Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:04 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for flowStats on nebbiolo2


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? 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 706/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 4.10.0  (landing page)
Greg Finak , Mike Jiang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/flowStats
git_branch: RELEASE_3_16
git_last_commit: 19e0ce5
git_last_commit_date: 2022-11-01 11:04:25 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flowStats
Version: 4.10.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings flowStats_4.10.0.tar.gz
StartedAt: 2023-04-10 20:46:35 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:52:11 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 335.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowStats.Rcheck
Warnings: 4

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings flowStats_4.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/flowStats.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘4.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flowStats’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
See ‘/home/biocbuild/bbs-3.16-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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
Missing or unexported object: ‘flowWorkspace::plotGate’
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
.combinePriorsForChildNodes: no visible global function definition for
  ‘adj’
.combinePriorsForChildNodes: no visible global function definition for
  ‘nodeData’
.graph_parent: no visible global function definition for ‘ugraph’
.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’
SimulateMixture: no visible global function definition for ‘rbox’
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:
  adj bogus cluster group hasPeak nodeData params rbox ugraph whichS y
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'SimulateMixture.Rd':
  ‘flowClust’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ellipse'
  ‘cov’ ‘centre’ ‘level’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
warpSet 18.345  0.212  18.557
* 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 ...
  ‘GettingStartedWithFlowStats.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/flowStats.Rcheck/00check.log’
for details.



Installation output

flowStats.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL flowStats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘flowStats’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** testing if installed package keeps a record of temporary installation path
* DONE (flowStats)

Tests output

flowStats.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
Warning message:
replacing previous import 'flowViz::contour' by 'graphics::contour' when loading 'flowStats' 
> 
> test_check("flowStats")

Estimating landmarks for channel CD4 ...
Registering curves for parameter CD4 ...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
 13.410   0.462  13.855 

Example timings

flowStats.Rcheck/flowStats-Ex.timings

nameusersystemelapsed
SimulateMixture0.0210.0000.021
autoGate3.0150.1043.118
binByRef1.920.061.98
calcPBChiSquare1.3950.0161.412
calcPearsonChi1.4930.0321.524
curv1Filter-class0.2540.0150.269
curv2Filter-class1.4180.0961.514
curvPeaks1.4000.0081.408
density1d3.2100.1363.347
gate_singlet000
gaussNorm4.0870.0994.187
gpaSet2.9520.0563.008
iProcrustes0.1130.0040.116
idFeaturesByBackgating0.7530.0400.794
landmarkMatrix1.4640.0321.496
lymphGate3.3870.0683.454
mkPrior000
norm2Filter-class0.1080.0040.112
normalize000
overton_like0.0060.0000.006
plotBins1.6430.0121.655
proBin1.4740.0031.477
quadrantGate000
rangeGate3.9470.0674.014
warpSet18.345 0.21218.557