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CHECK report for openCyto on malbec1

This page was generated on 2018-04-12 13:11:38 -0400 (Thu, 12 Apr 2018).

Package 976/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 1.16.1
Mike Jiang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/openCyto
Branch: RELEASE_3_6
Last Commit: 954c8f5
Last Changed Date: 2017-11-02 13:55:33 -0400 (Thu, 02 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: openCyto
Version: 1.16.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings openCyto_1.16.1.tar.gz
StartedAt: 2018-04-12 01:35:05 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:37:25 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 140.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: openCyto.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings openCyto_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/openCyto.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘openCyto’ version ‘1.16.1’
* 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 ‘openCyto’ 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:
  ‘flowWorkspace’
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
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘flowViz’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘flowClust:::.ellipsePoints’ ‘flowStats:::drvkde’
  ‘flowStats:::warpSetNCDF’ ‘flowWorkspace:::.cpp_addGate’
  ‘flowWorkspace:::.getAllDescendants’ ‘flowWorkspace:::trimWhiteSpace’
  ‘lattice:::updateList’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘groupBy’ ‘isCollapse’ ‘ppMethod’ ‘unlockNamespace’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘openCyto/R/pluginFramework.R’:
  unlockBinding(methodName, ENV)
  unlockBinding(methodName, ENV)

