Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-27 11:37:41 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 300/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.11.0  (landing page)
Waldir Leoncio
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: devel
git_last_commit: 1b666b3
git_last_commit_date: 2023-10-24 11:31:56 -0400 (Tue, 24 Oct 2023)
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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for cellmigRation on palomino3


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: 1.11.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cellmigRation.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings cellmigRation_1.11.0.tar.gz
StartedAt: 2024-03-27 00:06:00 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 00:08:19 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 138.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cellmigRation.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings cellmigRation_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cellmigRation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cellmigRation' version '1.11.0'
* 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 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
  'F:/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck/00check.log'
for details.


Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 Mar 27 00:08:05 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 
   2.53    0.37    2.93 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension000
CellMig-class0.020.000.01
CellMigPCA1.230.031.27
CellMigPCAclust0.020.000.01
CellMigPCAclustALL0.820.030.86
CellTracker0.000.030.03
CellTrackerMainLoop000
CentroidArray0.020.020.03
CentroidValidation0.420.000.43
ComputeTracksStats0.020.000.01
DetectRadii000
DiAutoCor1.110.001.11
DiRatio0.010.000.01
DiRatioPlot0.050.000.16
EstimateDiameterRange0.010.000.01
FMI0.360.020.38
FianlizeOptiParams000
FilterTrackedCells0.020.000.01
FinRes0.550.010.57
ForwardMigration0.750.020.76
GenAllCombos000
LinearConv20.020.000.01
LoadTiff000
MSD1.510.061.64
MakeHypercube000
MigrationStats000
NextOdd000
NonParallel4OptimizeParams0.020.000.02
NonParallelTrackLoop000
OptimizeParams0.010.000.01
OptimizeParamsMainLoop0.020.000.02
Parallel4OptimizeParams000
ParallelTrackLoop000
PerAndSpeed0.250.030.32
PlotTracksSeparately0.020.000.02
PostProcessTracking000
Prep4OptimizeParams0.110.000.11
ThreeConditions0.010.000.02
TrackCellsDataset0.020.020.03
TrajectoryDataset0.030.000.03
ValidateTrackingArgs000
VeAutoCor0.830.050.87
VisualizeCntr000
VisualizeImg0.010.000.02
VisualizeStackCentroids0.060.000.06
WSADataset000
aggregateFR0.520.000.51
aggregateTrackedCells0.010.000.02
bpass0.050.000.05
circshift000
cntrd0.700.030.73
fixDA000
fixExpName000
fixFM1000
fixFM2000
fixFM3000
fixFM4000
fixFM5000
fixFM6000
fixID1000
fixMSD000
fixPER1000
fixPER2000
fixPER3000
getAvailableAggrMetrics0.720.010.73
getCellImages0.360.520.88
getCellMigSlot0.470.300.76
getCellTrackMeta0.030.000.03
getCellTrackStats0.010.000.02
getCellTracks0.040.000.03
getCellsMeta0.010.000.01
getCellsStats0.000.020.02
getDACtable1.450.061.52
getDiRatio0.020.020.03
getFMItable0.360.000.36
getForMigtable0.480.010.50
getImageCentroids0.020.020.03
getImageStacks0.060.000.06
getMSDtable3.330.013.34
getOptimizedParameters0.000.020.02
getOptimizedParams0.020.010.03
getPerAndSpeed0.230.070.30
getPopulationStats0.020.010.03
getProcessedImages0.500.420.92
getProcessingStatus0.000.020.02
getResults0.530.060.59
getTracks0.010.000.02
getVACtable0.820.050.86
initializeTrackParams000
innerBondRaster000
internalPermutation000
matfix000
nontrivialBondTracking000
pkfnd0.630.010.64
plot3DAllTracks0.030.070.08
plot3DTracks0.000.010.02
plotAllTracks0.010.000.01
plotSampleTracks0.000.030.03
preProcCellMig000
rmPreProcessing0.070.020.08
runTrackingPermutation000
setAnalyticParams0.010.010.03
setCellMigSlot0.030.000.03
setCellTracks0.020.000.02
setCellsMeta0.000.020.01
setExpName0.000.030.04
setOptimizedParams0.000.020.01
setProcessedImages0.010.010.03
setProcessingStatus0.020.000.02
setTrackedCellsMeta0.000.030.03
setTrackedCentroids0.010.000.01
setTrackedPositions0.040.000.04
setTrackingStats0.010.000.01
sinkAway0.020.000.02
subNetworkTracking000
track000
trackHypercubeBuild000
trackSlideProcessing000
trackSlideWrapUp000
trivialBondRaster000
trivialBondTracking000
visualizeCellTracks0.070.000.07
visualizeTrcks0.010.000.01
warnMessage000
wsaPreProcessing0.030.020.04