Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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: 2024-06-19 14:00 -0400 (Wed, 19 Jun 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
merida1macOS 12.7.4 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 nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cellmigRation_1.12.0.tar.gz
StartedAt: 2024-06-19 21:26:42 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 21:30:24 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 222.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cellmigRation_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 Jun 19 21:28:26 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 
  2.645   0.176   2.811 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.002
CellMig-class0.0250.0040.029
CellMigPCA1.1960.0521.249
CellMigPCAclust0.0080.0000.008
CellMigPCAclustALL0.6250.0040.629
CellTracker0.0190.0000.019
CellTrackerMainLoop0.0050.0040.031
CentroidArray0.0190.0000.019
CentroidValidation0.4540.0000.454
ComputeTracksStats0.0140.0120.027
DetectRadii0.0030.0000.003
DiAutoCor1.3010.1121.413
DiRatio0.0130.0040.017
DiRatioPlot0.0310.0040.036
EstimateDiameterRange0.0160.0000.015
FMI0.4650.0120.477
FianlizeOptiParams0.0000.0010.001
FilterTrackedCells0.0000.0030.003
FinRes0.6020.0070.609
ForwardMigration0.8760.0320.908
GenAllCombos0.0030.0000.003
LinearConv20.0190.0000.019
LoadTiff0.0020.0000.002
MSD1.3850.0401.426
MakeHypercube0.0020.0000.001
MigrationStats0.0010.0000.001
NextOdd000
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop0.0010.0000.001
OptimizeParams0.0180.0000.018
OptimizeParamsMainLoop0.0050.0030.025
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.3160.0360.353
PlotTracksSeparately0.0100.0000.009
PostProcessTracking000
Prep4OptimizeParams0.0920.0040.096
ThreeConditions0.0090.0040.013
TrackCellsDataset0.0160.0000.016
TrajectoryDataset0.0220.0000.023
ValidateTrackingArgs0.0000.0010.001
VeAutoCor1.0190.0631.081
VisualizeCntr0.0020.0000.002
VisualizeImg0.0020.0030.005
VisualizeStackCentroids0.0590.0080.068
WSADataset0.0070.0000.008
aggregateFR0.6280.0400.668
aggregateTrackedCells0.0220.0040.026
bpass0.0620.0000.062
circshift0.0000.0000.001
cntrd0.7260.0240.750
fixDA000
fixExpName000
fixFM1000
fixFM20.0010.0000.000
fixFM30.0000.0000.001
fixFM4000
fixFM5000
fixFM60.0010.0000.000
fixID10.0010.0000.001
fixMSD0.0010.0000.001
fixPER10.0000.0000.001
fixPER2000
fixPER3000
getAvailableAggrMetrics0.9320.0400.972
getCellImages0.2361.0011.237
getCellMigSlot0.3080.5870.895
getCellTrackMeta0.0140.0040.018
getCellTrackStats0.0220.0000.022
getCellTracks0.0050.0130.018
getCellsMeta0.0120.0060.018
getCellsStats0.0290.0260.056
getDACtable2.1240.1362.261
getDiRatio0.0180.0000.018
getFMItable0.4020.0000.402
getForMigtable0.4910.0000.491
getImageCentroids0.0230.0000.024
getImageStacks0.0670.0000.067
getMSDtable3.2800.0483.328
getOptimizedParameters0.0170.0000.017
getOptimizedParams0.0150.0030.019
getPerAndSpeed0.2660.0100.276
getPopulationStats0.0130.0040.018
getProcessedImages0.2720.9921.265
getProcessingStatus0.0180.0010.017
getResults0.5670.0060.573
getTracks0.0170.0020.018
getVACtable0.9720.0361.008
initializeTrackParams000
innerBondRaster0.0010.0000.002
internalPermutation0.0010.0000.001
matfix0.0010.0000.001
nontrivialBondTracking0.0010.0000.001
pkfnd0.6560.0120.668
plot3DAllTracks0.0760.0200.097
plot3DTracks0.0010.0080.008
plotAllTracks0.0190.0000.019
plotSampleTracks0.0110.0040.015
preProcCellMig0.0070.0000.007
rmPreProcessing0.0790.0000.080
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0140.0040.018
setCellMigSlot0.0230.0000.023
setCellTracks0.0140.0040.017
setCellsMeta0.0180.0000.017
setExpName0.0200.0040.023
setOptimizedParams0.0170.0000.018
setProcessedImages0.0140.0040.018
setProcessingStatus0.0060.0120.017
setTrackedCellsMeta0.0180.0000.017
setTrackedCentroids0.0290.0000.028
setTrackedPositions0.0120.0040.017
setTrackingStats0.0170.0000.016
sinkAway0.0010.0000.001
subNetworkTracking0.0010.0000.002
track0.010.000.01
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0000.0000.001
trackSlideWrapUp0.0010.0000.001
trivialBondRaster0.0020.0000.001
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0650.0040.068
visualizeTrcks0.0240.0000.025
warnMessage0.0000.0000.001
wsaPreProcessing0.0460.0000.047