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CHECK report for flowBin on celaya2

This page was generated on 2020-01-16 13:38:11 -0500 (Thu, 16 Jan 2020).

Package 579/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowBin 1.23.0
Kieran O'Neill
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/flowBin
Branch: master
Last Commit: 97b42ee
Last Changed Date: 2019-10-29 13:37:15 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowBin
Version: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2020-01-16 04:28:40 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 04:30:48 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 128.2 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_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/flowBin.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.23.0’
* 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 (user + system) or elapsed time > 5s
             user system elapsed
flowBin    11.550  0.152  11.834
getBinExpr 11.195  0.213  11.733
* 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-3.11-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/4.0/Resources/library’
* installing *source* package ‘flowBin’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowBin)

Tests output


Example timings

flowBin.Rcheck/flowBin-Ex.timings

nameusersystemelapsed
checkQNorm0.8780.0520.932
flowBin11.550 0.15211.834
flowFPBin0.5460.0180.565
getBinExpr11.195 0.21311.733
kMeansBin0.6540.0150.669
mapBinsKNN0.3870.0120.399
quantileNormalise0.7500.0270.777