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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 835/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggcyto 1.33.0  (landing page)
Mike Jiang
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/ggcyto
git_branch: devel
git_last_commit: 09c942f
git_last_commit_date: 2024-04-30 10:47:37 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for ggcyto on palomino6

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: 1.33.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ggcyto_1.33.0.tar.gz
StartedAt: 2024-07-16 00:26:24 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 00:29:18 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 174.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ggcyto.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ggcyto_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/ggcyto.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ggcyto/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ggcyto' version '1.33.0'
* 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 ... 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 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 ... 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
ggcyto     13.22   0.37   13.80
autoplot    9.97   0.43   10.49
ggcyto_add  7.69   0.59    8.31
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/ggcyto.Rcheck/00check.log'
for details.


Installation output

ggcyto.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ggcyto
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   9.79    0.70   12.18 

Example timings

ggcyto.Rcheck/ggcyto-Ex.timings

nameusersystemelapsed
as.ggplot1.510.031.57
autoplot 9.97 0.4310.49
axis_x_inverse_trans1.630.161.74
compute_stats1.110.051.15
faust_gating_plot000
flowCore_asinht_trans000
fortify.ellipsoidGate000
fortify.filterList0.030.000.03
fortify.flowSet0.140.030.18
fortify.multiRangeGate0.000.010.01
fortify.polygonGate000
fortify.rectangleGate000
fortify_fs0.990.041.02
gate_null0.370.030.40
geom_gate2.210.092.31
geom_hvline0.250.000.25
geom_overlay1.900.112.20
geom_stats1.210.091.30
getFlowFrame3.630.213.83
ggcyto13.22 0.3713.80
ggcyto_add7.690.598.31
ggcyto_arrange000
ggcyto_par_default0.010.000.02
ggcyto_par_set0.750.130.87
is.ggcyto0.990.061.05
is.ggcyto_flowSet0.980.111.05
is.ggcyto_par000
labs_cyto1.550.121.67
marginalFilter1.720.051.77
merge.quad.gates0.070.020.09
replace_data0.910.061.00
scale_x_flowCore_fasinh1.360.081.44
scale_x_logicle2.470.062.51
scales_flowjo_biexp1.190.081.27
scales_flowjo_fasinh1.290.001.30
stat_position0.970.031.00
stats_null0.110.040.15