Multiple platform build/check report for BioC 3.14 - CHECK results for cellmigRation on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: cellmigRation

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellmigRation.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cellmigRation_1.2.0.tar.gz

StartedAt: 2022-04-12 16:59:21 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 17:04:28 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 306.9 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellmigRation.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cellmigRation_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cellmigRation.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellmigRation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cellmigRation' version '1.2.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cellmigRation_1.2.0.tar.gz && rm -rf cellmigRation.buildbin-libdir && mkdir cellmigRation.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellmigRation.buildbin-libdir cellmigRation_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cellmigRation_1.2.0.zip && rm cellmigRation_1.2.0.tar.gz cellmigRation_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 56  907k   56  512k    0     0   913k      0 --:--:-- --:--:-- --:--:--  913k
100  907k  100  907k    0     0  1103k      0 --:--:-- --:--:-- --:--:-- 1103k

install for i386

* installing *source* package 'cellmigRation' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cellmigRation'
    finding HTML links ... done
    AddDimension                            html  
    CellMig-class                           html  
    CellMigPCA                              html  
    CellMigPCAclust                         html  
    CellMigPCAclustALL                      html  
    CellTracker                             html  
    CellTrackerMainLoop                     html  
    CentroidArray                           html  
    CentroidValidation                      html  
    ComputeTracksStats                      html  
    DetectRadii                             html  
    DiAutoCor                               html  
    DiRatio                                 html  
    DiRatioPlot                             html  
    EstimateDiameterRange                   html  
    FMI                                     html  
    FianlizeOptiParams                      html  
    FilterTrackedCells                      html  
    FinRes                                  html  
    ForwardMigration                        html  
    GenAllCombos                            html  
    LinearConv2                             html  
    LoadTiff                                html  
    MSD                                     html  
    MakeHypercube                           html  
    MigrationStats                          html  
    NextOdd                                 html  
    NonParallel4OptimizeParams              html  
    NonParallelTrackLoop                    html  
    OptimizeParams                          html  
    OptimizeParamsMainLoop                  html  
    Parallel4OptimizeParams                 html  
    ParallelTrackLoop                       html  
    PerAndSpeed                             html  
    PlotTracksSeparately                    html  
    PostProcessTracking                     html  
    Prep4OptimizeParams                     html  
    ThreeConditions                         html  
    TrackCellsDataset                       html  
    TrajectoryDataset                       html  
    ValidateTrackingArgs                    html  
    VeAutoCor                               html  
    VisualizeCntr                           html  
    VisualizeImg                            html  
    VisualizeStackCentroids                 html  
    WSADataset                              html  
    aggregateFR                             html  
    aggregateTrackedCells                   html  
    bpass                                   html  
    cellmigRation-package                   html  
    circshift                               html  
    cntrd                                   html  
    fixDA                                   html  
    fixExpName                              html  
    fixFM1                                  html  
    fixFM2                                  html  
    fixFM3                                  html  
    fixFM4                                  html  
    fixFM5                                  html  
    fixFM6                                  html  
    fixID1                                  html  
    fixID2                                  html  
    fixID3                                  html  
    fixID4                                  html  
    fixID5                                  html  
    fixID6                                  html  
    fixMSD                                  html  
    fixPER1                                 html  
    fixPER2                                 html  
    fixPER3                                 html  
    getAvailableAggrMetrics                 html  
    getCellImages                           html  
    getCellMigSlot                          html  
    getCellTrackMeta                        html  
    getCellTrackStats                       html  
    getCellTracks                           html  
    getCellsMeta                            html  
    getCellsStats                           html  
    getDACtable                             html  
    getDiRatio                              html  
    getFMItable                             html  
    getForMigtable                          html  
    getImageCentroids                       html  
    getImageStacks                          html  
    getMSDtable                             html  
    getOptimizedParameters                  html  
    getOptimizedParams                      html  
    getPerAndSpeed                          html  
    getPopulationStats                      html  
    getProcessedImages                      html  
    getProcessingStatus                     html  
    getResults                              html  
    getTracks                               html  
    getVACtable                             html  
    initializeTrackParams                   html  
    innerBondRaster                         html  
    internalPermutation                     html  
    matfix                                  html  
    nontrivialBondTracking                  html  
    pkfnd                                   html  
    plot3DAllTracks                         html  
    plot3DTracks                            html  
    plotAllTracks                           html  
    plotSampleTracks                        html  
    preProcCellMig                          html  
    rmPreProcessing                         html  
    runTrackingPermutation                  html  
    setAnalyticParams                       html  
    setCellMigSlot                          html  
    setCellTracks                           html  
    setCellsMeta                            html  
    setExpName                              html  
    setOptimizedParams                      html  
    setProcessedImages                      html  
    setProcessingStatus                     html  
    setTrackedCellsMeta                     html  
    setTrackedCentroids                     html  
    setTrackedPositions                     html  
    setTrackingStats                        html  
    sinkAway                                html  
    subNetworkTracking                      html  
    track                                   html  
    trackHypercubeBuild                     html  
    trackSlideProcessing                    html  
    trackSlideWrapUp                        html  
    trackedCells-class                      html  
    trivialBondRaster                       html  
    trivialBondTracking                     html  
    visualizeCellTracks                     html  
    visualizeTrcks                          html  
    warnMessage                             html  
    wsaPreProcessing                        html  
** 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

