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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 303/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.14.0  (landing page)
Waldir Leoncio
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_20
git_last_commit: 49990de
git_last_commit_date: 2024-10-29 10:58:18 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for cellmigRation on kjohnson1

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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2024-12-20 13:58:00 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 14:00:18 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 137.4 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.14.0’
* 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-3.20-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-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 Dec 20 14:00:03 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 
  3.444   0.306   3.764 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0010.002
CellMig-class0.0390.0030.042
CellMigPCA1.4710.0311.508
CellMigPCAclust0.0110.0020.013
CellMigPCAclustALL0.7040.0070.711
CellTracker0.0290.0030.032
CellTrackerMainLoop0.0070.0120.023
CentroidArray0.0280.0030.031
CentroidValidation0.5250.0130.540
ComputeTracksStats0.0350.0030.038
DetectRadii0.0030.0010.003
DiAutoCor1.5240.0191.549
DiRatio0.0200.0020.022
DiRatioPlot0.0380.0130.052
EstimateDiameterRange0.0160.0020.019
FMI0.5120.0040.518
FianlizeOptiParams0.0010.0000.001
FilterTrackedCells0.0030.0010.004
FinRes0.7450.0150.766
ForwardMigration1.0530.0071.070
GenAllCombos0.0020.0010.003
LinearConv20.0200.0010.021
LoadTiff0.0010.0000.001
MSD1.8460.0531.907
MakeHypercube0.0010.0010.001
MigrationStats0.0010.0010.001
NextOdd000
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop000
OptimizeParams0.0260.0030.029
OptimizeParamsMainLoop0.0050.0090.017
Parallel4OptimizeParams0.0000.0000.001
ParallelTrackLoop0.0000.0000.001
PerAndSpeed0.3100.0300.341
PlotTracksSeparately0.0130.0020.015
PostProcessTracking000
Prep4OptimizeParams0.0980.0040.105
ThreeConditions0.0210.0030.024
TrackCellsDataset0.0230.0030.026
TrajectoryDataset0.0320.0020.035
ValidateTrackingArgs0.0010.0000.001
VeAutoCor0.9940.0191.033
VisualizeCntr0.0020.0010.003
VisualizeImg0.0030.0010.003
VisualizeStackCentroids0.0270.0050.034
WSADataset0.0030.0010.004
aggregateFR0.4230.0070.440
aggregateTrackedCells0.0190.0030.022
bpass0.0620.0030.065
circshift0.0010.0000.000
cntrd0.6670.0150.692
fixDA0.0000.0000.001
fixExpName0.0010.0000.001
fixFM1000
fixFM20.0000.0000.001
fixFM3000
fixFM40.0010.0000.000
fixFM5000
fixFM60.0010.0000.001
fixID10.0000.0000.001
fixMSD0.0000.0000.001
fixPER10.0000.0000.001
fixPER20.0000.0000.001
fixPER30.0000.0010.001
getAvailableAggrMetrics0.9530.0090.968
getCellImages0.2460.7751.051
getCellMigSlot0.4120.4930.910
getCellTrackMeta0.0250.0030.028
getCellTrackStats0.0280.0030.032
getCellTracks0.0250.0030.028
getCellsMeta0.0230.0020.027
getCellsStats0.0250.0030.028
getDACtable1.9790.0242.016
getDiRatio0.0230.0030.025
getFMItable0.5010.0070.511
getForMigtable0.5990.0070.627
getImageCentroids0.0280.0040.033
getImageStacks0.0660.0070.074
getMSDtable3.6310.0483.701
getOptimizedParameters0.0230.0020.025
getOptimizedParams0.0250.0040.029
getPerAndSpeed0.3220.0310.355
getPopulationStats0.0250.0030.028
getProcessedImages0.2401.1491.414
getProcessingStatus0.0260.0020.028
getResults0.6710.0160.691
getTracks0.0280.0020.030
getVACtable1.1240.0101.138
initializeTrackParams0.0010.0000.000
innerBondRaster0.0020.0010.002
internalPermutation0.0020.0000.001
matfix0.0010.0000.002
nontrivialBondTracking0.0010.0000.002
pkfnd0.7840.0300.818
plot3DAllTracks0.0010.0000.001
plot3DTracks0.0000.0000.001
plotAllTracks0.0210.0030.025
plotSampleTracks0.0200.0040.024
preProcCellMig0.0100.0020.013
rmPreProcessing0.0980.0040.102
runTrackingPermutation0.0020.0000.003
setAnalyticParams0.0230.0030.027
setCellMigSlot0.0330.0020.035
setCellTracks0.0230.0020.026
setCellsMeta0.0250.0030.028
setExpName0.0330.0020.035
setOptimizedParams0.0240.0030.027
setProcessedImages0.0240.0030.027
setProcessingStatus0.0260.0030.028
setTrackedCellsMeta0.0240.0030.026
setTrackedCentroids0.0230.0030.027
setTrackedPositions0.0230.0030.026
setTrackingStats0.0240.0020.026
sinkAway0.0010.0000.001
subNetworkTracking0.0020.0000.002
track0.0240.0020.027
trackHypercubeBuild0.0020.0000.002
trackSlideProcessing0.0010.0010.001
trackSlideWrapUp000
trivialBondRaster0.0030.0000.002
trivialBondTracking0.0000.0000.001
visualizeCellTracks0.0710.0070.079
visualizeTrcks0.0470.0020.050
warnMessage000
wsaPreProcessing0.0550.0020.057