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This page was generated on 2024-05-04 11:38:58 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 303/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.12.0  (landing page)
Waldir Leoncio
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_19
git_last_commit: 38ab506
git_last_commit_date: 2024-04-30 11:33:08 -0400 (Tue, 30 Apr 2024)
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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-05-03 20:43:57 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 20:46:22 -0400 (Fri, 03 May 2024)
EllapsedTime: 145.0 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* 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 ‘1.12.0’
* 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 version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
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 -- Fri May  3 20:46:09 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 
  3.313   0.363   3.694 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.002
CellMig-class0.0330.0030.036
CellMigPCA1.5610.0401.618
CellMigPCAclust0.0070.0020.009
CellMigPCAclustALL0.8360.0150.857
CellTracker0.0190.0040.023
CellTrackerMainLoop0.0050.0090.031
CentroidArray0.0190.0030.022
CentroidValidation0.5710.0170.593
ComputeTracksStats0.0270.0020.030
DetectRadii0.0020.0000.003
DiAutoCor1.6820.0241.722
DiRatio0.0210.0020.023
DiRatioPlot0.0370.0140.055
EstimateDiameterRange0.0250.0020.027
FMI0.6180.0110.634
FianlizeOptiParams0.0000.0000.001
FilterTrackedCells0.0030.0000.004
FinRes0.8320.0190.861
ForwardMigration1.2720.0171.301
GenAllCombos0.0030.0000.003
LinearConv20.0210.0020.023
LoadTiff0.0010.0000.001
MSD2.0970.0692.190
MakeHypercube0.0000.0010.002
MigrationStats0.0010.0010.001
NextOdd000
NonParallel4OptimizeParams0.0010.0000.002
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0140.0020.015
OptimizeParamsMainLoop0.0040.0080.020
Parallel4OptimizeParams0.0000.0000.001
ParallelTrackLoop0.0010.0010.001
PerAndSpeed0.3200.0290.361
PlotTracksSeparately0.0080.0010.009
PostProcessTracking000
Prep4OptimizeParams0.1050.0050.110
ThreeConditions0.0120.0030.015
TrackCellsDataset0.0160.0020.018
TrajectoryDataset0.0200.0020.022
ValidateTrackingArgs0.0010.0010.000
VeAutoCor1.1940.0221.229
VisualizeCntr0.0020.0010.004
VisualizeImg0.0050.0010.006
VisualizeStackCentroids0.0570.0110.072
WSADataset0.0070.0010.009
aggregateFR0.7390.0100.755
aggregateTrackedCells0.0180.0050.023
bpass0.0600.0030.063
circshift000
cntrd0.7790.0250.826
fixDA0.0010.0000.001
fixExpName0.0000.0000.001
fixFM1000
fixFM20.0000.0000.001
fixFM30.0000.0000.001
fixFM40.0000.0000.001
fixFM50.0000.0000.001
fixFM6000
fixID10.0000.0000.001
fixMSD0.0000.0000.001
fixPER1000
fixPER20.0000.0000.001
fixPER30.0010.0000.000
getAvailableAggrMetrics0.9750.0120.992
getCellImages0.2740.8091.203
getCellMigSlot0.3800.5460.936
getCellTrackMeta0.0140.0010.016
getCellTrackStats0.0180.0040.023
getCellTracks0.0170.0030.021
getCellsMeta0.0160.0020.018
getCellsStats0.0190.0030.022
getDACtable2.2700.0312.320
getDiRatio0.0230.0020.026
getFMItable0.5380.0080.548
getForMigtable0.6740.0090.689
getImageCentroids0.0220.0030.026
getImageStacks0.0490.0070.058
getMSDtable4.1950.0614.291
getOptimizedParameters0.0150.0020.017
getOptimizedParams0.0200.0020.021
getPerAndSpeed0.3100.0270.348
getPopulationStats0.0180.0020.021
getProcessedImages0.2710.8521.133
getProcessingStatus0.0140.0010.015
getResults0.7080.0170.733
getTracks0.0160.0020.018
getVACtable1.2860.0151.310
initializeTrackParams0.0000.0010.001
innerBondRaster0.0020.0000.002
internalPermutation0.0020.0000.001
matfix0.0010.0010.001
nontrivialBondTracking0.0010.0000.001
pkfnd0.8390.0250.870
plot3DAllTracks000
plot3DTracks0.0000.0000.001
plotAllTracks0.0160.0040.020
plotSampleTracks0.0140.0030.018
preProcCellMig0.0070.0010.008
rmPreProcessing0.1000.0080.109
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0130.0020.015
setCellMigSlot0.0240.0020.027
setCellTracks0.0150.0020.017
setCellsMeta0.0160.0020.018
setExpName0.0220.0020.024
setOptimizedParams0.0150.0020.018
setProcessedImages0.0150.0020.016
setProcessingStatus0.0310.0040.037
setTrackedCellsMeta0.0150.0020.016
setTrackedCentroids0.0160.0020.019
setTrackedPositions0.0150.0020.017
setTrackingStats0.0150.0020.016
sinkAway0.0010.0000.001
subNetworkTracking0.0010.0000.002
track0.0100.0010.011
trackHypercubeBuild0.0000.0000.001
trackSlideProcessing0.0000.0000.001
trackSlideWrapUp0.0000.0000.001
trivialBondRaster0.0010.0000.001
trivialBondTracking000
visualizeCellTracks0.0540.0090.064
visualizeTrcks0.0300.0040.037
warnMessage0.0000.0000.001
wsaPreProcessing0.0630.0030.069