Multiple platform build/check report for BioC 3.19 - CHECK results for ggcyto on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: ggcyto

Version: 1.31.2

Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ggcyto_1.31.2.tar.gz

StartedAt: 2024-03-27 22:57:25 -0400 (Wed, 27 Mar 2024)

EndedAt: 2024-03-27 23:01:34 -0400 (Wed, 27 Mar 2024)

EllapsedTime: 248.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ggcyto.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ggcyto_1.31.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ggcyto.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ggcyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggcyto’ version ‘1.31.2’
* 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 ... NOTE
Found the following non-portable file path:
  ggcyto/docs/articles/advanced/ggplot.flowSet.overlay_files/accessible-code-block-0.0.1/empty-anchor.js

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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 code 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 loading without being on the library search path ... 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:::guides_list’ ‘ggplot2:::hex_binwidth’ ‘ggplot2:::is.waive’
  ‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_labels’
  ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’
  ‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
grid.draw:
  function(x, recording)
grid.draw.ggcyto_GatingLayout:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fr2dt: no visible binding for global variable ‘axis’
.fr2dt: no visible binding for global variable ‘name’
.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 ‘count’
as.ggplot: no visible global function definition for ‘densCols’
as.ggplot: no visible global function definition for ‘colorRampPalette’
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.cytoframe: no visible global function definition for
  ‘getS3method’
autoplot.cytoset: 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’
faust_gating_plot: no visible global function definition for ‘gray’
fortify.GatingSetList: no visible global function definition for
  ‘getS3method’
fortify.cytoframe: no visible global function definition for
  ‘getS3method’
fortify.cytoset: 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.cytoset: 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.cytoset: no visible global function definition for ‘getS3method’
ggcyto.flowSet: no visible binding for global variable ‘axis’
ggcyto.flowSet: no visible binding for global variable ‘name’
ggcyto.ncdfFlowList: no visible global function definition for
  ‘getS3method’
ggcyto_arrange: no visible binding for global variable ‘name’
stat_position.filter: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  axis colorRampPalette count densCols density desc getS3method gray
  modifyList name setNames
Consider adding
  importFrom("grDevices", "colorRampPalette", "densCols", "gray")
  importFrom("graphics", "axis")
  importFrom("stats", "density", "setNames")
  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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'faust_gating_plot.Rd'
  ‘gh’ ‘...’

Documented arguments not in \usage in Rd file 'fortify.multiRangeGate.Rd':
  ‘nPoints’

Undocumented arguments in Rd file 'geom_multi_range.Rd'
  ‘stat’ ‘linejoin’ ‘na.rm’ ‘inherit.aes’

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     11.094  0.207  11.219
ggcyto        9.574  0.153   9.575
ggcyto_add    8.373  0.080   8.335
getFlowFrame  5.356  0.176   5.532
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ggcyto.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ggcyto
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘ggcyto’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: 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")
Coordinate system already present. Adding new coordinate system, which will
replace the existing one.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
[ FAIL 0 | WARN 0 | SKIP 8 | PASS 1 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On CRAN (8): 'test-autoplot.R:9:3', 'test-autoplot.R:14:3',
  'test-autoplot.R:25:3', 'test-ggcyto-fs.R:17:3', 'test-ggcyto-gs.R:31:3',
  'test-ggcyto-gs.R:83:3', 'test-ggcyto-gs.R:99:3',
  'test-multiRangeGate.R:14:3'

