autoplot                  32.714 29.593  15.027
plus-.ggcyto_GatingLayout 15.044  7.938   7.406
ggcyto.flowSet            14.405  7.732   9.532
ggcyto                    13.054  5.431   6.973
geom_stats                 5.864  6.242   2.907
geom_gate                  6.639  3.821   3.319
geom_overlay               5.784  4.488   2.133
ggcyto_flowSet_add         5.109  3.515   3.463
labs_cyto                  5.767  2.735   2.386
marginalFilter             3.889  3.734   2.379
ggcyto_par_set             4.239  3.220   1.986
replace_data               4.941  2.121   2.095
ggcyto.GatingSet           3.783  3.081   1.495
axis_x_inverse_trans       4.334  2.316   1.309
ggcyto_GatingSet_add       2.903  2.784   1.403
* 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-3.10-bioc/meat/ggcyto.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ggcyto
###
##############################################################################
##############################################################################


* 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
100.624  56.524  75.300 

name	user	system	elapsed
as.ggplot	2.423	1.770	1.232
autoplot	32.714	29.593	15.027
axis_x_inverse_trans	4.334	2.316	1.309
compute_stats	2.398	0.234	1.224
flowCore_asinht_trans	0.003	0.001	0.003
fortify.ellipsoidGate	0.123	0.001	0.010
fortify.filterList	0.461	0.003	0.042
fortify.flowSet	0.774	1.118	0.229
fortify.polygonGate	0.017	0.025	0.005
fortify.rectangleGate	0.042	0.066	0.015
fortify_fs	1.059	0.851	0.752
geom_gate	6.639	3.821	3.319
geom_hvline	0.391	0.007	0.403
geom_overlay	5.784	4.488	2.133
geom_stats	5.864	6.242	2.907
getFlowFrame	0.74	0.07	0.82
ggcyto.GatingSet	3.783	3.081	1.495
ggcyto	13.054	5.431	6.973
ggcyto.flowSet	14.405	7.732	9.532
ggcyto_GatingSet_add	2.903	2.784	1.403
ggcyto_arrange	0.001	0.000	0.001
ggcyto_flowSet_add	5.109	3.515	3.463
ggcyto_par_default	0.013	0.000	0.013
ggcyto_par_set	4.239	3.220	1.986
is.ggcyto	0.835	0.207	0.869
is.ggcyto_flowSet	1.224	1.040	0.800
is.ggcyto_par	0.009	0.013	0.003
labs_cyto	5.767	2.735	2.386
marginalFilter	3.889	3.734	2.379
merge.quad.gates	0.169	0.004	0.176
plus-.ggcyto_GatingLayout	15.044	7.938	7.406
replace_data	4.941	2.121	2.095
scale_x_flowCore_fasinh	3.414	0.799	1.855
scale_x_flowjo_biexp	3.755	0.823	1.891
scale_x_flowjo_fasinh	2.283	1.364	1.750
scale_x_logicle	1.931	1.095	1.601
stat_position	0.869	0.096	1.108