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This page was generated on 2024-03-28 11:38:55 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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

Package 301/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.11.0  (landing page)
Waldir Leoncio
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: devel
git_last_commit: 1b666b3
git_last_commit_date: 2023-10-24 11:31:56 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for cellmigRation on lconway


To the developers/maintainers of the cellmigRation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellmigRation.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cellmigRation
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.11.0.tar.gz
StartedAt: 2024-03-27 20:04:34 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:07:02 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 148.3 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.11.0’
* 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 ‘cellmigRation’ 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 code 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'fixDA.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM1.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM2.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM3.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM4.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM5.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM6.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixID2.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixID3.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixID4.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixMSD.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixPER1.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'fixPER2.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'innerBondRaster.Rd':
  ‘i’

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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.


Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘cellmigRation’ ...
** using staged installation
** R
** data
** inst
** 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 (cellmigRation)

Tests output

cellmigRation.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> BiocGenerics:::testPackage("cellmigRation")


RUNIT TEST PROTOCOL -- Wed Mar 27 20:06:49 2024 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
cellmigRation RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.300   0.371   3.688 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.002
CellMig-class0.0310.0030.034
CellMigPCA1.7090.0431.767
CellMigPCAclust0.0070.0020.009
CellMigPCAclustALL1.0480.0521.109
CellTracker0.0190.0030.022
CellTrackerMainLoop0.0070.0080.025
CentroidArray0.0200.0030.023
CentroidValidation0.5540.0240.584
ComputeTracksStats0.0250.0040.029
DetectRadii0.0030.0000.003
DiAutoCor1.6130.0281.658
DiRatio0.0200.0020.022
DiRatioPlot0.0390.0170.060
EstimateDiameterRange0.0190.0020.022
FMI0.5780.0110.594
FianlizeOptiParams0.0010.0010.001
FilterTrackedCells0.0020.0010.003
FinRes0.7830.0180.810
ForwardMigration1.1540.0171.181
GenAllCombos0.0020.0000.002
LinearConv20.0250.0020.027
LoadTiff0.0000.0010.002
MSD1.7990.0291.844
MakeHypercube0.0020.0000.003
MigrationStats0.0010.0010.002
NextOdd000
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop0.0010.0000.000
OptimizeParams0.0160.0030.019
OptimizeParamsMainLoop0.0040.0100.023
Parallel4OptimizeParams0.0000.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.3410.0300.384
PlotTracksSeparately0.0100.0020.012
PostProcessTracking0.0010.0000.000
Prep4OptimizeParams0.1410.0110.153
ThreeConditions0.0120.0030.015
TrackCellsDataset0.0150.0020.016
TrajectoryDataset0.0210.0020.023
ValidateTrackingArgs0.0010.0000.001
VeAutoCor1.2810.0321.325
VisualizeCntr0.0020.0010.005
VisualizeImg0.0040.0010.006
VisualizeStackCentroids0.0600.0090.070
WSADataset0.0080.0030.012
aggregateFR0.8330.0110.852
aggregateTrackedCells0.0210.0060.028
bpass0.0720.0020.075
circshift0.0000.0000.001
cntrd0.8630.0220.891
fixDA0.0010.0000.000
fixExpName0.0000.0000.001
fixFM10.0000.0010.000
fixFM20.0000.0000.001
fixFM30.0000.0000.001
fixFM40.0010.0000.000
fixFM5000
fixFM6000
fixID10.0010.0000.001
fixMSD0.0000.0000.001
fixPER10.0010.0010.000
fixPER2000
fixPER30.0000.0000.001
getAvailableAggrMetrics1.1130.0121.130
getCellImages0.2900.8771.179
getCellMigSlot0.3730.5551.051
getCellTrackMeta0.0130.0020.016
getCellTrackStats0.0170.0020.020
getCellTracks0.0140.0030.017
getCellsMeta0.0140.0020.015
getCellsStats0.0340.0050.039
getDACtable2.3560.0302.415
getDiRatio0.0200.0020.022
getFMItable0.5620.0070.572
getForMigtable0.8920.0110.908
getImageCentroids0.0210.0060.028
getImageStacks0.0570.0120.071
getMSDtable4.0620.0574.150
getOptimizedParameters0.0140.0010.016
getOptimizedParams0.0160.0030.019
getPerAndSpeed0.3160.0280.359
getPopulationStats0.0140.0030.017
getProcessedImages0.2751.2761.562
getProcessingStatus0.0140.0020.017
getResults0.6750.0190.706
getTracks0.0150.0020.017
getVACtable1.0680.0121.086
initializeTrackParams0.0000.0000.001
innerBondRaster0.0010.0010.002
internalPermutation0.0010.0000.002
matfix0.0020.0000.002
nontrivialBondTracking0.0010.0000.001
pkfnd0.7900.0150.812
plot3DAllTracks000
plot3DTracks0.0000.0010.001
plotAllTracks0.0170.0030.021
plotSampleTracks0.0140.0040.018
preProcCellMig0.0060.0010.008
rmPreProcessing0.1000.0040.104
runTrackingPermutation0.0010.0000.002
setAnalyticParams0.0150.0010.016
setCellMigSlot0.0250.0020.027
setCellTracks0.0120.0010.014
setCellsMeta0.0160.0010.018
setExpName0.0220.0020.025
setOptimizedParams0.0140.0020.016
setProcessedImages0.0140.0020.016
setProcessingStatus0.0140.0020.017
setTrackedCellsMeta0.0150.0020.018
setTrackedCentroids0.0140.0030.017
setTrackedPositions0.0160.0020.018
setTrackingStats0.0160.0020.017
sinkAway0.0010.0000.001
subNetworkTracking0.0020.0010.002
track0.0110.0000.012
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp0.0010.0000.001
trivialBondRaster0.0010.0000.002
trivialBondTracking000
visualizeCellTracks0.0880.0170.107
visualizeTrcks0.0290.0030.032
warnMessage0.0000.0010.001
wsaPreProcessing0.0550.0020.057