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This page was generated on 2023-04-12 11:06:09 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 lconway


To the developers/maintainers of the ggcyto package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 811/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggcyto 1.26.4  (landing page)
Mike Jiang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/ggcyto
git_branch: RELEASE_3_16
git_last_commit: 114d68d
git_last_commit_date: 2022-12-13 13:00:39 -0400 (Tue, 13 Dec 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ggcyto
Version: 1.26.4
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_1.26.4.tar.gz
StartedAt: 2023-04-10 20:27:27 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:30:13 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 166.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ggcyto.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### 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_1.26.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ggcyto.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.26.4’
* 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 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 ‘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 ‘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’
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 documentation object 'faust_gating_plot'
  ‘gh’ ‘...’

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   10.200  0.437  10.694
ggcyto      8.155  0.376   8.557
ggcyto_add  8.021  0.396   8.467
* 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-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/4.2/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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 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 7 | PASS 1 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (7)

[ FAIL 0 | WARN 0 | SKIP 7 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 10.590   0.672  11.313 

Example timings

ggcyto.Rcheck/ggcyto-Ex.timings

nameusersystemelapsed
as.ggplot2.0500.0452.105
autoplot10.200 0.43710.694
axis_x_inverse_trans0.6900.0430.738
compute_stats1.7860.0401.832
faust_gating_plot0.0010.0010.001
flowCore_asinht_trans0.0020.0010.002
fortify.ellipsoidGate0.0060.0020.008
fortify.filterList0.0200.0050.026
fortify.flowSet0.1000.0240.124
fortify.polygonGate0.0040.0000.004
fortify.rectangleGate0.0100.0010.010
fortify_fs1.5890.0281.630
gate_null0.6770.0490.732
geom_gate2.9650.1133.118
geom_hvline0.2730.0100.285
geom_overlay1.2580.0781.344
geom_stats1.4210.0831.519
getFlowFrame4.2050.0974.320
ggcyto8.1550.3768.557
ggcyto_add8.0210.3968.467
ggcyto_arrange0.0000.0010.001
ggcyto_par_default0.0120.0010.012
ggcyto_par_set1.3920.1011.498
is.ggcyto1.5820.0151.607
is.ggcyto_flowSet1.5730.0121.594
is.ggcyto_par0.0020.0010.002
labs_cyto0.8050.0880.904
marginalFilter2.2760.0962.481
merge.quad.gates0.0790.0030.082
replace_data0.8440.0430.890
scale_x_flowCore_fasinh1.8590.0181.904
scale_x_logicle1.7870.0561.852
scales_flowjo_biexp1.9260.0211.955
scales_flowjo_fasinh1.9880.0312.027
stat_position1.7100.0161.731
stats_null0.2060.0650.271