BioC 3.4: CHECK report for CytoML on morelia

Package: CytoML

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CytoML_1.0.1.tar.gz

StartedAt: 2017-04-15 00:45:17 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:48:51 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 213.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: CytoML.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CytoML_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CytoML.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CytoML’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.4-bioc/meat/CytoML.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
* 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:::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
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’
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’
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’
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’
subPopulationNode : <anonymous>: no visible global function definition
  for ‘is’
subPopulationNode : <anonymous> : <anonymous>: no visible global
  function definition for ‘is’
xmlTag: no visible global function definition for ‘is’
compensate,GatingSet-graphGML: no visible global function definition
  for ‘is’
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 name pData<- parent parent_count population rgb slot x y
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "as", "extends", "is", "slot")
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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
cytobank2GatingSet 4.800  0.305   7.476
compare.counts     4.557  0.283  10.131
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CytoML)
  Warning messages:
  1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
  2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
  > 
  > 
  > test_check("CytoML")
  Error in test_files(paths, reporter = reporter, env = env, ...) : 
    No matching test file in dir
  Calls: test_check ... run_tests -> with_top_env -> test_dir -> test_files
  Execution halted
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/CytoML.Rcheck/00check.log’
for details.

R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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)
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
> 
> 
> test_check("CytoML")
Error in test_files(paths, reporter = reporter, env = env, ...) : 
  No matching test file in dir
Calls: test_check ... run_tests -> with_top_env -> test_dir -> test_files
Execution halted

* installing *source* package ‘CytoML’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (CytoML)

name	user	system	elapsed
GatingSet2cytobank	2.392	0.077	3.503
GatingSet2flowJo	1.981	0.053	3.940
compare.counts	4.557	0.283	10.131
cytobank2GatingSet	4.800	0.305	7.476
extend	0.113	0.004	0.116
getChildren-graphGML-character-method	0.833	0.003	0.836
getNodes-graphGML-method	0.811	0.003	0.886
plot-graphGML-missing-method	0.910	0.004	1.153
read.gatingML.cytobank	0.944	0.004	0.949