.boundary: no visible global function definition for ‘rectangleGate’
.center_mode: no visible global function definition for ‘density’
.find_peaks: no visible global function definition for ‘density’
.find_peaks: no visible global function definition for ‘points’
.find_valleys: no visible global function definition for ‘density’
.gateToFilterResult: no visible global function definition for ‘exprs’
.gateToFilterResult: no visible global function definition for ‘as’
.gatingTemplate: no visible global function definition for ‘as’
.gatingTemplate: no visible global function definition for ‘new’
.gatingTemplate: no visible binding for global variable ‘pop’
.gatingTemplate: no visible binding for global variable ‘gating_method’
.gatingTemplate: no visible binding for global variable ‘gating_args’
.gatingTemplate: no visible binding for global variable
  ‘collapseDataForGating’
.gatingTemplate: no visible binding for global variable
  ‘preprocessing_method’
.gatingTemplate: no visible binding for global variable
  ‘preprocessing_args’
.gatingTemplate: no visible global function definition for ‘extends’
.gating_adaptor: no visible global function definition for ‘as’
.gating_adaptor: no visible global function definition for ‘na.omit’
.gating_adaptor: no visible global function definition for
  ‘rectangleGate’
.gating_adaptor: no visible global function definition for ‘filters’
.gating_adaptor: no visible global function definition for ‘extends’
.gating_gtMethod : <anonymous>: no visible global function definition
  for ‘extends’
.gating_gtMethod: no visible global function definition for ‘extends’
.gating_refGate : <anonymous>: no visible global function definition
  for ‘rectangleGate’
.gating_refGate: no visible global function definition for ‘filterList’
.gen_1dgate : <anonymous>: no visible binding for global variable
  ‘parent’
.gen_1dgate : <anonymous>: no visible binding for global variable
  ‘gating_method’
.gen_1dgate : <anonymous>: no visible binding for global variable
  ‘gating_args’
.gen_1dgate : <anonymous>: no visible binding for global variable
  ‘collapseDataForGating’
.gen_1dgate : <anonymous>: no visible binding for global variable
  ‘preprocessing_method’
.gen_1dgate : <anonymous>: no visible binding for global variable
  ‘preprocessing_args’
.gen_dummy_ref_gate: no visible binding for global variable ‘parent’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable ‘pop’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable ‘gating_method’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable ‘gating_args’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable ‘collapseDataForGating’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable ‘preprocessing_method’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable ‘preprocessing_args’
.gen_refGate: no visible binding for global variable ‘parent’
.gen_refGate: no visible binding for global variable ‘gating_args’
.getEllipse: no visible global function definition for ‘qf’
.getEllipse: no visible global function definition for ‘qchisq’
.getEllipseGate: no visible global function definition for ‘qf’
.getEllipseGate: no visible global function definition for ‘qchisq’
.getEllipseGate: no visible global function definition for
  ‘polygonGate’
.getEllipseGate: no visible global function definition for
  ‘ellipsoidGate’
.getFullPath: no visible binding for global variable ‘parent’
.improvedMindensity: no visible global function definition for
  ‘density’
.improvedMindensity: no visible global function definition for
  ‘smooth.spline’
.improvedMindensity: no visible global function definition for
  ‘predict’
.improvedMindensity: no visible global function definition for ‘median’
.improvedMindensity : .plots: no visible global function definition for
  ‘abline’
.improvedMindensity: no visible global function definition for ‘par’
.improvedMindensity: no visible global function definition for ‘abline’
.plotTree: no visible global function definition for ‘as’
.plotTree: no visible global function definition for ‘par’
.plotTree: no visible global function definition for ‘legend’
.preprocess_csv: no visible binding for global variable ‘pop’
.preprocess_csv: no visible binding for global variable ‘parent’
.preprocess_csv: no visible binding for global variable ‘gating_method’
.preprocess_csv: no visible binding for global variable ‘gating_args’
.preprocess_csv: no visible binding for global variable
  ‘collapseDataForGating’
.preprocess_csv: no visible binding for global variable
  ‘preprocessing_method’
.preprocess_csv: no visible binding for global variable
  ‘preprocessing_args’
.preprocess_row: no visible binding for global variable ‘pop’
.preprocess_row: no visible binding for global variable ‘gating_method’
.preprocess_row: no visible binding for global variable ‘parent’
.preprocess_row: no visible binding for global variable ‘gating_args’
.preprocess_row: no visible binding for global variable
  ‘preprocessing_method’
.preprocess_row: no visible binding for global variable
  ‘preprocessing_args’
.prior_flowClust1d: no visible global function definition for ‘fsApply’
.prior_flowClust1d : <anonymous>: no visible global function definition
  for ‘exprs’
.prior_flowClust1d: no visible global function definition for ‘hclust’
.prior_flowClust1d: no visible global function definition for ‘dist’
.prior_flowClust1d: no visible global function definition for ‘median’
.prior_flowClust1d: no visible global function definition for ‘cutree’
.prior_flowClust1d: no visible global function definition for ‘kmeans’
.prior_flowClust1d : <anonymous>: no visible global function definition
  for ‘sd’
.prior_flowClust1d: no visible binding for global variable ‘var’
.prior_flowClust1d : <anonymous>: no visible global function definition
  for ‘embed’
.prior_flowClust1d : <anonymous>: no visible binding for global
  variable ‘var’
.prior_kmeans : <anonymous>: no visible global function definition for
  ‘exprs’
.prior_kmeans : <anonymous>: no visible global function definition for
  ‘kmeans’
.prior_kmeans : <anonymous> : <anonymous>: no visible global function
  definition for ‘cov’
.prior_kmeans : <anonymous>: no visible global function definition for
  ‘dist’
.prior_kmeans: no visible binding for global variable ‘cov.wt’
.quadGate2rectangleGates: no visible global function definition for
  ‘rectangleGate’
.quadGate2rectangleGates: no visible global function definition for
  ‘filters’
.quantile_flowClust : cdf_target : <anonymous>: no visible global
  function definition for ‘pt’
.quantile_flowClust : cdf_target: no visible global function definition
  for ‘weighted.mean’
.quantile_flowClust: no visible global function definition for
  ‘uniroot’
.read.FCS.csv: no visible global function definition for ‘new’
.read.FCS.csv: no visible global function definition for ‘parameters<-’
.read.flowSet.csv: no visible global function definition for ‘flowSet’
.standardize_flowFrame: no visible global function definition for
  ‘exprs’
.standardize_flowFrame: no visible global function definition for
  ‘exprs<-’
.standardize_flowset: no visible global function definition for
  ‘fsApply’
.standardize_flowset: no visible global function definition for
  ‘flowSet’
.standardize_flowset: no visible global function definition for ‘as’
.tailgate: no visible global function definition for ‘exprs’
.tailgate: no visible global function definition for ‘exprs<-’
.tailgate: no visible global function definition for ‘rectangleGate’
.truncate_flowframe: no visible global function definition for
  ‘rectangleGate’
.truncate_flowframe: no visible global function definition for ‘Subset’
.truncate_flowset: no visible global function definition for
  ‘rectangleGate’
.truncate_flowset: no visible global function definition for ‘Subset’
.unique_check_alias: no visible binding for global variable ‘parent’
as.data.table.gatingTemplate : <anonymous>: no visible global function
