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This page was generated on 2024-04-18 11:32:07 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 299/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.10.0  (landing page)
Waldir Leoncio
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 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)
kjohnson1macOS 13.6.1 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:
- 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: 2024-04-17 08:25:33 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 08:27:50 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 136.5 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-mac-arm64/meat/cellmigRation.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-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 Ventura 13.6.1
* 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
* 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-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 -- Wed Apr 17 08:27:36 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 
  3.500   0.297   3.835 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0030.0010.004
CellMig-class0.0420.0040.047
CellMigPCA1.4610.0311.508
CellMigPCAclust0.0110.0020.013
CellMigPCAclustALL0.9210.0340.969
CellTracker0.0280.0020.031
CellTrackerMainLoop0.0060.0090.017
CentroidArray0.0270.0020.030
CentroidValidation0.4650.0160.484
ComputeTracksStats0.0340.0030.037
DetectRadii0.0020.0000.003
DiAutoCor1.3050.0171.337
DiRatio0.0200.0020.021
DiRatioPlot0.0370.0120.050
EstimateDiameterRange0.0170.0020.020
FMI0.4440.0030.449
FianlizeOptiParams0.0000.0000.001
FilterTrackedCells0.0020.0010.003
FinRes0.6340.0160.655
ForwardMigration0.9250.0090.944
GenAllCombos0.0020.0010.003
LinearConv20.0190.0010.020
LoadTiff0.0010.0000.002
MSD1.4600.0351.507
MakeHypercube0.0020.0000.002
MigrationStats0.0010.0000.002
NextOdd0.0000.0000.001
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop000
OptimizeParams0.0240.0020.027
OptimizeParamsMainLoop0.0060.0100.017
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0000.0010.001
PerAndSpeed0.3100.0350.351
PlotTracksSeparately0.0110.0020.014
PostProcessTracking000
Prep4OptimizeParams0.1060.0050.111
ThreeConditions0.0210.0030.023
TrackCellsDataset0.0400.0040.043
TrajectoryDataset0.0330.0030.035
ValidateTrackingArgs0.0010.0000.001
VeAutoCor1.0550.0171.077
VisualizeCntr0.0020.0000.003
VisualizeImg0.0050.0000.005
VisualizeStackCentroids0.0670.0070.075
WSADataset0.0100.0020.012
aggregateFR0.6220.0080.658
aggregateTrackedCells0.0340.0060.040
bpass0.0790.0030.082
circshift0.0000.0000.001
cntrd0.7060.0160.727
fixDA0.0010.0000.001
fixExpName0.0010.0000.000
fixFM10.0010.0000.000
fixFM2000
fixFM3000
fixFM40.0010.0000.001
fixFM50.0000.0000.001
fixFM60.0000.0000.001
fixID10.0010.0000.001
fixMSD0.0000.0000.001
fixPER10.0000.0000.001
fixPER20.0000.0000.001
fixPER30.0000.0000.001
getAvailableAggrMetrics0.9180.0090.934
getCellImages0.2510.7841.056
getCellMigSlot0.4050.4850.900
getCellTrackMeta0.0260.0030.030
getCellTrackStats0.0280.0030.032
getCellTracks0.0260.0030.029
getCellsMeta0.0250.0020.027
getCellsStats0.0290.0030.032
getDACtable1.9190.0221.957
getDiRatio0.0210.0020.024
getFMItable0.4490.0050.455
getForMigtable0.8670.0080.880
getImageCentroids0.0310.0040.035
getImageStacks0.0690.0070.076
getMSDtable3.4070.0443.475
getOptimizedParameters0.0270.0020.030
getOptimizedParams0.0270.0020.030
getPerAndSpeed0.2910.0290.321
getPopulationStats0.0280.0030.031
getProcessedImages0.2400.7851.042
getProcessingStatus0.0270.0040.030
getResults0.6250.0160.649
getTracks0.0230.0030.025
getVACtable1.0370.0111.056
initializeTrackParams0.0000.0000.001
innerBondRaster0.0010.0010.002
internalPermutation0.0010.0000.002
matfix0.0010.0010.002
nontrivialBondTracking0.0010.0000.002
pkfnd0.6840.0150.701
plot3DAllTracks000
plot3DTracks000
plotAllTracks0.0220.0040.025
plotSampleTracks0.0190.0040.023
preProcCellMig0.0110.0020.013
rmPreProcessing0.0960.0030.099
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0270.0020.030
setCellMigSlot0.0330.0020.036
setCellTracks0.0240.0020.027
setCellsMeta0.0240.0030.027
setExpName0.0330.0020.035
setOptimizedParams0.0270.0020.030
setProcessedImages0.0240.0020.027
setProcessingStatus0.0240.0030.027
setTrackedCellsMeta0.0630.0100.076
setTrackedCentroids0.0280.0020.030
setTrackedPositions0.0240.0030.027
setTrackingStats0.0270.0020.029
sinkAway0.0010.0000.001
subNetworkTracking0.0010.0010.002
track0.0100.0010.011
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.000
trackSlideWrapUp0.0000.0000.001
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0690.0090.082
visualizeTrcks0.0480.0020.050
warnMessage0.0010.0000.000
wsaPreProcessing0.0530.0020.057