Multiple platform build/check report for BioC 3.11 - CHECK report for ggcyto on tokay2

Package: ggcyto

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ggcyto_1.16.0.tar.gz

StartedAt: 2020-10-17 04:30:38 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 04:37:02 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 383.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ggcyto.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ggcyto_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ggcyto.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggcyto/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ggcyto' version '1.16.0'
* 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 ... OK
* checking whether package 'ggcyto' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWc0M05/R.INSTALL226c305088f/ggcyto/man/marginalFilter.Rd:14: file link 'boundaryFilter' in package 'flowCore' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ggcyto.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
Undefined global functions or variables:
  axis colorRampPalette count densCols density desc getS3method gray
  modifyList name
Consider adding
  importFrom("grDevices", "colorRampPalette", "densCols", "gray")
  importFrom("graphics", "axis")
  importFrom("stats", "density")
  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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
autoplot   12.90   0.50   13.26
ggcyto     11.91   0.28   12.18
ggcyto_add 10.61   0.39   11.00
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
autoplot   12.05   0.45   12.50
ggcyto     10.30   0.25   10.55
ggcyto_add  8.55   0.34    8.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/ggcyto.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ggcyto_1.16.0.tar.gz && rm -rf ggcyto.buildbin-libdir && mkdir ggcyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggcyto.buildbin-libdir ggcyto_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ggcyto_1.16.0.zip && rm ggcyto_1.16.0.tar.gz ggcyto_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 13.7M  100 13.7M    0     0  58.6M      0 --:--:-- --:--:-- --:--:-- 60.3M

install for i386

* installing *source* package 'ggcyto' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ggcyto'
    finding HTML links ... done
    as.ggplot                               html  
    autoplot                                html  
    finding level-2 HTML links ... done

    axis_x_inverse_trans                    html  
    compute_stats                           html  
    flowCore_asinht_trans                   html  
    fortify.ellipsoidGate                   html  
    fortify.filterList                      html  
    fortify.flowSet                         html  
    fortify.polygonGate                     html  
    fortify.rectangleGate                   html  
    fortify_fs                              html  
    geom_gate                               html  
    geom_hvline                             html  
    geom_overlay                            html  
    geom_stats                              html  
    getFlowFrame                            html  
    ggcyto                                  html  
    ggcyto_add                              html  
    ggcyto_arrange                          html  
    ggcyto_par_default                      html  
    ggcyto_par_set                          html  
    is.ggcyto                               html  
    is.ggcyto_flowSet                       html  
    is.ggcyto_par                           html  
    labs_cyto                               html  
    marginalFilter                          html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpWc0M05/R.INSTALL226c305088f/ggcyto/man/marginalFilter.Rd:14: file link 'boundaryFilter' in package 'flowCore' does not exist and so has been treated as a topic
    merge.quad.gates                        html  
    print.ggcyto                            html  
    print.ggcyto_GatingLayout               html  
    replace_data                            html  
    scale_x_flowCore_fasinh                 html  
    scale_x_logicle                         html  
    scales_flowjo_biexp                     html  
    scales_flowjo_fasinh                    html  
    stat_position                           html  
    transform-gate                          html  
*** 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

install for x64

* installing *source* package 'ggcyto' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggcyto' as ggcyto_1.16.0.zip
* DONE (ggcyto)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ggcyto' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 0 ]
There were 36 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  48.93    4.31   53.59


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 0 ]
There were 36 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  51.64    3.57   55.23

name	user	system	elapsed
as.ggplot	1.58	0.03	1.61
autoplot	12.90	0.50	13.26
axis_x_inverse_trans	1.08	0.02	1.10
compute_stats	1.27	0.07	1.34
flowCore_asinht_trans	0	0	0
fortify.ellipsoidGate	0	0	0
fortify.filterList	0.02	0.00	0.01
fortify.flowSet	0.11	0.08	0.19
fortify.polygonGate	0	0	0
fortify.rectangleGate	0.01	0.00	0.01
fortify_fs	0.94	0.03	0.97
geom_gate	2.62	0.12	2.75
geom_hvline	0.33	0.00	0.32
geom_overlay	1.61	0.13	1.74
geom_stats	1.98	0.08	2.06
getFlowFrame	1.20	0.06	1.27
ggcyto	11.91	0.28	12.18
ggcyto_add	10.61	0.39	11.00
ggcyto_arrange	0	0	0
ggcyto_par_default	0.02	0.00	0.02
ggcyto_par_set	1.40	0.08	1.47
is.ggcyto	1.10	0.01	1.11
is.ggcyto_flowSet	0.84	0.08	0.92
is.ggcyto_par	0.02	0.00	0.02
labs_cyto	1.14	0.10	1.23
marginalFilter	2.32	0.11	2.44
merge.quad.gates	0.19	0.00	0.19
replace_data	1.38	0.09	1.46
scale_x_flowCore_fasinh	1.51	0.03	1.55
scale_x_logicle	1.46	0.06	1.52
scales_flowjo_biexp	1.75	0.05	1.79
scales_flowjo_fasinh	1.53	0.02	1.55
stat_position	0.78	0.01	0.80

name	user	system	elapsed
as.ggplot	0.91	0.05	0.95
autoplot	12.05	0.45	12.50
axis_x_inverse_trans	0.82	0.11	0.94
compute_stats	0.71	0.03	0.73
flowCore_asinht_trans	0	0	0
fortify.ellipsoidGate	0	0	0
fortify.filterList	0.03	0.00	0.04
fortify.flowSet	0.20	0.05	0.25
fortify.polygonGate	0.02	0.00	0.01
fortify.rectangleGate	0	0	0
fortify_fs	0.71	0.01	0.72
geom_gate	2.37	0.08	2.45
geom_hvline	0.23	0.00	0.24
geom_overlay	1.50	0.09	1.59
geom_stats	1.69	0.12	1.82
getFlowFrame	0.61	0.02	0.62
ggcyto	10.30	0.25	10.55
ggcyto_add	8.55	0.34	8.89
ggcyto_arrange	0	0	0
ggcyto_par_default	0	0	0
ggcyto_par_set	1.48	0.05	1.53
is.ggcyto	0.56	0.03	0.59
is.ggcyto_flowSet	0.67	0.06	0.74
is.ggcyto_par	0	0	0
labs_cyto	1.19	0.05	1.24
marginalFilter	1.79	0.11	1.90
merge.quad.gates	0.11	0.00	0.11
replace_data	1.21	0.09	1.30
scale_x_flowCore_fasinh	0.97	0.02	0.98
scale_x_logicle	0.81	0.03	0.84
scales_flowjo_biexp	1.00	0.08	1.08
scales_flowjo_fasinh	1.10	0.06	1.16
stat_position	1.01	0.05	1.06

CHECK report for ggcyto on tokay2

Summary

Command output

Installation output

Tests output

Example timings