install for x64

* installing *source* package 'cellmigRation' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellmigRation' as cellmigRation_1.2.0.zip
* DONE (cellmigRation)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cellmigRation' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 12 17:04:14 2022 
*********************************************** 
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 
   3.48    0.32    3.79


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 12 17:04:18 2022 
*********************************************** 
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 
   4.39    0.31    4.68

name	user	system	elapsed
AddDimension	0	0	0
CellMig-class	0.03	0.00	0.05
CellMigPCA	1.21	0.03	1.24
CellMigPCAclust	0.01	0.00	0.01
CellMigPCAclustALL	0.75	0.00	0.75
CellTracker	0.00	0.04	0.03
CellTrackerMainLoop	0	0	0
CentroidArray	0.02	0.01	0.04
CentroidValidation	0.51	0.00	0.51
ComputeTracksStats	0.04	0.00	0.03
DetectRadii	0.01	0.00	0.02
DiAutoCor	1.45	0.00	1.45
DiRatio	0.02	0.00	0.02
DiRatioPlot	0.04	0.00	0.05
EstimateDiameterRange	0.02	0.00	0.01
FMI	0.51	0.00	0.52
FianlizeOptiParams	0	0	0
FilterTrackedCells	0	0	0
FinRes	0.72	0.00	0.72
ForwardMigration	1.05	0.00	1.05
GenAllCombos	0	0	0
LinearConv2	0.02	0.00	0.01
LoadTiff	0	0	0
MSD	1.81	0.00	1.92
MakeHypercube	0	0	0
MigrationStats	0	0	0
NextOdd	0	0	0
NonParallel4OptimizeParams	0	0	0
NonParallelTrackLoop	0	0	0
OptimizeParams	0.02	0.00	0.01
OptimizeParamsMainLoop	0	0	0
Parallel4OptimizeParams	0	0	0
ParallelTrackLoop	0	0	0
PerAndSpeed	0.41	0.00	0.59
PlotTracksSeparately	0.03	0.00	0.04
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.25	0.00	0.25
ThreeConditions	0.03	0.00	0.03
TrackCellsDataset	0.03	0.00	0.03
TrajectoryDataset	0.06	0.00	0.06
ValidateTrackingArgs	0	0	0
VeAutoCor	1.41	0.00	1.41
VisualizeCntr	0.00	0.01	0.01
VisualizeImg	0	0	0
VisualizeStackCentroids	0.12	0.00	0.13
WSADataset	0.02	0.00	0.01
aggregateFR	0.72	0.00	0.72
aggregateTrackedCells	0.03	0.00	0.03
