Multiple platform build/check report for BioC 3.9 - CHECK report for ggcyto on tokay2

Package: ggcyto

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ggcyto_1.12.0.tar.gz

StartedAt: 2019-10-16 04:03:29 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:11:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 455.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ggcyto.Rcheck

Warnings: 3

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ggcyto_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ggcyto.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.12.0'
* 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 ... OK
* 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-3.9-bioc/tmpdir/RtmpIbJzzE/R.INSTALL16742d9d4b20/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-3.9-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:::isNegated'
  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' 'ggplot2:::update_theme'
  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 : : no visible binding for global variable 'axis'
as.ggplot : : no visible binding for global variable 'name'
as.ggplot: no visible binding for global variable 'density'
autoplot.GatingHierarchy : : 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 : : 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 density desc getS3method gray modifyList name
Consider adding
  importFrom("grDevices", "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 ... WARNING
Undocumented S4 methods:
  generic '%+%' and siglist 'ggcyto'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'fortify.filterList'
  'data' 'nPoints'

Undocumented arguments in documentation object 'fortify.polygonGate'
  'nPoints'

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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
autoplot                  13.89   0.61   14.27
ggcyto.flowSet             9.66   0.08    9.87
plus-.ggcyto_GatingLayout  6.20   0.29    6.48
ggcyto                     5.42   0.09    5.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
autoplot                  12.64   0.54   13.64
ggcyto.flowSet             7.64   0.09    7.61
plus-.ggcyto_GatingLayout  6.30   0.31    6.34
ggcyto                     5.45   0.03    5.48
* 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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-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/3.9/bioc/src/contrib/ggcyto_1.12.0.tar.gz && rm -rf ggcyto.buildbin-libdir && mkdir ggcyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggcyto.buildbin-libdir ggcyto_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ggcyto_1.12.0.zip && rm ggcyto_1.12.0.tar.gz ggcyto_1.12.0.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 9878k  100 9878k    0     0  56.6M      0 --:--:-- --:--:-- --:--:-- 58.8M

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.GatingSet                        html  
    ggcyto                                  html  
    ggcyto.flowSet                          html  
    ggcyto_GatingSet_add                    html  
    ggcyto_arrange                          html  
    ggcyto_flowSet_add                      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-3.9-bioc/tmpdir/RtmpIbJzzE/R.INSTALL16742d9d4b20/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  
    plus-.ggcyto_GatingLayout               html  
    print.ggcyto                            html  
    print.ggcyto_GatingLayout               html  
    replace_data                            html  
    scale_x_flowCore_fasinh                 html  
    scale_x_flowJo_biexp                    html  
    scale_x_flowJo_fasinh                   html  
    scale_x_logicle                         html  
    stat_position                           html  
    transform-gate                          html  
** 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_1.12.0.zip
* DONE (ggcyto)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ggcyto' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
> library(vdiffr)
> 
> test_check("ggcyto")
loading R object...
loading tree object...
Done
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  77.48    5.15   82.71


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
> library(vdiffr)
> 
> test_check("ggcyto")
loading R object...
loading tree object...
Done
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  77.04    4.82   81.78

name	user	system	elapsed
as.ggplot	1.35	0.08	1.42
autoplot	13.89	0.61	14.27
axis_x_inverse_trans	1.20	0.03	1.23
compute_stats	1.27	0.04	1.31
flowCore_asinht_trans	0.02	0.00	0.02
fortify.ellipsoidGate	0	0	0
fortify.filterList	0.01	0.02	0.03
fortify.flowSet	0.45	0.08	0.47
fortify.polygonGate	0.02	0.00	0.01
fortify.rectangleGate	0	0	0
fortify_fs	0.84	0.04	0.89
geom_gate	3.08	0.22	3.29
geom_hvline	0.26	0.00	0.27
geom_overlay	1.71	0.15	1.86
geom_stats	2.40	0.13	2.47
getFlowFrame	0.96	0.03	1.01
ggcyto.GatingSet	0.92	0.02	0.94
ggcyto	5.42	0.09	5.50
ggcyto.flowSet	9.66	0.08	9.87
ggcyto_GatingSet_add	1.36	0.01	1.33
ggcyto_arrange	0	0	0
ggcyto_flowSet_add	3.50	0.05	3.61
ggcyto_par_default	0.01	0.00	0.02
ggcyto_par_set	1.72	0.05	1.83
is.ggcyto	1.05	0.08	1.15
is.ggcyto_flowSet	1.06	0.04	1.11
is.ggcyto_par	0	0	0
labs_cyto	1.75	0.03	1.78
marginalFilter	2.47	0.10	2.52
merge.quad.gates	0.11	0.00	0.11
plus-.ggcyto_GatingLayout	6.20	0.29	6.48
replace_data	1.67	0.08	1.72
scale_x_flowCore_fasinh	1.74	0.08	1.74
scale_x_flowJo_biexp	1.61	0.06	1.70
scale_x_flowJo_fasinh	1.51	0.08	1.61
scale_x_logicle	1.78	0.08	1.86
stat_position	1.08	0.02	1.09

name	user	system	elapsed
as.ggplot	1.02	0.03	1.05
autoplot	12.64	0.54	13.64
axis_x_inverse_trans	1.28	0.03	1.32
compute_stats	1.18	0.08	1.21
flowCore_asinht_trans	0	0	0
fortify.ellipsoidGate	0.01	0.00	0.02
fortify.filterList	0.03	0.00	0.03
fortify.flowSet	0.21	0.03	0.24
fortify.polygonGate	0.01	0.00	0.01
fortify.rectangleGate	0	0	0
fortify_fs	0.81	0.04	0.84
geom_gate	2.91	0.04	2.97
geom_hvline	0.29	0.00	0.30
geom_overlay	1.97	0.08	2.00
geom_stats	2.58	0.05	2.59
getFlowFrame	0.58	0.06	0.64
ggcyto.GatingSet	0.97	0.00	0.97
ggcyto	5.45	0.03	5.48
ggcyto.flowSet	7.64	0.09	7.61
ggcyto_GatingSet_add	1.38	0.04	1.41
ggcyto_arrange	0	0	0
ggcyto_flowSet_add	2.67	0.04	2.73
ggcyto_par_default	0	0	0
ggcyto_par_set	1.81	0.05	1.89
is.ggcyto	0.62	0.02	0.65
is.ggcyto_flowSet	0.66	0.04	0.70
is.ggcyto_par	0	0	0
labs_cyto	1.47	0.05	1.51
marginalFilter	2.14	0.05	2.16
merge.quad.gates	0.14	0.00	0.14
plus-.ggcyto_GatingLayout	6.30	0.31	6.34
replace_data	1.26	0.03	1.29
scale_x_flowCore_fasinh	1.39	0.03	1.42
scale_x_flowJo_biexp	1.07	0.06	1.11
scale_x_flowJo_fasinh	1.4	0.0	1.4
scale_x_logicle	1.41	0.02	1.41
stat_position	0.73	0.00	0.73

CHECK report for ggcyto on tokay2

Summary

Command output

Installation output

Tests output

Example timings