| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:02:52 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (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 303/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cellmigRation 1.12.0 (landing page) Waldir Leoncio
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| 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: 2024-05-31 02:04:36 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 02:08:22 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 225.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cellmigRation.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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.
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)
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 -- Fri May 31 02:06:20 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
2.758 0.214 2.962
cellmigRation.Rcheck/cellmigRation-Ex.timings
| name | user | system | elapsed | |
| AddDimension | 0.002 | 0.000 | 0.002 | |
| CellMig-class | 0.028 | 0.000 | 0.029 | |
| CellMigPCA | 1.186 | 0.056 | 1.241 | |
| CellMigPCAclust | 0.004 | 0.004 | 0.008 | |
| CellMigPCAclustALL | 0.615 | 0.003 | 0.618 | |
| CellTracker | 0.016 | 0.004 | 0.020 | |
| CellTrackerMainLoop | 0.010 | 0.000 | 0.029 | |
| CentroidArray | 0.017 | 0.004 | 0.020 | |
| CentroidValidation | 0.440 | 0.007 | 0.447 | |
| ComputeTracksStats | 0.023 | 0.005 | 0.027 | |
| DetectRadii | 0.002 | 0.000 | 0.003 | |
| DiAutoCor | 1.241 | 0.051 | 1.293 | |
| DiRatio | 0.017 | 0.001 | 0.018 | |
| DiRatioPlot | 0.033 | 0.003 | 0.036 | |
| EstimateDiameterRange | 0.011 | 0.005 | 0.016 | |
| FMI | 0.436 | 0.000 | 0.437 | |
| FianlizeOptiParams | 0.001 | 0.000 | 0.000 | |
| FilterTrackedCells | 0.003 | 0.000 | 0.003 | |
| FinRes | 0.609 | 0.000 | 0.609 | |
| ForwardMigration | 0.896 | 0.008 | 0.905 | |
| GenAllCombos | 0.003 | 0.000 | 0.003 | |
| LinearConv2 | 0.018 | 0.000 | 0.017 | |
| LoadTiff | 0.000 | 0.001 | 0.001 | |
| MSD | 1.415 | 0.014 | 1.429 | |
| MakeHypercube | 0.002 | 0.000 | 0.002 | |
| MigrationStats | 0.001 | 0.000 | 0.002 | |
| NextOdd | 0.000 | 0.000 | 0.001 | |
| NonParallel4OptimizeParams | 0.001 | 0.000 | 0.001 | |
| NonParallelTrackLoop | 0 | 0 | 0 | |
| OptimizeParams | 0.009 | 0.007 | 0.018 | |
| OptimizeParamsMainLoop | 0.003 | 0.004 | 0.030 | |
| Parallel4OptimizeParams | 0.000 | 0.000 | 0.001 | |
| ParallelTrackLoop | 0.000 | 0.001 | 0.001 | |
| PerAndSpeed | 0.274 | 0.013 | 0.287 | |
| PlotTracksSeparately | 0.005 | 0.004 | 0.009 | |
| PostProcessTracking | 0 | 0 | 0 | |
| Prep4OptimizeParams | 0.126 | 0.012 | 0.138 | |
| ThreeConditions | 0.010 | 0.004 | 0.014 | |
| TrackCellsDataset | 0.013 | 0.003 | 0.017 | |
| TrajectoryDataset | 0.022 | 0.000 | 0.022 | |
| ValidateTrackingArgs | 0.001 | 0.000 | 0.001 | |
| VeAutoCor | 0.984 | 0.011 | 0.996 | |
| VisualizeCntr | 0.003 | 0.001 | 0.003 | |
| VisualizeImg | 0.006 | 0.000 | 0.006 | |
| VisualizeStackCentroids | 0.062 | 0.003 | 0.066 | |
| WSADataset | 0.007 | 0.000 | 0.007 | |
| aggregateFR | 0.594 | 0.001 | 0.594 | |
| aggregateTrackedCells | 0.020 | 0.004 | 0.024 | |
| bpass | 0.049 | 0.007 | 0.057 | |
| circshift | 0.001 | 0.000 | 0.001 | |
| cntrd | 0.686 | 0.005 | 0.690 | |
