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CHECK report for flowBin on tokay2

This page was generated on 2020-10-17 11:56:34 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE flowBin PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 604/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowBin 1.24.0
Kieran O'Neill
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/flowBin
Branch: RELEASE_3_11
Last Commit: 8e86624
Last Changed Date: 2020-04-27 14:37:48 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowBin
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowBin.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowBin_1.24.0.tar.gz
StartedAt: 2020-10-17 04:04:05 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:06:04 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 119.4 seconds
RetCode: 0
Status:  OK  
CheckDir: flowBin.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowBin.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowBin_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowBin.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowBin/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowBin' version '1.24.0'
* 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 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
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
getBinExpr 5.78   0.03    5.82
flowBin    5.45   0.06    5.51
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
getBinExpr 7.16   0.02    7.17
flowBin    6.15   0.00    6.16
* 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-3.11-bioc/meat/flowBin.Rcheck/00check.log'
for details.



Installation output

flowBin.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/flowBin_1.24.0.tar.gz && rm -rf flowBin.buildbin-libdir && mkdir flowBin.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowBin.buildbin-libdir flowBin_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL flowBin_1.24.0.zip && rm flowBin_1.24.0.tar.gz flowBin_1.24.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  158k  100  158k    0     0   962k      0 --:--:-- --:--:-- --:--:-- 1006k

install for i386

* installing *source* package 'flowBin' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowBin'
    finding HTML links ... done
    BinnedFlowSample                        html  
    FlowSample                              html  
    amlsample                               html  
    checkQNorm                              html  
    eventsInBins                            html  
    flowBin                                 html  
    flowFPBin                               html  
    getBinExpr                              html  
    kMeansBin                               html  
    mapBinsKNN                              html  
    quantileNormalise                       html  
    removeSparseBins                        html  
    show-methods                            html  
** 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

install for x64

* installing *source* package 'flowBin' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowBin' as flowBin_1.24.0.zip
* DONE (flowBin)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'flowBin' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowBin.Rcheck/examples_i386/flowBin-Ex.timings

nameusersystemelapsed
checkQNorm0.720.050.77
flowBin5.450.065.51
flowFPBin0.360.020.37
getBinExpr5.780.035.82
kMeansBin0.520.030.54
mapBinsKNN0.280.000.28
quantileNormalise0.700.000.71

flowBin.Rcheck/examples_x64/flowBin-Ex.timings

nameusersystemelapsed
checkQNorm0.570.060.63
flowBin6.150.006.16
flowFPBin0.370.000.38
getBinExpr7.160.027.17
kMeansBin0.440.000.44
mapBinsKNN0.260.000.26
quantileNormalise0.460.000.45