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This page was generated on 2021-10-22 12:04:01 -0400 (Fri, 22 Oct 2021).

CHECK results for ggcyto on nebbiolo2

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? here 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 772/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggcyto 1.21.0  (landing page)
Mike Jiang ,Jake Wagner
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/ggcyto
git_branch: master
git_last_commit: 834a4c4
git_last_commit_date: 2021-05-19 12:17:22 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: ggcyto
Version: 1.21.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ggcyto_1.21.0.tar.gz
StartedAt: 2021-10-21 20:16:37 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 20:18:52 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 134.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ggcyto.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ggcyto_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ggcyto.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.21.0’
* 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 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.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’
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 ... OK
* 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   8.778  0.307   8.852
ggcyto     8.605  0.176   8.642
ggcyto_add 6.600  0.136   6.607
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/ggcyto.Rcheck/00check.log’
for details.



Installation output

ggcyto.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ggcyto
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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`.
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (6)

[ FAIL 0 | WARN 0 | SKIP 6 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  8.881   0.395   9.181 

Example timings

ggcyto.Rcheck/ggcyto-Ex.timings

nameusersystemelapsed
as.ggplot1.0510.0281.066
autoplot8.7780.3078.852
axis_x_inverse_trans0.9620.0360.975
compute_stats0.6430.0400.682
flowCore_asinht_trans0.0020.0000.001
fortify.ellipsoidGate0.0060.0000.005
fortify.filterList0.0200.0000.019
fortify.flowSet0.1350.0240.131
fortify.polygonGate0.0030.0000.003
fortify.rectangleGate0.0160.0000.007
fortify_fs0.5440.0240.567
gate_null0.4000.0120.402
geom_gate1.8400.0281.842
geom_hvline0.1840.0000.183
geom_overlay1.1210.0401.119
geom_stats1.3970.0161.371
getFlowFrame3.2110.1323.343
ggcyto8.6050.1768.642
ggcyto_add6.6000.1366.607
ggcyto_arrange000
ggcyto_par_default0.0070.0000.007
ggcyto_par_set1.4680.0761.504
is.ggcyto0.5410.0200.561
is.ggcyto_flowSet0.5490.0320.581
is.ggcyto_par0.0020.0000.002
labs_cyto0.8320.0200.812
marginalFilter1.2340.0201.236
merge.quad.gates0.0860.0000.086
replace_data0.8200.0200.814
scale_x_flowCore_fasinh0.8390.0320.855
scale_x_logicle0.8810.0400.905
scales_flowjo_biexp0.8370.0320.852
scales_flowjo_fasinh0.8250.0240.834
stat_position0.5210.0280.549
stats_null0.1380.0040.141