| fixDA | 0.001 | 0.000 | 0.001 | |
| fixExpName | 0.001 | 0.000 | 0.001 | |
| fixFM1 | 0.000 | 0.000 | 0.001 | |
| fixFM2 | 0.000 | 0.000 | 0.001 | |
| fixFM3 | 0 | 0 | 0 | |
| fixFM4 | 0 | 0 | 0 | |
| fixFM5 | 0.000 | 0.001 | 0.000 | |
| fixFM6 | 0.000 | 0.000 | 0.001 | |
| fixID1 | 0.000 | 0.000 | 0.001 | |
| fixMSD | 0 | 0 | 0 | |
| fixPER1 | 0 | 0 | 0 | |
| fixPER2 | 0.000 | 0.001 | 0.000 | |
| fixPER3 | 0.000 | 0.001 | 0.001 | |
| getAvailableAggrMetrics | 0.857 | 0.012 | 0.869 | |
| getCellImages | 0.281 | 1.027 | 1.309 | |
| getCellMigSlot | 0.314 | 0.619 | 0.935 | |
| getCellTrackMeta | 0.014 | 0.004 | 0.017 | |
| getCellTrackStats | 0.016 | 0.004 | 0.020 | |
| getCellTracks | 0.014 | 0.004 | 0.018 | |
| getCellsMeta | 0.013 | 0.004 | 0.017 | |
| getCellsStats | 0.024 | 0.008 | 0.033 | |
| getDACtable | 1.981 | 0.052 | 2.033 | |
| getDiRatio | 0.018 | 0.000 | 0.018 | |
| getFMItable | 0.410 | 0.000 | 0.411 | |
| getForMigtable | 0.486 | 0.000 | 0.487 | |
| getImageCentroids | 0.023 | 0.000 | 0.023 | |
| getImageStacks | 0.066 | 0.000 | 0.065 | |
| getMSDtable | 3.227 | 0.007 | 3.235 | |
| getOptimizedParameters | 0.009 | 0.008 | 0.017 | |
| getOptimizedParams | 0.019 | 0.000 | 0.018 | |
| getPerAndSpeed | 0.250 | 0.003 | 0.252 | |
| getPopulationStats | 0.018 | 0.000 | 0.018 | |
| getProcessedImages | 0.235 | 1.072 | 1.306 | |
| getProcessingStatus | 0.013 | 0.004 | 0.018 | |
| getResults | 0.602 | 0.020 | 0.622 | |
| getTracks | 0.013 | 0.004 | 0.018 | |
| getVACtable | 0.970 | 0.004 | 0.975 | |
| initializeTrackParams | 0.000 | 0.000 | 0.001 | |
| innerBondRaster | 0.002 | 0.000 | 0.002 | |
| internalPermutation | 0.001 | 0.000 | 0.001 | |
| matfix | 0.001 | 0.000 | 0.001 | |
| nontrivialBondTracking | 0.001 | 0.000 | 0.001 | |
| pkfnd | 0.669 | 0.004 | 0.672 | |
| plot3DAllTracks | 0.069 | 0.028 | 0.097 | |
| plot3DTracks | 0.005 | 0.003 | 0.008 | |
| plotAllTracks | 0.018 | 0.000 | 0.018 | |
| plotSampleTracks | 0.015 | 0.000 | 0.015 | |
| preProcCellMig | 0.008 | 0.000 | 0.008 | |
| rmPreProcessing | 0.078 | 0.000 | 0.078 | |
| runTrackingPermutation | 0.002 | 0.000 | 0.002 | |
| setAnalyticParams | 0.016 | 0.000 | 0.017 | |
| setCellMigSlot | 0.023 | 0.000 | 0.023 | |
| setCellTracks | 0.017 | 0.000 | 0.018 | |
| setCellsMeta | 0.014 | 0.004 | 0.017 | |
| setExpName | 0.023 | 0.000 | 0.023 | |
| setOptimizedParams | 0.013 | 0.005 | 0.018 | |
| setProcessedImages | 0.014 | 0.003 | 0.017 | |
| setProcessingStatus | 0.013 | 0.005 | 0.017 | |
| setTrackedCellsMeta | 0.011 | 0.006 | 0.017 | |
| setTrackedCentroids | 0.014 | 0.004 | 0.017 | |
| setTrackedPositions | 0.018 | 0.000 | 0.017 | |
| setTrackingStats | 0.010 | 0.008 | 0.018 | |
| sinkAway | 0.001 | 0.000 | 0.001 | |
| subNetworkTracking | 0.002 | 0.000 | 0.001 | |
| track | 0.01 | 0.00 | 0.01 | |
| trackHypercubeBuild | 0.001 | 0.000 | 0.001 | |
| trackSlideProcessing | 0.001 | 0.000 | 0.000 | |
| trackSlideWrapUp | 0.001 | 0.000 | 0.001 | |
| trivialBondRaster | 0.001 | 0.000 | 0.002 | |
| trivialBondTracking | 0.001 | 0.000 | 0.001 | |
| visualizeCellTracks | 0.079 | 0.000 | 0.079 | |
| visualizeTrcks | 0.025 | 0.000 | 0.025 | |
| warnMessage | 0.001 | 0.000 | 0.001 | |
| wsaPreProcessing | 0.044 | 0.004 | 0.047 | |