Package: CytoML

Version: 1.6.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CytoML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CytoML_1.6.5.tar.gz

StartedAt: 2018-10-16 20:47:06 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:51:34 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 267.9 seconds

RetCode: 0

Status:  OK

CheckDir: CytoML.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CytoML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CytoML_1.6.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CytoML.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoML’ version ‘1.6.5’
* 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 ‘CytoML’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
Unexported objects imported by ':::' calls:
  ‘flowUtils:::.fuEnv’ ‘flowUtils:::smartTreeParse’
  ‘flowWorkspace:::.cpp_getCompensation’
  ‘flowWorkspace:::.fix_channel_slash’ ‘flowWorkspace:::.groupByTree’
  ‘flowWorkspace:::compute.timestep’ ‘flowWorkspace:::isHidden’
  ‘flowWorkspace:::isNegated’
  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
.preprocessorDiva: no visible binding for global variable ‘specimen’
.preprocessorDiva: no visible binding for global variable
  ‘sampleSelected’
GatingSet2flowJo: no visible global function definition for ‘pData<-’
addGate: no visible binding for global variable ‘id’
addGate: no visible binding for global variable ‘gate_id’
addGate: no visible binding for global variable ‘fcs’
addGate: no visible binding for global variable ‘gate_def’
addGate: no visible binding for global variable ‘name’
compare.counts: no visible binding for global variable ‘population’
compare.counts: no visible binding for global variable ‘parent’
compare.counts: no visible binding for global variable ‘count’
compare.counts: no visible binding for global variable ‘parent_count’
compare.counts: no visible global function definition for ‘.’
compare.counts: no visible binding for global variable ‘fcs_filename’
constructTree: no visible binding for global variable ‘id’
constructTree: no visible binding for global variable ‘name’
export_comp_trans: no visible global function definition for ‘logtGml2’
extend.polygonGate: no visible binding for global variable ‘..dim’
extend.polygonGate : <anonymous>: no visible binding for global
  variable ‘y’
extend.polygonGate : <anonymous>: no visible binding for global
  variable ‘x’
extend.polygonGate: no visible binding for global variable ‘id’
extend.polygonGate: no visible binding for global variable ‘x’
extend.polygonGate: no visible binding for global variable ‘y’
extend.polygonGate: no visible binding for global variable ‘is.smaller’
read.gatingML.cytobank: no visible binding for global variable ‘id’
read.gatingML.cytobank: no visible binding for global variable
  ‘comp_ref’
getTransformations,graphGML : <anonymous>: no visible global function
  definition for ‘logtGml2_trans’
Undefined global functions or variables:
  . ..dim comp_ref count fcs fcs_filename gate_def gate_id id
  is.smaller logtGml2 logtGml2_trans name pData<- parent parent_count
  population sampleSelected specimen x y
* 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
compare.counts     7.685  0.384   6.010
cytobank2GatingSet 7.303  0.504   5.462
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/CytoML.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CytoML
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CytoML’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CytoML)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(CytoML)
> 
> 
> test_check("CytoML")
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: ggplot2
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 26 SKIPPED: 0 FAILED: 0
> 
> #devtools::test()
> 
> 
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
> 
> proc.time()
   user  system elapsed 
124.986   5.951 104.602 

name	user	system	elapsed
GatingSet2cytobank	2.488	0.186	2.691
GatingSet2flowJo	1.829	0.097	1.945
compare.counts	7.685	0.384	6.010
cytobank2GatingSet	7.303	0.504	5.462
extend	0.093	0.001	0.095
getChildren-graphGML-character-method	1.147	0.008	1.167
getNodes-graphGML-method	1.179	0.010	1.196
openDiva	0.002	0.000	0.001
plot-graphGML-missing-method	1.318	0.006	1.335
range.GatingHierarchy	0.002	0.000	0.002
read.gatingML.cytobank	1.211	0.004	1.227