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This page was generated on 2024-04-17 11:37:34 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 299/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.10.0  (landing page)
Waldir Leoncio
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_18
git_last_commit: b06828e
git_last_commit_date: 2023-10-24 11:31:56 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for cellmigRation on merida1


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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-04-16 00:27:53 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 00:32:27 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 274.5 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/cellmigRation.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘1.10.0’
* 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 ‘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 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 ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
getMSDtable 10.040  0.071  10.590
getDACtable  5.654  0.034   5.939
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK


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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.

> BiocGenerics:::testPackage("cellmigRation")


RUNIT TEST PROTOCOL -- Tue Apr 16 00:32:07 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 
  5.951   0.562   7.115 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0030.0010.004
CellMig-class0.0470.0040.057
CellMigPCA3.2550.0533.483
CellMigPCAclust0.0120.0040.021
CellMigPCAclustALL2.1180.1162.284
CellTracker0.0280.0060.036
CellTrackerMainLoop0.0070.0100.026
CentroidArray0.0300.0040.035
CentroidValidation1.4000.0421.630
ComputeTracksStats0.0480.0050.055
DetectRadii0.0050.0010.007
DiAutoCor3.8790.0424.117
DiRatio0.0360.0030.044
DiRatioPlot0.0600.0210.088
EstimateDiameterRange0.0300.0030.033
FMI1.3540.0151.429
FianlizeOptiParams0.0010.0010.001
FilterTrackedCells0.0060.0010.008
FinRes1.8160.0241.945
ForwardMigration2.7460.0162.868
GenAllCombos0.0050.0010.007
LinearConv20.0460.0030.052
LoadTiff0.0020.0000.002
MSD4.2190.0514.798
MakeHypercube0.0030.0020.004
MigrationStats0.0010.0020.005
NextOdd0.0010.0000.001
NonParallel4OptimizeParams0.0010.0000.002
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0240.0030.030
OptimizeParamsMainLoop0.0070.0090.022
Parallel4OptimizeParams0.0010.0010.001
ParallelTrackLoop0.0010.0010.002
PerAndSpeed0.6400.0450.816
PlotTracksSeparately0.0150.0030.020
PostProcessTracking0.0010.0000.001
Prep4OptimizeParams0.2220.0160.279
ThreeConditions0.0180.0040.027
TrackCellsDataset0.0360.0040.047
TrajectoryDataset0.0350.0030.042
ValidateTrackingArgs0.0010.0010.002
VeAutoCor3.1420.0253.671
VisualizeCntr0.0040.0020.007
VisualizeImg0.0090.0020.013
VisualizeStackCentroids0.0890.0150.114
WSADataset0.0100.0020.014
aggregateFR1.8910.0132.161
aggregateTrackedCells0.0350.0100.049
bpass0.1470.0050.179
circshift0.0010.0010.002
cntrd2.1600.0232.217
fixDA0.0010.0010.001
fixExpName0.0000.0010.001
fixFM10.0010.0010.002
fixFM20.0010.0010.001
fixFM30.0000.0000.001
fixFM40.0010.0000.001
fixFM50.0000.0000.001
fixFM60.0000.0000.001
fixID10.0010.0000.002
fixMSD0.0010.0000.001
fixPER10.0010.0000.001
fixPER20.0000.0000.001
fixPER30.0010.0010.002
getAvailableAggrMetrics2.7280.0182.839
getCellImages0.8012.4553.389
getCellMigSlot0.8731.5872.625
getCellTrackMeta0.0220.0040.027
getCellTrackStats0.0300.0060.037
getCellTracks0.0240.0070.033
getCellsMeta0.0220.0030.026
getCellsStats0.0280.0060.037
getDACtable5.6540.0345.939
getDiRatio0.0410.0040.046
getFMItable1.3680.0101.443
getForMigtable1.9020.0121.980
getImageCentroids0.0360.0070.045
getImageStacks0.0900.0130.110
getMSDtable10.040 0.07110.590
getOptimizedParameters0.0220.0040.026
getOptimizedParams0.0260.0050.035
getPerAndSpeed0.6140.0410.740
getPopulationStats0.0250.0040.030
getProcessedImages0.8333.3644.374
getProcessingStatus0.0230.0030.025
getResults1.8000.0241.905
getTracks0.0260.0040.032
getVACtable3.0690.0173.342
initializeTrackParams0.0000.0000.001
innerBondRaster0.0030.0010.004
internalPermutation0.0020.0010.002
matfix0.0020.0000.003
nontrivialBondTracking0.0020.0000.003
pkfnd2.0960.0162.275
plot3DAllTracks0.0000.0010.001
plot3DTracks0.0010.0010.000
plotAllTracks0.0320.0060.041
plotSampleTracks0.0250.0050.034
preProcCellMig0.0110.0020.015
rmPreProcessing0.2230.0040.246
runTrackingPermutation0.0030.0010.005
setAnalyticParams0.0620.0050.073
setCellMigSlot0.0370.0030.048
setCellTracks0.0220.0030.027
setCellsMeta0.0230.0030.027
setExpName0.0360.0030.041
setOptimizedParams0.0240.0040.029
setProcessedImages0.0230.0030.028
setProcessingStatus0.0240.0030.030
setTrackedCellsMeta0.0230.0040.031
setTrackedCentroids0.0230.0030.027
setTrackedPositions0.0230.0030.028
setTrackingStats0.0240.0040.029
sinkAway0.0010.0010.002
subNetworkTracking0.0020.0010.005
track0.0190.0010.023
trackHypercubeBuild0.0010.0000.002
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp0.0020.0000.002
trivialBondRaster0.0040.0000.004
trivialBondTracking0.0010.0000.003
visualizeCellTracks0.0950.0150.118
visualizeTrcks0.0450.0030.054
warnMessage0.0010.0000.001
wsaPreProcessing0.1380.0040.147