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This page was generated on 2021-10-22 12:04:58 -0400 (Fri, 22 Oct 2021).

CHECK results for flowStats on merida1

To the developers/maintainers of the flowStats package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowStats.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 668/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 4.5.1  (landing page)
Greg Finak , Mike Jiang , Jake Wagner
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/flowStats
git_branch: master
git_last_commit: 5932e47
git_last_commit_date: 2021-07-30 14:05:12 -0400 (Fri, 30 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: flowStats
Version: 4.5.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowStats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowStats_4.5.1.tar.gz
StartedAt: 2021-10-22 03:56:10 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 04:00:40 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 270.6 seconds
RetCode: 0
Status:   OK  
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowStats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowStats_4.5.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowStats.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘4.5.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flowStats’ 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
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 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
warpSet   18.403  1.369  19.801
gaussNorm  5.612  0.204   5.826
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowStats.Rcheck/00check.log’
for details.



Installation output

flowStats.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowStats
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘flowStats’ ...
** using staged installation
** R
** data
** 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 (flowStats)

Tests output

flowStats.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
 19.261   1.117  20.359 

Example timings

flowStats.Rcheck/flowStats-Ex.timings

nameusersystemelapsed
autoGate2.5770.1162.701
binByRef1.3060.0401.348
calcPBChiSquare0.9400.0310.972
calcPearsonChi1.0170.0291.048
curv1Filter-class0.4000.0160.416
curv2Filter-class2.1110.3052.418
curvPeaks0.8160.0220.839
density1d3.5790.1563.743
gate_singlet000
gaussNorm5.6120.2045.826
gpaSet3.3360.0723.419
iProcrustes0.1170.0030.120
idFeaturesByBackgating0.8880.0130.901
landmarkMatrix1.3140.0241.345
lymphGate3.0320.0623.108
norm2Filter-class0.1660.0020.169
normalize0.0000.0000.001
overton_like0.0170.0050.022
plotBins1.0800.0241.107
proBin1.2240.0461.272
quadrantGate000
rangeGate3.0760.0993.184
warpSet18.403 1.36919.801