Multiple platform build/check report for BioC 3.21 - CHECK results for ggcyto on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4350
kjohnson3	macOS 13.6.5 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4108
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*

CHECK results for ggcyto on kjohnson3

To the developers/maintainers of the ggcyto package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggcyto.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: ggcyto

Version: 1.35.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggcyto_1.35.0.tar.gz

StartedAt: 2024-11-25 22:58:01 -0500 (Mon, 25 Nov 2024)

EndedAt: 2024-11-25 23:02:43 -0500 (Mon, 25 Nov 2024)

EllapsedTime: 281.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ggcyto.Rcheck

Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggcyto_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ggcyto.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggcyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggcyto’ version ‘1.35.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.Rd: gs_get_pop_paths
  geom_hvline.Rd: geom_hline, geom_vline, aes, aes_string, layer,
    aes_colour_fill_alpha, aes_group_order, aes_linetype_size_shape
  geom_multi_range.Rd: geom_rect, aes, aes_string, layer,
    aes_colour_fill_alpha, aes_group_order, aes_linetype_size_shape
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ggcyto.Rcheck/00check.log’
for details.

Installation output

ggcyto.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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)

Tests output

ggcyto.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  3.398   0.149   3.545

Example timings

ggcyto.Rcheck/ggcyto-Ex.timings

name	user	system	elapsed
as.ggplot	0.668	0.008	0.676
autoplot	3.100	0.056	3.157
axis_x_inverse_trans	0.352	0.008	0.361
compute_stats	0.525	0.008	0.533
faust_gating_plot	0	0	0
flowCore_asinht_trans	0.001	0.000	0.000
fortify.ellipsoidGate	0.001	0.000	0.002
fortify.filterList	0.007	0.001	0.008
fortify.flowSet	0.030	0.006	0.035
fortify.multiRangeGate	0.001	0.000	0.001
fortify.polygonGate	0.001	0.000	0.001
fortify.rectangleGate	0.002	0.000	0.002
fortify_fs	0.508	0.005	0.512
gate_null	0.122	0.005	0.127
geom_gate	0.946	0.021	0.968
geom_hvline	0.090	0.001	0.091
geom_overlay	0.399	0.022	0.422
geom_stats	0.579	0.038	0.619
getFlowFrame	1.801	0.043	1.844
ggcyto	3.257	0.088	3.354
ggcyto_add	2.536	0.099	2.635
ggcyto_arrange	0	0	0
ggcyto_par_default	0.004	0.000	0.004
ggcyto_par_set	0.279	0.022	0.302
is.ggcyto	0.491	0.004	0.495
is.ggcyto_flowSet	0.496	0.004	0.501
is.ggcyto_par	0.000	0.000	0.001
labs_cyto	0.274	0.015	0.291
marginalFilter	0.816	0.021	0.838
merge.quad.gates	0.030	0.001	0.031
replace_data	0.299	0.009	0.309
scale_x_flowCore_fasinh	0.621	0.005	0.626
scale_x_logicle	0.882	0.015	0.897
scales_flowjo_biexp	0.629	0.013	0.641
scales_flowjo_fasinh	0.594	0.009	0.603
stat_position	0.479	0.009	0.488
stats_null	0.046	0.005	0.050