  definition for ‘extends’
fcEllipsoidGate: no visible global function definition for ‘as’
fcFilterList : <anonymous>: no visible global function definition for
  ‘extends’
fcFilterList: no visible global function definition for ‘filterList’
fcFilterList: no visible global function definition for ‘as’
fcPolygonGate: no visible global function definition for ‘as’
fcRectangleGate: no visible global function definition for ‘as’
fcTree: no visible global function definition for ‘as’
fcTree: no visible global function definition for ‘new’
flowClust.1d: no visible global function definition for ‘exprs’
flowClust.1d: no visible global function definition for ‘rectangleGate’
flowClust.1d: no visible global function definition for ‘abline’
flowClust.1d: no visible global function definition for ‘rainbow’
flowClust.1d: no visible global function definition for ‘lines’
flowClust.2d: no visible global function definition for ‘new’
flowClust.2d: no visible global function definition for ‘dist’
flowClust.2d: no visible global function definition for ‘qchisq’
flowClust.2d: no visible global function definition for ‘exprs’
flowClust.2d: no visible global function definition for ‘sd’
flowClust.2d: no visible global function definition for ‘polygonGate’
flowClust.2d: no visible global function definition for ‘lines’
flowClust.2d: no visible global function definition for ‘points’
gate_flowClust_1d: no visible global function definition for ‘exprs’
gate_flowClust_1d: no visible global function definition for
  ‘rectangleGate’
gate_flowClust_1d: no visible global function definition for ‘abline’
gate_flowClust_1d: no visible global function definition for ‘rainbow’
gate_flowClust_1d: no visible global function definition for ‘lines’
gate_flowClust_2d: no visible global function definition for ‘new’
gate_flowClust_2d: no visible global function definition for ‘dist’
gate_flowClust_2d: no visible global function definition for ‘qchisq’
gate_flowClust_2d: no visible global function definition for ‘exprs’
gate_flowClust_2d: no visible global function definition for ‘sd’
gate_flowClust_2d: no visible global function definition for
  ‘polygonGate’
gate_flowClust_2d: no visible global function definition for ‘lines’
gate_flowClust_2d: no visible global function definition for ‘points’
gate_mindensity: no visible global function definition for ‘exprs’
gate_mindensity: no visible global function definition for
  ‘rectangleGate’
gate_mindensity2: no visible global function definition for ‘exprs’
gate_mindensity2: no visible global function definition for
  ‘rectangleGate’
gate_quad_sequential : <anonymous>: no visible global function
  definition for ‘exprs’
gate_quad_sequential: no visible global function definition for
  ‘filter’
gate_quad_sequential: no visible global function definition for ‘as’
gate_quad_sequential : <anonymous>: no visible global function
  definition for ‘rectangleGate’
gate_quad_sequential: no visible global function definition for
  ‘filters’
gate_quad_tmix: no visible global function definition for ‘filter’
gate_quad_tmix: no visible global function definition for ‘as’
gate_quad_tmix: no visible global function definition for ‘polygonGate’
gate_quad_tmix: no visible global function definition for ‘filters’
gate_quantile: no visible global function definition for ‘exprs’
gate_quantile: no visible global function definition for ‘quantile’
gate_quantile: no visible global function definition for ‘hist’
gate_quantile: no visible global function definition for ‘density’
gate_quantile: no visible global function definition for ‘abline’
gate_quantile: no visible global function definition for ‘text’
gate_quantile: no visible global function definition for
  ‘rectangleGate’
gate_tail: no visible global function definition for ‘exprs’
gate_tail: no visible global function definition for ‘rectangleGate’
mindensity: no visible global function definition for ‘exprs’
mindensity: no visible global function definition for ‘rectangleGate’
mindensity2: no visible global function definition for ‘exprs’
mindensity2: no visible global function definition for ‘rectangleGate’
ocRectRefGate: no visible global function definition for ‘as’
quadGate.seq : <anonymous>: no visible global function definition for
  ‘exprs’
quadGate.seq: no visible global function definition for ‘filter’
quadGate.seq: no visible global function definition for ‘as’
quadGate.seq : <anonymous>: no visible global function definition for
  ‘rectangleGate’
quadGate.seq: no visible global function definition for ‘filters’
quadGate.tmix: no visible global function definition for ‘filter’
quadGate.tmix: no visible global function definition for ‘as’
quadGate.tmix: no visible global function definition for ‘polygonGate’
quadGate.tmix: no visible global function definition for ‘filters’
quantileGate: no visible global function definition for ‘exprs’
quantileGate: no visible global function definition for ‘quantile’
quantileGate: no visible global function definition for ‘hist’
quantileGate: no visible global function definition for ‘density’
quantileGate: no visible global function definition for ‘abline’
quantileGate: no visible global function definition for ‘text’
quantileGate: no visible global function definition for ‘rectangleGate’
tailgate: no visible global function definition for ‘exprs’
tailgate: no visible global function definition for ‘rectangleGate’
add,GatingHierarchy-ocRectRefGate: no visible global function
  definition for ‘selectMethod’
coerce,ncdfFlowList-flowFrame: no visible global function definition
  for ‘selectMethod’
coerce,ncdfFlowSet-flowFrame: no visible global function definition for
  ‘fsApply’
coerce,ncdfFlowSet-flowFrame : <anonymous>: no visible global function
  definition for ‘exprs’
coerce,ncdfFlowSet-flowFrame: no visible global function definition for
  ‘new’
gatingTemplate,character: no visible binding for global variable
  ‘isMultiPops’
gatingTemplate,character: no visible binding for global variable ‘pop’
gatingTemplate,character: no visible binding for global variable
  ‘gating_args’
plot,fcFilterList-ANY : <anonymous>: no visible global function
  definition for ‘dnorm’
plot,fcFilterList-ANY: no visible global function definition for ‘hist’
plot,fcFilterList-ANY: no visible global function definition for
  ‘exprs’
plot,fcFilterList-ANY: no visible global function definition for
  ‘lines’
plot,fcFilterList-ANY: no visible global function definition for
  ‘rainbow’
plot,fcFilterList-ANY: no visible global function definition for
  ‘abline’
show,fcFilter: no visible global function definition for
  ‘callNextMethod’
Undefined global functions or variables:
  Subset abline as callNextMethod collapseDataForGating cov cov.wt
  cutree density dist dnorm ellipsoidGate embed exprs exprs<- extends
  filter filterList filters flowSet fsApply gating_args gating_method
  hclust hist isMultiPops kmeans legend lines median na.omit new par
  parameters<- parent points polygonGate pop predict preprocessing_args
  preprocessing_method pt qchisq qf quantile rainbow rectangleGate sd
  selectMethod smooth.spline text uniroot var weighted.mean
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "hist", "legend", "lines", "par",
             "points", "text")
  importFrom("methods", "as", "callNextMethod", "extends", "new",
             "selectMethod")
  importFrom("stats", "cov", "cov.wt", "cutree", "density", "dist",
             "dnorm", "embed", "filter", "hclust", "kmeans", "median",
             "na.omit", "predict", "pt", "qchisq", "qf", "quantile",
             "sd", "smooth.spline", "uniroot", "var", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
checkRd: (5) openCyto.options.Rd:0-20: Must have a \description
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘gridExtra’
* 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 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/openCyto.Rcheck/00check.log’
for details.

