Back to Multiple platform build/check report for BioC 3.19:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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: 2024-06-12 14:00 -0400 (Wed, 12 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


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: 2024-06-12 21:25:45 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 21:29:27 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 222.5 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 12 21:27:29 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 
  2.868   0.278   3.134 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0000.0010.002
CellMig-class0.0280.0000.028
CellMigPCA1.1040.0841.189
CellMigPCAclust0.0080.0000.008
CellMigPCAclustALL0.6090.0000.610
CellTracker0.0190.0000.019
CellTrackerMainLoop0.0080.0000.025
CentroidArray0.0180.0020.020
CentroidValidation0.4510.0020.452
ComputeTracksStats0.0270.0000.027
DetectRadii0.0030.0000.003
DiAutoCor1.2370.0441.281
DiRatio0.0160.0000.016
DiRatioPlot0.0290.0040.033
EstimateDiameterRange0.0100.0040.014
FMI0.4200.0040.424
FianlizeOptiParams0.0010.0000.001
FilterTrackedCells0.0010.0010.003
FinRes0.6010.0020.602
ForwardMigration0.8460.0160.862
GenAllCombos0.0030.0000.003
LinearConv20.0180.0000.018
LoadTiff0.0000.0010.001
MSD1.4030.0031.407
MakeHypercube0.0020.0000.001
MigrationStats0.0000.0010.001
NextOdd0.0000.0010.000
NonParallel4OptimizeParams0.0000.0010.001
NonParallelTrackLoop000
OptimizeParams0.0100.0080.018
OptimizeParamsMainLoop0.0070.0020.024
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.3370.0000.339
PlotTracksSeparately0.0060.0040.010
PostProcessTracking0.0000.0000.001
Prep4OptimizeParams0.0970.0040.101
ThreeConditions0.0020.0120.014
TrackCellsDataset0.0170.0000.017
TrajectoryDataset0.0220.0000.023
ValidateTrackingArgs0.0010.0000.001
VeAutoCor1.0340.0361.070
VisualizeCntr0.0020.0000.003
VisualizeImg0.0010.0040.006
VisualizeStackCentroids0.0580.0080.066
WSADataset0.0030.0040.007
aggregateFR0.6160.0000.616
aggregateTrackedCells0.0240.0000.023
bpass0.0550.0030.059
circshift0.0010.0000.000
cntrd0.6990.0000.699
fixDA0.0000.0000.001
fixExpName0.0000.0000.001
fixFM10.0000.0000.001
fixFM2000
fixFM3000
fixFM4000
fixFM50.0000.0010.001
fixFM6000
fixID1000
fixMSD0.0010.0000.000
fixPER1000
fixPER20.0000.0000.001
fixPER30.0000.0000.001
getAvailableAggrMetrics0.8590.0120.871
getCellImages0.3210.9401.262
getCellMigSlot0.2940.6130.906
getCellTrackMeta0.0100.0070.017
getCellTrackStats0.0130.0080.020
getCellTracks0.0140.0030.019
getCellsMeta0.0130.0040.018
getCellsStats0.0310.0040.035
getDACtable2.0980.0512.149
getDiRatio0.0180.0000.019
getFMItable0.4020.0050.406
getForMigtable0.4950.0000.496
getImageCentroids0.0230.0000.024
getImageStacks0.0540.0110.066
getMSDtable3.2720.0203.292
getOptimizedParameters0.0140.0040.018
getOptimizedParams0.0190.0000.019
getPerAndSpeed0.2800.0070.287
getPopulationStats0.0130.0040.018
getProcessedImages0.2321.0331.263
getProcessingStatus0.0140.0030.017
getResults0.5580.0340.590
getTracks0.0110.0070.018
getVACtable1.0010.0081.008
initializeTrackParams0.0010.0000.001
innerBondRaster0.0020.0000.002
internalPermutation0.0010.0000.001
matfix0.0010.0000.001
nontrivialBondTracking0.0020.0000.001
pkfnd0.6730.0000.673
plot3DAllTracks0.0650.0390.105
plot3DTracks0.0050.0030.008
plotAllTracks0.0180.0000.019
plotSampleTracks0.0110.0040.015
preProcCellMig0.0070.0000.007
rmPreProcessing0.0820.0000.082
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0120.0040.016
setCellMigSlot0.0220.0000.023
setCellTracks0.0090.0080.018
setCellsMeta0.0140.0040.018
setExpName0.0230.0000.023
setOptimizedParams0.0180.0000.018
setProcessedImages0.0140.0040.017
setProcessingStatus0.0140.0040.018
setTrackedCellsMeta0.0130.0040.018
setTrackedCentroids0.0310.0000.031
setTrackedPositions0.0090.0080.017
setTrackingStats0.0170.0000.017
sinkAway0.0010.0000.001
subNetworkTracking0.0010.0000.001
track0.0090.0000.009
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.000
trackSlideWrapUp0.0000.0010.000
trivialBondRaster0.0000.0010.002
trivialBondTracking0.0000.0000.001
visualizeCellTracks0.0650.0030.069
visualizeTrcks0.0240.0000.025
warnMessage000
wsaPreProcessing0.0460.0000.046