| Back to Build/check report for BioC 3.17 | 
  | 
This page was generated on 2023-02-08 01:14:55 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 | 
| 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 | ||||
| 
To the developers/maintainers of the cellmigRation package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page.  | 
| Package 276/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cellmigRation 1.7.0  (landing page) Waldir Leoncio 
  | kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: cellmigRation | 
| Version: 1.7.0 | 
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cellmigRation_1.7.0.tar.gz | 
| StartedAt: 2023-02-06 20:26:27 -0000 (Mon, 06 Feb 2023) | 
| EndedAt: 2023-02-06 20:31:52 -0000 (Mon, 06 Feb 2023) | 
| EllapsedTime: 325.4 seconds | 
| RetCode: 0 | 
| Status: OK | 
| CheckDir: cellmigRation.Rcheck | 
| Warnings: 0 | 
##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cellmigRation_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.7.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getMSDtable 5.328  0.004   5.333
* 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 ...
  ‘cellmigRation.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
cellmigRation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cellmigRation ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
cellmigRation.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 -- Mon Feb  6 20:28:44 2023 
*********************************************** 
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 
  3.618   0.136   3.745 
cellmigRation.Rcheck/cellmigRation-Ex.timings
| name | user | system | elapsed | |
| AddDimension | 0.002 | 0.000 | 0.002 | |
| CellMig-class | 0.027 | 0.000 | 0.027 | |
| CellMigPCA | 1.825 | 0.011 | 1.839 | |
| CellMigPCAclust | 0.007 | 0.000 | 0.008 | |
| CellMigPCAclustALL | 1.014 | 0.004 | 1.019 | |
| CellTracker | 0.020 | 0.000 | 0.021 | |
| CellTrackerMainLoop | 0.006 | 0.000 | 0.005 | |
| CentroidArray | 0.021 | 0.000 | 0.022 | |
| CentroidValidation | 0.742 | 0.004 | 0.746 | |
| ComputeTracksStats | 0.031 | 0.000 | 0.031 | |
| DetectRadii | 0.004 | 0.000 | 0.004 | |
| DiAutoCor | 2.185 | 0.000 | 2.185 | |
| DiRatio | 0.020 | 0.000 | 0.021 | |
| DiRatioPlot | 0.035 | 0.004 | 0.040 | |
| EstimateDiameterRange | 0.018 | 0.000 | 0.019 | |
| FMI | 0.736 | 0.008 | 0.744 | |
| FianlizeOptiParams | 0.000 | 0.000 | 0.001 | |
| FilterTrackedCells | 0.003 | 0.000 | 0.003 | |
| FinRes | 1.020 | 0.008 | 1.028 | |
| ForwardMigration | 1.504 | 0.000 | 1.504 | |
| GenAllCombos | 0.003 | 0.000 | 0.004 | |
| LinearConv2 | 0.026 | 0.000 | 0.026 | |
| LoadTiff | 0.001 | 0.000 | 0.000 | |
| MSD | 2.530 | 0.048 | 2.581 | |
| MakeHypercube | 0.002 | 0.000 | 0.001 | |
| MigrationStats | 0.000 | 0.001 | 0.001 | |
| NextOdd | 0 | 0 | 0 | |
| NonParallel4OptimizeParams | 0.000 | 0.001 | 0.001 | |
| NonParallelTrackLoop | 0 | 0 | 0 | |
| OptimizeParams | 0.014 | 0.004 | 0.018 | |
| OptimizeParamsMainLoop | 0.005 | 0.000 | 0.004 | |
| Parallel4OptimizeParams | 0.000 | 0.000 | 0.001 | |
| ParallelTrackLoop | 0.001 | 0.000 | 0.001 | |
| PerAndSpeed | 0.377 | 0.008 | 0.387 | |
| PlotTracksSeparately | 0.009 | 0.000 | 0.009 | |
| PostProcessTracking | 0.000 | 0.000 | 0.001 | |
| Prep4OptimizeParams | 0.125 | 0.004 | 0.130 | |
| ThreeConditions | 0.017 | 0.000 | 0.018 | |
| TrackCellsDataset | 0.018 | 0.000 | 0.018 | |
| TrajectoryDataset | 0.021 | 0.000 | 0.020 | |
| ValidateTrackingArgs | 0.000 | 0.000 | 0.001 | |
| VeAutoCor | 1.639 | 0.004 | 1.644 | |
| VisualizeCntr | 0.003 | 0.000 | 0.003 | |