Installation output

openCyto.Rcheck/00install.out

* installing *source* package ‘openCyto’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c unlockNamespace.c -o unlockNamespace.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o openCyto.so RcppExports.o misc.o unlockNamespace.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/openCyto.Rcheck/openCyto/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (openCyto)

Tests output

openCyto.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(openCyto)
Loading required package: flowWorkspace
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
> 
> test_check("openCyto")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 83 SKIPPED: 0 FAILED: 0
> 
> #devtools::test("˜/rglab/workspace/openCyto")
> 
> #taking quite some time , thus only for internal testing
> #test_file("˜/rglab/workspace/openCyto/tests/testthat/gating-testSuite.R")
> 
> proc.time()
   user  system elapsed 
 16.904   0.260  16.926

Example timings

openCyto.Rcheck/openCyto-Ex.timings

nameusersystemelapsed
add_pop000
flowClust1d000
flowClust2d000
gate_mindensity000
gate_mindensity2000
gate_quantile000
gate_tail0.0000.0000.001
gating-methods0.0000.0000.001
gatingTemplate-class000
getChildren-gatingTemplate-character-method000
getGate-gatingTemplate-character-method000
getNodes000
getParent-gatingTemplate-character-method0.0000.0000.001
gtMethod-class0.0000.0000.001
gtPopulation-class0.0040.0000.001
names-gtMethod-method000
openCyto0.0000.0000.001
openCyto.options0.0040.0000.000
plot-fcFilterList-ANY-method0.0000.0000.001
plot-gatingTemplate-missing-method0.0000.0000.001
ppMethod-class0.0040.0000.000
ppMethod-gatingTemplate-character-method000
toggle.helperGates000