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CHECK report for ggcyto on malbec2

This page was generated on 2018-10-17 08:28:24 -0400 (Wed, 17 Oct 2018).

Package 614/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggcyto 1.8.2
Mike Jiang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ggcyto
Branch: RELEASE_3_7
Last Commit: ad88ca1
Last Changed Date: 2018-07-13 03:07:15 -0400 (Fri, 13 Jul 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ggcyto
Version: 1.8.2
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ggcyto_1.8.2.tar.gz
StartedAt: 2018-10-16 00:50:07 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:52:38 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 150.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ggcyto.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ggcyto_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ggcyto.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.2’
* 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 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.
Unexported objects imported by ':::' calls:
  ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’
  ‘flowWorkspace:::fix_y_axis’ ‘flowWorkspace:::isNegated’
  ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’ ‘ggplot2:::as_gg_data_frame’
  ‘ggplot2:::check_aesthetics’ ‘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 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 ‘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.polygonGate : <anonymous>: no visible global function
  definition for ‘dist’
fortify.polygonGate : <anonymous>: no visible global function
  definition for ‘approx’
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:
  approx axis density desc dist getS3method gray modifyList name
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis")
  importFrom("stats", "approx", "density", "dist")
  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 or elapsed time > 5s
                 user system elapsed
autoplot       10.280  0.092  10.391
ggcyto.flowSet  5.316  0.008   5.332
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/ggcyto.Rcheck/00check.log’
for details.



Installation output

ggcyto.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ggcyto
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ggcyto’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘%+%’ from package ‘ggplot2’ in package ‘ggcyto’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggcyto)

Tests output

ggcyto.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
> library(vdiffr)
> 
> test_check("ggcyto")
loading R object...
loading tree object...
Done
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 41 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 38.844   0.720  39.791 

Example timings

ggcyto.Rcheck/ggcyto-Ex.timings

nameusersystemelapsed
as.ggplot0.8840.0240.910
autoplot10.280 0.09210.391
axis_x_inverse_trans0.8320.0040.836
compute_stats0.6280.0120.640
flowCore_asinht_trans0.0000.0040.002
fortify.ellipsoidGate0.0080.0000.007
fortify.filterList0.0160.0000.018
fortify.flowSet0.1000.0160.116
fortify.polygonGate0.0040.0000.007
fortify.rectangleGate0.0040.0000.008
fortify_fs0.5080.0160.529
geom_gate2.6680.0162.688
geom_hvline0.2760.0040.278
geom_overlay1.2280.0041.234
geom_stats1.6840.0121.700
getFlowFrame0.5040.0160.521
ggcyto.GatingSet0.6600.0040.664
ggcyto3.6320.0083.644
ggcyto.flowSet5.3160.0085.332
ggcyto_GatingSet_add0.8880.0080.897
ggcyto_arrange0.0000.0000.001
ggcyto_flowSet_add2.1720.0242.199
ggcyto_par_default0.0040.0000.006
ggcyto_par_set1.0920.0081.104
is.ggcyto0.5160.0200.536
is.ggcyto_flowSet0.5280.0200.548
is.ggcyto_par0.0040.0000.002
labs_cyto1.2360.0001.236
marginalFilter1.3640.0081.372
merge.quad.gates0.1040.0000.103
plus-.ggcyto_GatingLayout4.3240.0124.345
replace_data1.0120.0001.015
scale_x_flowCore_fasinh0.8800.0280.907
scale_x_flowJo_biexp0.8840.0080.895
scale_x_flowJo_fasinh0.8600.0240.889
scale_x_logicle1.1080.0161.127
stat_position0.5160.0200.535