Package: CytoML

Version: 1.4.1

Command: rm -rf CytoML.buildbin-libdir CytoML.Rcheck && mkdir CytoML.buildbin-libdir CytoML.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CytoML.buildbin-libdir CytoML_1.4.1.tar.gz >CytoML.Rcheck\00install.out 2>&1 && cp CytoML.Rcheck\00install.out CytoML-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CytoML.buildbin-libdir --install="check:CytoML-install.out" --force-multiarch --no-vignettes --timings CytoML_1.4.1.tar.gz

StartedAt: 2018-04-11 23:20:11 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:27:50 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 458.4 seconds

RetCode: 0

Status:  OK

CheckDir: CytoML.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf CytoML.buildbin-libdir CytoML.Rcheck && mkdir CytoML.buildbin-libdir CytoML.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CytoML.buildbin-libdir CytoML_1.4.1.tar.gz >CytoML.Rcheck\00install.out 2>&1 && cp CytoML.Rcheck\00install.out CytoML-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CytoML.buildbin-libdir --install="check:CytoML-install.out" --force-multiarch --no-vignettes --timings CytoML_1.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CytoML.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CytoML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoML' version '1.4.1'
* 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 'CytoML' 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 global function definition for 'menu'
.preprocessorDiva: no visible binding for global variable 'specimen'
.preprocessorDiva: no visible binding for global variable
  'sampleSelected'
GatingSet2flowJo: no visible global function definition for 'pData<-'
addCustomInfo : <anonymous>: no visible global function definition for
  'is'
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'
constructPopNode: no visible global function definition for 'is'
constructPopNode : <anonymous>: no visible global function definition
  for 'is'
constructTree : <anonymous>: no visible binding for global variable
  'slot'
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.ellipsoidGate: no visible global function definition for 'as'
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'
extend.polygonGate: no visible global function definition for 'rgb'
extend.rectangleGate: no visible global function definition for 'as'
gateNode.ellipsoidGate: no visible global function definition for 'as'
inverse.ellipsoidGate: no visible global function definition for 'as'
inverse.rectangleGate: no visible global function definition for 'as'
openDiva: no visible global function definition for 'new'
read.gatingML.cytobank: no visible global function definition for 'is'
read.gatingML.cytobank: no visible binding for global variable 'id'
read.gatingML.cytobank: no visible binding for global variable
  'comp_ref'
read.gatingML.cytobank : <anonymous>: no visible global function
  definition for 'is'
read.gatingML.cytobank: no visible global function definition for 'as'
xmlTag: no visible global function definition for 'is'
compensate,GatingSet-graphGML: no visible global function definition
  for 'is'
getSamples,divaWorkspace: no visible global function definition for
  'selectMethod'
getTransformations,graphGML : <anonymous>: no visible global function
  definition for 'extends'
transform,ellipsoidGate: no visible global function definition for 'as'
Undefined global functions or variables:
  . as comp_ref count extends fcs fcs_filename gate_def gate_id id is
  is.smaller logtGml2 menu name new pData<- parent parent_count
  population rgb sampleSelected selectMethod slot specimen x y
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "as", "extends", "is", "new", "selectMethod",
             "slot")
  importFrom("utils", "menu")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
compare.counts 5.75   0.23   12.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
compare.counts     8.12   0.35    9.05
cytobank2GatingSet 6.72   0.25    7.11
GatingSet2cytobank 3.73   0.13    5.07
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/CytoML.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'CytoML' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CytoML'
    finding HTML links ... done
    GatingSet2cytobank                      html  
    GatingSet2flowJo                        html  
    addCustomInfo                           html  
    compare.counts                          html  
    compensate-GatingSet-graphGML-method    html  
    constructTree                           html  
    cytobank2GatingSet                      html  
    divaWorkspace-class                     html  
    finding level-2 HTML links ... done

    extend                                  html  
    gating-methods                          html  
    getChildren-graphGML-character-method   html  
    getCompensationMatrices-graphGML-method
                                            html  
    getGate-graphGML-character-method       html  
    getNodes-graphGML-method                html  
    getParent-graphGML-character-method     html  
    getTransformations-graphGML-method      html  
    graphGML-class                          html  
    matchPath                               html  
    openDiva                                html  
    parse.gateInfo                          html  
    plot-graphGML-missing-method            html  
    range.GatingHierarchy                   html  
    read.gatingML.cytobank                  html  
    show-graphGML-method                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CytoML' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoML' as CytoML_1.4.1.zip
* DONE (CytoML)
In R CMD INSTALL
In R CMD INSTALL

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(CytoML)
> 
> 
> test_check("CytoML")
Loading required package: flowCore

Attaching package: 'flowCore'

The following object is masked from 'package:base':

    sort

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: 12127 SKIPPED: 0 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/CytoML")
> 
> 
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> 
> proc.time()
   user  system elapsed 
  87.34    4.09   93.37 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(CytoML)
> 
> 
> test_check("CytoML")
Loading required package: flowCore

Attaching package: 'flowCore'

The following object is masked from 'package:base':

    sort

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: 12127 SKIPPED: 0 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/CytoML")
> 
> 
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> 
> proc.time()
   user  system elapsed 
 112.09    3.32  116.67