Sojourner Developer
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/sojourner |
| Branch: RELEASE_3_12 |
| Last Commit: 8242813 |
| Last Changed Date: 2021-03-27 23:05:09 -0400 (Sat, 27 Mar 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:53 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the sojourner package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1750/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sojourner 1.4.2 (landing page) Sojourner Developer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: sojourner |
| Version: 1.4.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sojourner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sojourner_1.4.2.tar.gz |
| StartedAt: 2021-05-06 06:27:05 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:39:03 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 718.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sojourner.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sojourner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sojourner_1.4.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/sojourner.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sojourner/DESCRIPTION’ ... OK
* this is package ‘sojourner’ version ‘1.4.2’
* 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 ‘sojourner’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotLocalizations_Density-methods 50.326 0.268 50.659
plotTrackOverlay_Dcoef-methods 39.104 0.159 39.408
fitNormDistr-methods 35.288 0.194 35.531
Dcoef-methods 14.353 0.107 14.483
maskTracks-methods 13.918 0.252 14.199
plotIndividual_Tracks-methods 11.047 0.240 11.299
plotTrack-methods 6.120 0.175 6.318
fitRT-methods 5.218 0.063 5.290
combineTrackll-methods 4.591 0.046 138.488
compare_RT_CDF-methods 4.276 0.102 141.354
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
sojourner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sojourner ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘sojourner’ ... ** using staged installation ** R ** 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 (sojourner)
sojourner.Rcheck/tests/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("sojourner")
Reading ParticleTracker file: SWR1_WT_140mW_image6.csv ...
mage6 read and processed.
Process complete.
Reading ParticleTracker file: SWR1_WT_140mW_image6.csv ...
mage6 read and processed.
Process complete.
applying filter, min 5 max Inf
Reading ParticleTracker file: SWR1_WT_140mW_image6.csv ...
mage6 read and processed.
Process complete.
applying filter, min 5 max Inf
applying filter, min 7 max Inf
45 tracks length > & = 1
45 tracks length > & = 2
45 tracks length > & = 3
45 tracks length > & = 4
45 tracks length > & = 5
45 tracks length > & = 6
...
Reading ParticleTracker file: SWR1_WT_140mW_image6.csv ...
mage6 read and processed.
Process complete.
applying trimmer, min 1 max 20
RUNIT TEST PROTOCOL -- Thu May 6 06:38:55 2021
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
sojourner RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.878 0.490 13.365
sojourner.Rcheck/sojourner-Ex.timings
| name | user | system | elapsed | |
| Dcoef-methods | 14.353 | 0.107 | 14.483 | |
| combineTrackll-methods | 4.591 | 0.046 | 138.488 | |
| compareFolder-methods | 0.226 | 0.027 | 0.254 | |
| compare_RT_CDF-methods | 4.276 | 0.102 | 141.354 | |
| createTrackll-methods | 0.051 | 0.005 | 0.057 | |
| dispVariance-methods | 1.458 | 0.026 | 1.486 | |
| displacementCDF-methods | 2.713 | 0.112 | 2.863 | |
| dwellTime-methods | 0.458 | 0.025 | 0.509 | |
| exportTrackll-methods | 0.112 | 0.016 | 0.130 | |
| filterTrack-methods | 0.098 | 0.005 | 0.104 | |
| fitNormDistr-methods | 35.288 | 0.194 | 35.531 | |
| fitRT-methods | 5.218 | 0.063 | 5.290 | |
| linkSkippedFrames-methods | 0.208 | 0.013 | 0.221 | |
| maskTracks-methods | 13.918 | 0.252 | 14.199 | |
| mergeTracks-methods | 0.067 | 0.007 | 0.075 | |
| msd-methods | 4.891 | 0.041 | 4.975 | |
| plotIndividual_Tracks-methods | 11.047 | 0.240 | 11.299 | |
| plotLocalizations_Density-methods | 50.326 | 0.268 | 50.659 | |
| plotTrack-methods | 6.120 | 0.175 | 6.318 | |
| plotTrackOverlay_Dcoef-methods | 39.104 | 0.159 | 39.408 | |
| sojournerGUI-methods | 0 | 0 | 0 | |
| squareDisp-methods | 0.256 | 0.014 | 0.271 | |