bpass	0.06	0.00	0.07
circshift	0	0	0
cntrd	1	0	1
fixDA	0	0	0
fixExpName	0	0	0
fixFM1	0	0	0
fixFM2	0.00	0.02	0.01
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0	0	0
fixID1	0	0	0
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.96	0.01	0.97
getCellImages	1.12	0.13	1.25
getCellMigSlot	0.77	0.25	1.02
getCellTrackMeta	0.01	0.01	0.03
getCellTrackStats	0.03	0.00	0.03
getCellTracks	0.03	0.00	0.03
getCellsMeta	0.04	0.00	0.03
getCellsStats	0.01	0.02	0.03
getDACtable	2.02	0.00	2.02
getDiRatio	0.01	0.00	0.01
getFMItable	0.50	0.02	0.52
getForMigtable	0.64	0.00	0.64
getImageCentroids	0.03	0.00	0.03
getImageStacks	0.21	0.00	0.20
getMSDtable	3.93	0.01	3.96
getOptimizedParameters	0.02	0.00	0.01
getOptimizedParams	0.02	0.02	0.03
getPerAndSpeed	0.31	0.03	0.35
getPopulationStats	0.01	0.01	0.03
getProcessedImages	0.86	0.33	1.19
getProcessingStatus	0.02	0.02	0.03
getResults	0.72	0.00	0.72
getTracks	0.01	0.01	0.03
getVACtable	1.53	0.00	1.53
initializeTrackParams	0	0	0
innerBondRaster	0	0	0
internalPermutation	0	0	0
matfix	0	0	0
nontrivialBondTracking	0	0	0
pkfnd	0.80	0.00	0.79
plot3DAllTracks	0.19	0.05	1.74
plot3DTracks	0.02	0.00	0.02
plotAllTracks	0.03	0.01	0.04
plotSampleTracks	0.03	0.02	0.05
preProcCellMig	0.02	0.01	0.03
rmPreProcessing	0.19	0.02	0.21
runTrackingPermutation	0	0	0
setAnalyticParams	0.03	0.01	0.04
setCellMigSlot	0.06	0.00	0.07
setCellTracks	0.03	0.00	0.03
setCellsMeta	0.02	0.04	0.04
setExpName	0.04	0.00	0.05
setOptimizedParams	0.03	0.01	0.05
setProcessedImages	0.02	0.03	0.04
setProcessingStatus	0.05	0.00	0.05
setTrackedCellsMeta	0.04	0.00	0.04
setTrackedCentroids	0.05	0.00	0.05
setTrackedPositions	0.03	0.01	0.05
setTrackingStats	0.05	0.02	0.06
sinkAway	0	0	0
subNetworkTracking	0	0	0
track	0.01	0.00	0.02
trackHypercubeBuild	0	0	0
trackSlideProcessing	0	0	0
trackSlideWrapUp	0	0	0
trivialBondRaster	0	0	0
trivialBondTracking	0	0	0
visualizeCellTracks	0.22	0.01	0.24
visualizeTrcks	0.05	0.00	0.04
warnMessage	0	0	0
wsaPreProcessing	0.09	0.00	0.10

