Sojourner Developer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/sojourner |
| Branch: RELEASE_3_10 |
| Last Commit: 2c59633 |
| Last Changed Date: 2020-04-05 19:54:57 -0400 (Sun, 05 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:49:53 -0400 (Wed, 15 Apr 2020).
| Package 1629/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sojourner 1.0.2 Sojourner Developer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: sojourner |
| Version: 1.0.2 |
| 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_1.0.2.tar.gz |
| StartedAt: 2020-04-15 05:50:17 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:01:54 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 696.7 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_1.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/sojourner.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sojourner/DESCRIPTION’ ... OK
* this is package ‘sojourner’ version ‘1.0.2’
* 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 or elapsed time > 5s
user system elapsed
plotLocalizations_Density-methods 54.501 0.383 56.169
plotTrackOverlay_Dcoef-methods 44.980 0.135 45.884
fitNormDistr-methods 38.313 0.299 39.078
plotTrack-methods 20.091 0.415 21.056
maskTracks-methods 17.853 0.423 18.743
selComponentTracks-methods 16.715 0.183 17.056
Dcoef-methods 15.887 0.237 16.249
plotIndividualTracks-methods 14.609 0.186 15.055
fitCDF-methods 13.780 0.556 14.464
getCI-methods 13.151 0.089 13.404
fitRT-methods 6.007 0.773 5.643
compare_RT_CDF-methods 5.009 0.453 124.451
combineTrackll-methods 5.047 0.092 127.487
* 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/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Wed Apr 15 06:01:46 2020
***********************************************
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
9.579 0.522 10.228
sojourner.Rcheck/sojourner-Ex.timings
| name | user | system | elapsed | |
| Dcoef-methods | 15.887 | 0.237 | 16.249 | |
| bootstrap-methods | 3.219 | 0.029 | 3.302 | |
| combineTrackll-methods | 5.047 | 0.092 | 127.487 | |
| compareFolder-methods | 0.195 | 0.012 | 0.207 | |
| compare_RT_CDF-methods | 5.009 | 0.453 | 124.451 | |
| createTrackll-methods | 0.228 | 0.281 | 0.073 | |
| densityMaskTracks-methods | 3.136 | 0.554 | 3.068 | |
| dispVariance-methods | 1.531 | 0.018 | 1.589 | |
| displacementCDF-methods | 3.214 | 0.099 | 3.374 | |
| dwellTime-methods | 0.590 | 0.007 | 0.600 | |
| exportTrackll-methods | 0.112 | 0.015 | 0.130 | |
| filterTrack-methods | 0.132 | 0.007 | 0.144 | |
| fitCDF-methods | 13.780 | 0.556 | 14.464 | |
| fitNormDistr-methods | 38.313 | 0.299 | 39.078 | |
| fitRT-methods | 6.007 | 0.773 | 5.643 | |
| getCI-methods | 13.151 | 0.089 | 13.404 | |
| hmmTrackll-methods | 0.929 | 0.015 | 0.948 | |
| linkSkippedFrames-methods | 0.201 | 0.011 | 0.215 | |
| maskTracks-methods | 17.853 | 0.423 | 18.743 | |
| mergeTracks-methods | 0.072 | 0.006 | 0.079 | |
| msd-methods | 4.076 | 0.040 | 4.230 | |
| plotIndividualTracks-methods | 14.609 | 0.186 | 15.055 | |
| plotLocalizations_Density-methods | 54.501 | 0.383 | 56.169 | |
| plotTrack-methods | 20.091 | 0.415 | 21.056 | |
| plotTrackOverlay_Dcoef-methods | 44.980 | 0.135 | 45.884 | |
| selComponentTracks-methods | 16.715 | 0.183 | 17.056 | |
| sojournerGUI-methods | 0 | 0 | 0 | |
| squareDisp-methods | 0.236 | 0.011 | 0.251 | |