Sojourner Developer
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/sojourner |
| Branch: master |
| Last Commit: fd85736 |
| Last Changed Date: 2019-10-29 13:43:38 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:55:07 -0500 (Thu, 16 Jan 2020).
| Package 1624/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sojourner 1.1.0 Sojourner Developer
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: sojourner |
| Version: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2020-01-16 09:04:48 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 09:19:31 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 883.2 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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/sojourner.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.1.0’
* 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 ‘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 72.968 1.137 75.314
plotTrackOverlay_Dcoef-methods 57.414 0.245 59.230
fitNormDistr-methods 50.346 0.507 50.871
maskTracks-methods 25.247 0.890 26.162
plotTrack-methods 23.716 0.833 25.548
selComponentTracks-methods 22.865 0.435 23.570
Dcoef-methods 20.840 0.357 21.214
plotIndividualTracks-methods 17.667 0.452 18.200
fitCDF-methods 15.973 1.460 17.444
getCI-methods 16.377 0.237 16.621
fitRT-methods 8.657 0.229 7.283
compare_RT_CDF-methods 7.047 0.454 162.672
combineTrackll-methods 7.076 0.172 157.907
* 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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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
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
...
RUNIT TEST PROTOCOL -- Thu Jan 16 09:19:23 2020
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
sojourner RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.423 0.940 13.079
sojourner.Rcheck/sojourner-Ex.timings
| name | user | system | elapsed | |
| Dcoef-methods | 20.840 | 0.357 | 21.214 | |
| bootstrap-methods | 4.377 | 0.144 | 4.523 | |
| combineTrackll-methods | 7.076 | 0.172 | 157.907 | |
| compareFolder-methods | 0.217 | 0.024 | 0.243 | |
| compare_RT_CDF-methods | 7.047 | 0.454 | 162.672 | |
| createTrackll-methods | 0.310 | 0.217 | 0.110 | |
| densityMaskTracks-methods | 4.450 | 0.320 | 3.979 | |
| dispVariance-methods | 2.022 | 0.028 | 2.052 | |
| displacementCDF-methods | 3.877 | 0.214 | 4.094 | |
| dwellTime-methods | 0.777 | 0.015 | 0.793 | |
| exportTrackll-methods | 0.181 | 0.036 | 0.217 | |
| filterTrack-methods | 0.102 | 0.012 | 0.115 | |
| fitCDF-methods | 15.973 | 1.460 | 17.444 | |
| fitNormDistr-methods | 50.346 | 0.507 | 50.871 | |
| fitRT-methods | 8.657 | 0.229 | 7.283 | |
| getCI-methods | 16.377 | 0.237 | 16.621 | |
| hmmTrackll-methods | 1.069 | 0.051 | 1.123 | |
| linkSkippedFrames-methods | 0.203 | 0.020 | 0.223 | |
| maskTracks-methods | 25.247 | 0.890 | 26.162 | |
| mergeTracks-methods | 0.090 | 0.012 | 0.102 | |
| msd-methods | 4.715 | 0.063 | 4.779 | |
| plotIndividualTracks-methods | 17.667 | 0.452 | 18.200 | |
| plotLocalizations_Density-methods | 72.968 | 1.137 | 75.314 | |
| plotTrack-methods | 23.716 | 0.833 | 25.548 | |
| plotTrackOverlay_Dcoef-methods | 57.414 | 0.245 | 59.230 | |
| selComponentTracks-methods | 22.865 | 0.435 | 23.570 | |
| sojournerGUI-methods | 0.000 | 0.001 | 0.000 | |
| squareDisp-methods | 0.229 | 0.024 | 0.253 | |