[ FAIL 0 | WARN 0 | SKIP 8 | PASS 1 ]
Deleting unused snapshots:
• autoplot/autoplot-fr-2d.svg
• autoplot/autoplot-fs-2d.svg
• autoplot/autoplot-gs-2-gate.svg
• autoplot/autoplot-gs-bool-gate.svg
• ggcyto-fs/ggcyto-fs-1d-den-stats.svg
• ggcyto-fs/ggcyto-fs-1d-density-alpha.svg
• ggcyto-fs/ggcyto-fs-1d-density-black.svg
• ggcyto-fs/ggcyto-fs-1d-density.svg
• ggcyto-fs/ggcyto-fs-1d-facet.svg
• ggcyto-fs/ggcyto-fs-2d-hex-1dgate-static-stats.svg
• ggcyto-fs/ggcyto-fs-2d-hex-1dgate.svg
• ggcyto-fs/ggcyto-fs-2d-hex-gradien.svg
• ggcyto-fs/ggcyto-fs-2d-hex-lim.svg
• ggcyto-fs/ggcyto-fs-2d-hex-polygates.svg
• ggcyto-fs/ggcyto-fs-2d-hex-rectgate-stats.svg
• ggcyto-fs/ggcyto-fs-2d-hex-rectgate.svg
• ggcyto-fs/ggcyto-fs-2d-hex.svg
• ggcyto-fs/ggcyto-fs-2d-multi-gates-single-stats.svg
• ggcyto-fs/ggcyto-fs-2d-multi-gates.svg
• ggcyto-gs/gate-null-2gates-geom-gate.svg
• ggcyto-gs/ggcyto-gs-1-gate.svg
• ggcyto-gs/ggcyto-gs-2-gate.svg
• ggcyto-gs/ggcyto-gs-all-children.svg
• ggcyto-gs/ggcyto-gs-axis-x-inverse-trans.svg
• ggcyto-gs/ggcyto-gs-custom-range.svg
• ggcyto-gs/ggcyto-gs-instrument-range.svg
• ggcyto-gs/ggcyto-gs-overlay-1d.svg
• ggcyto-gs/ggcyto-gs-overlay-2d.svg
• ggcyto-gs/ggcyto-gs-root.svg
• ggcyto-gs/ggcyto-gs-stats-all.svg
• ggcyto-gs/ggcyto-gs-stats-custom.svg
• ggcyto-gs/ggcyto-gs-stats.svg
• ggcyto-gs/stats-null-1gate-geom-stats.svg
• ggcyto-gs/stats-null-2gates-geom-stats.svg
• ggcyto-gs/stats-null-2gates.svg
• multiRangeGate/ggcyto-fs-2d-multirangegate-flip.svg
• multiRangeGate/ggcyto-fs-2d-multirangegate.svg
> 
> proc.time()
   user  system elapsed 
 10.088   0.464  10.463

name	user	system	elapsed
as.ggplot	1.840	0.035	1.868
autoplot	11.094	0.207	11.219
axis_x_inverse_trans	0.764	0.028	0.774
compute_stats	1.419	0.000	1.419
faust_gating_plot	0.000	0.000	0.001
flowCore_asinht_trans	0.002	0.000	0.002
fortify.ellipsoidGate	0.007	0.000	0.007
fortify.filterList	0.02	0.00	0.02
fortify.flowSet	0.151	0.036	0.159
fortify.multiRangeGate	0.004	0.000	0.005
fortify.polygonGate	0.003	0.000	0.003
fortify.rectangleGate	0.005	0.003	0.008
fortify_fs	1.295	0.020	1.315
gate_null	0.430	0.020	0.441
geom_gate	3.081	0.044	3.096
geom_hvline	0.291	0.004	0.295
geom_overlay	1.236	0.028	1.207
geom_stats	1.496	0.004	1.456
getFlowFrame	5.356	0.176	5.532
ggcyto	9.574	0.153	9.575
ggcyto_add	8.373	0.080	8.335
ggcyto_arrange	0.001	0.000	0.000
ggcyto_par_default	0.011	0.004	0.014
ggcyto_par_set	0.891	0.024	0.886
is.ggcyto	1.253	0.012	1.265
is.ggcyto_flowSet	1.257	0.008	1.265
is.ggcyto_par	0.003	0.000	0.002
labs_cyto	0.914	0.016	0.901
marginalFilter	2.096	0.012	2.089
merge.quad.gates	0.096	0.000	0.097
replace_data	1.058	0.024	1.057
scale_x_flowCore_fasinh	1.706	0.036	1.727
scale_x_logicle	2.227	0.036	2.248
scales_flowjo_biexp	1.656	0.007	1.633
scales_flowjo_fasinh	1.667	0.020	1.663
stat_position	1.309	0.001	1.310
stats_null	0.146	0.012	0.158

CHECK results for ggcyto on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings