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CHECK report for flowBin on merida1

This page was generated on 2019-04-16 11:57:18 -0400 (Tue, 16 Apr 2019).

Package 525/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowBin 1.18.1
Kieran O'Neill
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/flowBin
Branch: RELEASE_3_8
Last Commit: 11091fe
Last Changed Date: 2019-01-04 13:31:36 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowBin
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowBin.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowBin_1.18.1.tar.gz
StartedAt: 2019-04-15 23:56:40 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:58:10 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 90.0 seconds
RetCode: 0
Status:  OK 
CheckDir: flowBin.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowBin.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowBin_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowBin.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowBin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowBin’ version ‘1.18.1’
* 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 ‘flowBin’ 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
Package in Depends field not imported from: ‘flowCore’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getBinExpr.def : getBinFrame: no visible global function definition
  for ‘exprs<-’
.getBinExpr.def : getBinFrame: no visible global function definition
  for ‘exprs’
.getBinExpr.def : scaleData: no visible global function definition for
  ‘pData’
.getBinExpr.def : getOnePopExpr : extractOneTube : <anonymous>: no
  visible global function definition for ‘exprs’
.getBinExpr.def : getOnePopExpr : extractOneTube: no visible global
  function definition for ‘pData’
.getBinExpr.def : getOneBinMeds : <anonymous>: no visible global
  function definition for ‘median’
.getBinExpr.def : getOneBinMeds : <anonymous>: no visible global
  function definition for ‘exprs’
.getBinExpr.def : getOneBinMeds: no visible global function definition
  for ‘pData’
checkQNorm.func: no visible global function definition for ‘flowSet’
checkQNorm.func: no visible global function definition for ‘par’
checkQNorm.func: no visible binding for global variable ‘sd’
flowFPBin.def: no visible global function definition for ‘flowSet’
kMeansBin.def: no visible global function definition for ‘exprs’
kMeansBin.def: no visible global function definition for ‘pData’
kMeansBin.def: no visible global function definition for ‘kmeans’
mapBinsKNN.def : mapClustersKNN: no visible global function definition
  for ‘exprs’
mapBinsKNN.def: no visible global function definition for
  ‘capture.output’
mapBinsKNN.def: no visible global function definition for ‘parLapply’
medianFI: no visible global function definition for ‘median’
medianFIDist: no visible global function definition for ‘median’
proportionPositive: no visible global function definition for
  ‘quantile’
qnorm.func : normCol : <anonymous>: no visible global function
  definition for ‘exprs’
qnorm.func : normCol : getCol: no visible global function definition
  for ‘exprs’
qnorm.func : normCol : getCol: no visible global function definition
  for ‘runif’
qnorm.func : normCol : setCol: no visible global function definition
  for ‘exprs’
qnorm.func : normCol : setCol: no visible global function definition
  for ‘exprs<-’
checkQNorm,FlowSample-FlowSample: no visible global function definition
  for ‘flowSet’
checkQNorm,FlowSample-FlowSample: no visible global function definition
  for ‘par’
checkQNorm,FlowSample-FlowSample: no visible binding for global
  variable ‘sd’
flowFPBin,FlowSample: no visible global function definition for
  ‘flowSet’
getBinExpr,BinnedFlowSample : getBinFrame: no visible global function
  definition for ‘exprs<-’
getBinExpr,BinnedFlowSample : getBinFrame: no visible global function
  definition for ‘exprs’
getBinExpr,BinnedFlowSample : scaleData: no visible global function
  definition for ‘pData’
getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube :
  <anonymous>: no visible global function definition for ‘exprs’
getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube: no
  visible global function definition for ‘pData’
getBinExpr,BinnedFlowSample : getOneBinMeds : <anonymous>: no visible
  global function definition for ‘median’
getBinExpr,BinnedFlowSample : getOneBinMeds : <anonymous>: no visible
  global function definition for ‘exprs’
getBinExpr,BinnedFlowSample : getOneBinMeds: no visible global function
  definition for ‘pData’
kMeansBin,FlowSample: no visible global function definition for ‘exprs’
kMeansBin,FlowSample: no visible global function definition for ‘pData’
kMeansBin,FlowSample: no visible global function definition for
  ‘kmeans’
mapBinsKNN,FlowSample : mapClustersKNN: no visible global function
  definition for ‘exprs’
mapBinsKNN,FlowSample: no visible global function definition for
  ‘capture.output’
mapBinsKNN,FlowSample: no visible global function definition for
  ‘parLapply’
quantileNormalise,FlowSample : normCol : <anonymous>: no visible global
  function definition for ‘exprs’
quantileNormalise,FlowSample : normCol : getCol: no visible global
  function definition for ‘exprs’
quantileNormalise,FlowSample : normCol : getCol: no visible global
  function definition for ‘runif’
quantileNormalise,FlowSample : normCol : setCol: no visible global
  function definition for ‘exprs’
quantileNormalise,FlowSample : normCol : setCol: no visible global
  function definition for ‘exprs<-’
show,FlowSample: no visible global function definition for ‘str’
Undefined global functions or variables:
  capture.output exprs exprs<- flowSet kmeans median pData par
  parLapply quantile runif sd str
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "kmeans", "median", "quantile", "runif", "sd")
  importFrom("utils", "capture.output", "str")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
flowBin    9.238  0.057   9.379
getBinExpr 7.982  0.036   8.065
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowBin.Rcheck/00check.log’
for details.



Installation output

flowBin.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowBin
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowBin’ ...
** R
** data
** 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 (flowBin)

Tests output


Example timings

flowBin.Rcheck/flowBin-Ex.timings

nameusersystemelapsed
checkQNorm0.7150.0270.749
flowBin9.2380.0579.379
flowFPBin0.4370.0060.448
getBinExpr7.9820.0368.065
kMeansBin0.6290.0070.636
mapBinsKNN0.3360.0050.345
quantileNormalise0.5610.0070.576