| VisualizeImg | 0.003 | 0.004 | 0.006 | |
| VisualizeStackCentroids | 0.062 | 0.000 | 0.062 | |
| WSADataset | 0.006 | 0.000 | 0.006 | |
| aggregateFR | 0.957 | 0.004 | 0.961 | |
| aggregateTrackedCells | 0.020 | 0.004 | 0.024 | |
| bpass | 0.083 | 0.000 | 0.083 | |
| circshift | 0.001 | 0.000 | 0.001 | |
| cntrd | 1.083 | 0.004 | 1.088 | |
| fixDA | 0.000 | 0.000 | 0.001 | |
| fixExpName | 0.000 | 0.000 | 0.001 | |
| fixFM1 | 0 | 0 | 0 | |
| fixFM2 | 0 | 0 | 0 | |
| fixFM3 | 0 | 0 | 0 | |
| fixFM4 | 0.001 | 0.000 | 0.001 | |
| fixFM5 | 0.000 | 0.000 | 0.001 | |
| fixFM6 | 0 | 0 | 0 | |
| fixID1 | 0 | 0 | 0 | |
| fixMSD | 0.000 | 0.001 | 0.000 | |
| fixPER1 | 0.000 | 0.001 | 0.000 | |
| fixPER2 | 0 | 0 | 0 | |
| fixPER3 | 0.000 | 0.000 | 0.001 | |
| getAvailableAggrMetrics | 1.382 | 0.004 | 1.387 | |
| getCellImages | 0.227 | 0.328 | 0.554 | |
| getCellMigSlot | 0.257 | 0.196 | 0.453 | |
| getCellTrackMeta | 0.018 | 0.000 | 0.018 | |
| getCellTrackStats | 0.022 | 0.000 | 0.022 | |
| getCellTracks | 0.018 | 0.000 | 0.018 | |
| getCellsMeta | 0.018 | 0.000 | 0.018 | |
| getCellsStats | 0.021 | 0.000 | 0.020 | |
| getDACtable | 2.958 | 0.004 | 2.963 | |
| getDiRatio | 0.023 | 0.000 | 0.022 | |
| getFMItable | 0.699 | 0.000 | 0.699 | |
| getForMigtable | 0.875 | 0.000 | 0.876 | |
| getImageCentroids | 0.025 | 0.000 | 0.025 | |
| getImageStacks | 0.049 | 0.012 | 0.062 | |
| getMSDtable | 5.328 | 0.004 | 5.333 | |
| getOptimizedParameters | 0.013 | 0.004 | 0.017 | |
| getOptimizedParams | 0.019 | 0.000 | 0.019 | |
| getPerAndSpeed | 0.374 | 0.000 | 0.375 | |
| getPopulationStats | 0.010 | 0.008 | 0.019 | |
| getProcessedImages | 0.188 | 0.352 | 0.539 | |
| getProcessingStatus | 0.009 | 0.008 | 0.017 | |
| getResults | 0.957 | 0.000 | 0.956 | |
| getTracks | 0.015 | 0.004 | 0.019 | |
| getVACtable | 1.627 | 0.000 | 1.627 | |
| initializeTrackParams | 0 | 0 | 0 | |
| innerBondRaster | 0.001 | 0.000 | 0.001 | |
| internalPermutation | 0.001 | 0.000 | 0.001 | |
| matfix | 0.000 | 0.001 | 0.001 | |
| nontrivialBondTracking | 0.000 | 0.001 | 0.002 | |
| pkfnd | 1.084 | 0.001 | 1.085 | |
| plot3DAllTracks | 0.103 | 0.028 | 0.133 | |
| plot3DTracks | 0.008 | 0.000 | 0.008 | |
| plotAllTracks | 0.021 | 0.000 | 0.020 | |
| plotSampleTracks | 0.015 | 0.000 | 0.016 | |
| preProcCellMig | 0.003 | 0.004 | 0.007 | |
| rmPreProcessing | 0.136 | 0.004 | 0.139 | |
| runTrackingPermutation | 0.002 | 0.000 | 0.002 | |
| setAnalyticParams | 0.017 | 0.000 | 0.018 | |
| setCellMigSlot | 0.013 | 0.008 | 0.022 | |
| setCellTracks | 0.018 | 0.000 | 0.018 | |
| setCellsMeta | 0.018 | 0.000 | 0.018 | |
| setExpName | 0.017 | 0.004 | 0.021 | |
| setOptimizedParams | 0.015 | 0.004 | 0.018 | |
| setProcessedImages | 0.014 | 0.004 | 0.018 | |
| setProcessingStatus | 0.018 | 0.000 | 0.018 | |
| setTrackedCellsMeta | 0.018 | 0.000 | 0.018 | |
| setTrackedCentroids | 0.018 | 0.000 | 0.018 | |
| setTrackedPositions | 0.018 | 0.000 | 0.019 | |
| setTrackingStats | 0.010 | 0.008 | 0.019 | |
| sinkAway | 0.000 | 0.000 | 0.001 | |
| subNetworkTracking | 0.002 | 0.000 | 0.001 | |
| track | 0.012 | 0.000 | 0.012 | |
| trackHypercubeBuild | 0.001 | 0.000 | 0.001 | |
| trackSlideProcessing | 0.001 | 0.000 | 0.000 | |
| trackSlideWrapUp | 0.001 | 0.000 | 0.001 | |
| trivialBondRaster | 0.002 | 0.000 | 0.002 | |
| trivialBondTracking | 0.001 | 0.000 | 0.000 | |
| visualizeCellTracks | 0.098 | 0.000 | 0.098 | |
| visualizeTrcks | 0.032 | 0.000 | 0.032 | |
| warnMessage | 0.000 | 0.000 | 0.001 | |
| wsaPreProcessing | 0.072 | 0.002 | 0.075 | |