name	user	system	elapsed
AddDimension	0.00	0.02	0.02
CellMig-class	0.03	0.00	0.03
CellMigPCA	1.36	0.03	1.40
CellMigPCAclust	0.01	0.00	0.02
CellMigPCAclustALL	0.82	0.00	0.81
CellTracker	0.01	0.00	0.02
CellTrackerMainLoop	0	0	0
CentroidArray	0.03	0.00	0.03
CentroidValidation	0.60	0.00	0.59
ComputeTracksStats	0.03	0.00	0.03
DetectRadii	0	0	0
DiAutoCor	1.84	0.00	1.85
DiRatio	0.02	0.02	0.03
DiRatioPlot	0.04	0.00	0.05
EstimateDiameterRange	0.02	0.00	0.01
FMI	0.58	0.00	0.58
FianlizeOptiParams	0	0	0
FilterTrackedCells	0	0	0
FinRes	0.76	0.03	0.80
ForwardMigration	1.35	0.01	1.36
GenAllCombos	0	0	0
LinearConv2	0.03	0.00	0.03
LoadTiff	0	0	0
MSD	1.78	0.00	1.78
MakeHypercube	0	0	0
MigrationStats	0	0	0
NextOdd	0	0	0
NonParallel4OptimizeParams	0	0	0
NonParallelTrackLoop	0	0	0
OptimizeParams	0.02	0.00	0.02
OptimizeParamsMainLoop	0	0	0
Parallel4OptimizeParams	0	0	0
ParallelTrackLoop	0	0	0
PerAndSpeed	0.44	0.02	0.48
PlotTracksSeparately	0.01	0.00	0.02
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.14	0.00	0.15
ThreeConditions	0.02	0.00	0.01
TrackCellsDataset	0.00	0.03	0.03
TrajectoryDataset	0.03	0.00	0.03
ValidateTrackingArgs	0	0	0
VeAutoCor	1.54	0.00	1.55
VisualizeCntr	0	0	0
VisualizeImg	0	0	0
VisualizeStackCentroids	0.07	0.03	0.09
WSADataset	0.00	0.02	0.02
aggregateFR	0.79	0.00	0.80
aggregateTrackedCells	0.03	0.00	0.03
bpass	0.08	0.00	0.08
circshift	0	0	0
cntrd	1.14	0.00	1.14
fixDA	0	0	0
fixExpName	0	0	0
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0.02	0.00	0.01
fixFM6	0	0	0
fixID1	0	0	0
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	1.12	0.00	1.13
getCellImages	0.30	0.31	0.61
getCellMigSlot	0.36	0.09	0.45
getCellTrackMeta	0.02	0.00	0.02
getCellTrackStats	0.01	0.00	0.01
getCellTracks	0.01	0.00	0.01
getCellsMeta	0.02	0.00	0.02
getCellsStats	0.01	0.02	0.03
getDACtable	2.28	0.00	2.28
getDiRatio	0.02	0.00	0.02
getFMItable	0.73	0.02	0.75
getForMigtable	1.02	0.01	1.03
getImageCentroids	0.03	0.00	0.03
getImageStacks	0.08	0.02	0.09
getMSDtable	4.97	0.03	5.00
getOptimizedParameters	0.00	0.01	0.02
getOptimizedParams	0.00	0.02	0.01
getPerAndSpeed	0.31	0.05	0.36
getPopulationStats	0.02	0.00	0.02
getProcessedImages	0.29	0.37	0.67
getProcessingStatus	0.02	0.02	0.03
getResults	0.81	0.00	0.81
getTracks	0.02	0.01	0.04
getVACtable	1.65	0.02	1.67
initializeTrackParams	0	0	0
innerBondRaster	0.02	0.00	0.01
internalPermutation	0	0	0
matfix	0	0	0
nontrivialBondTracking	0	0	0
pkfnd	1.05	0.01	1.07
plot3DAllTracks	0.11	0.05	0.15
plot3DTracks	0.00	0.02	0.02
plotAllTracks	0.03	0.00	0.03
plotSampleTracks	0.01	0.00	0.01
preProcCellMig	0.02	0.00	0.02
rmPreProcessing	0.12	0.00	0.12
runTrackingPermutation	0	0	0
setAnalyticParams	0.00	0.01	0.02
setCellMigSlot	0.03	0.00	0.03
setCellTracks	0.04	0.00	0.03
setCellsMeta	0.01	0.00	0.02
setExpName	0.03	0.00	0.03
setOptimizedParams	0.02	0.00	0.02
setProcessedImages	0.01	0.00	0.01
setProcessingStatus	0.03	0.00	0.03
setTrackedCellsMeta	0.02	0.00	0.02
setTrackedCentroids	0.02	0.00	0.01
setTrackedPositions	0.03	0.00	0.03
setTrackingStats	0.01	0.00	0.02
sinkAway	0	0	0
subNetworkTracking	0	0	0
track	0.02	0.00	0.02
trackHypercubeBuild	0	0	0
trackSlideProcessing	0	0	0
trackSlideWrapUp	0	0	0
trivialBondRaster	0	0	0
trivialBondTracking	0	0	0
visualizeCellTracks	0.09	0.02	0.11
visualizeTrcks	0.03	0.00	0.03
warnMessage	0	0	0
wsaPreProcessing	0.10	0.00	0.09

CHECK results for cellmigRation on tokay2

Summary

Command output

Installation output

Tests output

Example timings