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CHECK report for flowStats on tokay1

This page was generated on 2021-05-06 12:31:20 -0400 (Thu, 06 May 2021).

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 634/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 4.2.0  (landing page)
Greg Finak , Mike Jiang , Jake Wagner
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowStats
Branch: RELEASE_3_12
Last Commit: dac2093
Last Changed Date: 2020-10-27 10:35:39 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: flowStats
Version: 4.2.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings flowStats_4.2.0.tar.gz
StartedAt: 2021-05-06 02:53:21 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:59:15 -0400 (Thu, 06 May 2021)
EllapsedTime: 353.4 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: flowStats.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings flowStats_4.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/flowStats.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '4.2.0'
* 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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-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   19.34   0.82   20.15
gaussNorm  4.87   0.20    5.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
warpSet   19.50   0.72   20.22
gaussNorm  5.09   0.44    5.53
* 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-3.12-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 http://172.29.0.3/BBS/3.12/bioc/src/contrib/flowStats_4.2.0.tar.gz && rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowStats.buildbin-libdir flowStats_4.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL flowStats_4.2.0.zip && rm flowStats_4.2.0.tar.gz flowStats_4.2.0.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 1519k  100 1519k    0     0  44.7M      0 --:--:-- --:--:-- --:--:-- 46.3M

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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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_4.2.0.zip
* DONE (flowStats)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'flowStats' successfully unpacked and MD5 sums checked

Tests output

flowStats.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 ...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
  15.50    1.03   16.53

flowStats.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 ...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
  14.43    0.51   15.01

Example timings

flowStats.Rcheck/examples_i386/flowStats-Ex.timings

nameusersystemelapsed
autoGate2.610.062.67
binByRef1.300.081.38
calcPBChiSquare1.050.051.09
calcPearsonChi1.000.011.01
curv1Filter-class0.310.000.32
curv2Filter-class1.720.181.89
curvPeaks0.780.030.81
density1d3.880.093.97
gate_singlet000
gaussNorm4.870.205.08
gpaSet3.320.043.34
iProcrustes0.110.000.11
idFeaturesByBackgating0.790.010.81
landmarkMatrix1.490.021.50
lymphGate4.610.084.69
norm2Filter-class0.170.000.17
normalize000
overton_like0.010.000.02
plotBins1.890.042.09
proBin1.020.021.03
quadrantGate000
rangeGate3.080.123.21
warpSet19.34 0.8220.15

flowStats.Rcheck/examples_x64/flowStats-Ex.timings

nameusersystemelapsed
autoGate3.090.063.16
binByRef1.140.081.22
calcPBChiSquare1.050.051.09
calcPearsonChi0.940.071.02
curv1Filter-class0.370.020.39
curv2Filter-class2.560.112.67
curvPeaks0.700.030.73
density1d3.830.083.91
gate_singlet000
gaussNorm5.090.445.53
gpaSet4.050.074.13
iProcrustes0.110.000.11
idFeaturesByBackgating1.360.021.37
landmarkMatrix0.620.080.71
lymphGate2.880.082.95
norm2Filter-class0.110.010.12
normalize000
overton_like0.000.020.02
plotBins1.090.061.17
proBin0.690.000.69
quadrantGate000
rangeGate4.720.124.84
warpSet19.50 0.7220.22