Sojourner Developer
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/sojourner |
| Branch: RELEASE_3_11 |
| Last Commit: f0a6b71 |
| Last Changed Date: 2020-05-29 20:21:02 -0400 (Fri, 29 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:48 -0400 (Sat, 17 Oct 2020).
| 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 1697/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sojourner 1.2.1 Sojourner Developer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: sojourner |
| Version: 1.2.1 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:sojourner.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings sojourner_1.2.1.tar.gz |
| StartedAt: 2020-10-17 05:40:13 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:48:50 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 517.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sojourner.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:sojourner.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings sojourner_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/sojourner.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sojourner/DESCRIPTION’ ... OK
* this is package ‘sojourner’ version ‘1.2.1’
* 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 39.195 0.201 39.414
plotTrackOverlay_Dcoef-methods 35.021 0.181 35.246
fitNormDistr-methods 30.182 0.428 30.618
Dcoef-methods 13.461 0.343 14.087
maskTracks-methods 13.529 0.259 14.286
plotIndividual_Tracks-methods 10.161 0.192 10.350
plotTrack-methods 7.089 0.424 7.997
combineTrackll-methods 4.819 0.370 105.741
compare_RT_CDF-methods 4.729 0.283 108.417
* 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: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL sojourner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("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 -- Sat Oct 17 05:48:46 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
9.022 0.371 9.379
sojourner.Rcheck/sojourner-Ex.timings
| name | user | system | elapsed | |
| Dcoef-methods | 13.461 | 0.343 | 14.087 | |
| combineTrackll-methods | 4.819 | 0.370 | 105.741 | |
| compareFolder-methods | 0.246 | 0.081 | 0.345 | |
| compare_RT_CDF-methods | 4.729 | 0.283 | 108.417 | |
| createTrackll-methods | 0.062 | 0.031 | 0.108 | |
| dispVariance-methods | 1.012 | 0.075 | 1.084 | |
| displacementCDF-methods | 1.930 | 0.172 | 2.116 | |
| dwellTime-methods | 0.600 | 0.098 | 0.717 | |
| exportTrackll-methods | 0.133 | 0.143 | 0.272 | |
| filterTrack-methods | 0.132 | 0.043 | 0.174 | |
| fitNormDistr-methods | 30.182 | 0.428 | 30.618 | |
| fitRT-methods | 4.011 | 0.127 | 4.030 | |
| linkSkippedFrames-methods | 0.197 | 0.103 | 0.317 | |
| maskTracks-methods | 13.529 | 0.259 | 14.286 | |
| mergeTracks-methods | 0.051 | 0.035 | 0.100 | |
| msd-methods | 3.177 | 0.387 | 3.597 | |
| plotIndividual_Tracks-methods | 10.161 | 0.192 | 10.350 | |
| plotLocalizations_Density-methods | 39.195 | 0.201 | 39.414 | |
| plotTrack-methods | 7.089 | 0.424 | 7.997 | |
| plotTrackOverlay_Dcoef-methods | 35.021 | 0.181 | 35.246 | |
| sojournerGUI-methods | 0 | 0 | 0 | |
| squareDisp-methods | 0.136 | 0.092 | 0.225 | |