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CHECK report for flowStats on tokay2

This page was generated on 2020-10-17 11:56:35 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE flowStats PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 626/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 4.0.0
Greg Finak , Mike Jiang , Jake Wagner
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/flowStats
Branch: RELEASE_3_11
Last Commit: b51b995
Last Changed Date: 2020-04-27 14:19:17 -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 [ WARNINGS ] 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: flowStats
Version: 4.0.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowStats_4.0.0.tar.gz
StartedAt: 2020-10-17 04:09:20 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:14:28 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 307.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowStats.Rcheck
Warnings: 1

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:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowStats_4.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowStats.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 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '4.0.0'
* package encoding: UTF-8
* 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 'flowStats' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/autoGate.Rd:21: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/autoGate.Rd:25: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/autoGate.Rd:54: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/gate_singlet.Rd:65: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/lymphGate.Rd:79: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/lymphGate.Rd:83: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/lymphGate.Rd:133: file link 'ellipsoidGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/lymphGate.Rd:141: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/normalize.Rd:58: file link 'ncdfFlowSet' in package 'ncdfFlow' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/quadrantGate.Rd:71: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/quadrantGate.Rd:79: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/rangeGate.Rd:135: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/rangeGate.Rd:145: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/spillover-flowSet.Rd:41: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowStats.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
* 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
Missing object imported by a ':::' call: 'flowWorkspace:::.isBooleanGate.graphNEL'
Unexported objects imported by ':::' calls:
  'flowCore:::checkClass' 'flowCore:::copyFlowSet'
  'flowCore:::findTimeChannel' 'flowCore:::inPolygon'
  'flowViz:::evalError' 'flowViz:::plotType'
  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
.plotGPAprocess: no visible binding for global variable 'whichS'
.plotGPAprocess: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'bogus'
.usingSVD: no visible binding for global variable 'params'
density1d_simple: no visible binding for global variable 'y'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
Undefined global functions or variables:
  bogus cluster group hasPeak params whichS y
* 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
warpSet   15.08   0.51   15.59
gaussNorm  5.67   0.32    5.98
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
warpSet   16.72   0.69   17.41
gaussNorm  5.47   0.27    5.73
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowStats.Rcheck/00check.log'
for details.

Installation output

flowStats.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/flowStats_4.0.0.tar.gz && rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowStats.buildbin-libdir flowStats_4.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL flowStats_4.0.0.zip && rm flowStats_4.0.0.tar.gz flowStats_4.0.0.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 1518k  100 1518k    0     0  13.1M      0 --:--:-- --:--:-- --:--:-- 13.9M

install for i386

* installing *source* package 'flowStats' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowStats'
    finding HTML links ... done
    BackGating                              html  
    ITN                                     html  
    addName-methods                         html  
    autoGate                                html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/autoGate.Rd:21: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/autoGate.Rd:25: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/autoGate.Rd:54: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
    binByRef                                html  
    calcPBChiSquare                         html  
    calcPearsonChi                          html  
    curv1Filter-class                       html  
    finding level-2 HTML links ... done

    curv2Filter-class                       html  
    curvPeaks                               html  
    density1d                               html  
    fdPar                                   html  
    flowStats-package                       html  
    gate_singlet                            html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/gate_singlet.Rd:65: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
    gaussNorm                               html  
    gpaSet                                  html  
    iProcrustes                             html  
    idFeaturesByBackgating                  html  
    landmarkMatrix                          html  
    lymphGate                               html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/lymphGate.Rd:79: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/lymphGate.Rd:83: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/lymphGate.Rd:133: file link 'ellipsoidGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/lymphGate.Rd:141: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
    norm2Filter-class                       html  
    normQA                                  html  
    normalize                               html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/normalize.Rd:58: file link 'ncdfFlowSet' in package 'ncdfFlow' does not exist and so has been treated as a topic
    overton_like                            html  
    plotBins                                html  
    proBin                                  html  
    quadrantGate                            html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/quadrantGate.Rd:71: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/quadrantGate.Rd:79: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
    rangeGate                               html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/rangeGate.Rd:135: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/rangeGate.Rd:145: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
    spillover-flowSet                       html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp88KeAZ/R.INSTALLdb41c1c6aac/flowStats/man/spillover-flowSet.Rd:41: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
    spillover_match-flowSet                 html  
    spillover_ng-flowSet                    html  
    warpSet                                 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 'flowStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowStats' as flowStats_4.0.0.zip
* DONE (flowStats)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'flowStats' successfully unpacked and MD5 sums checked

Tests output

flowStats.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(flowStats)
> 
> test_check("flowStats")

Estimating landmarks for channel CD4 ...
Registering curves for parameter CD4 ...
== testthat results  ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.09    1.04   14.12

flowStats.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(flowStats)
> 
> test_check("flowStats")

Estimating landmarks for channel CD4 ...
Registering curves for parameter CD4 ...
== testthat results  ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.34    0.78   16.81

Example timings

flowStats.Rcheck/examples_i386/flowStats-Ex.timings

nameusersystemelapsed
autoGate2.560.012.58
binByRef1.610.031.64
calcPBChiSquare1.530.051.57
calcPearsonChi1.270.091.36
curv1Filter-class0.730.020.75
curv2Filter-class1.860.061.92
curvPeaks1.110.051.16
density1d4.440.154.59
gate_singlet000
gaussNorm5.670.325.98
gpaSet2.970.153.13
iProcrustes0.080.020.09
idFeaturesByBackgating0.810.000.81
landmarkMatrix1.000.011.02
lymphGate2.990.073.04
norm2Filter-class0.140.000.14
normalize000
overton_like000
plotBins1.590.081.68
proBin1.060.011.07
quadrantGate000
rangeGate3.640.083.72
warpSet15.08 0.5115.59

flowStats.Rcheck/examples_x64/flowStats-Ex.timings

nameusersystemelapsed
autoGate2.310.042.35
binByRef1.220.021.24
calcPBChiSquare0.820.030.86
calcPearsonChi0.860.030.89
curv1Filter-class0.250.020.27
curv2Filter-class1.520.061.58
curvPeaks0.750.000.75
density1d3.610.063.67
gate_singlet000
gaussNorm5.470.275.73
gpaSet3.790.083.88
iProcrustes0.130.000.12
idFeaturesByBackgating1.010.001.02
landmarkMatrix1.320.001.31
lymphGate3.030.073.11
norm2Filter-class0.150.000.16
normalize000
overton_like0.020.000.01
plotBins1.230.041.27
proBin0.850.030.87
quadrantGate000
rangeGate3.110.143.25
warpSet16.72 0.6917.41