Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-04-13 12:08:49 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for sojourner on machv2


To the developers/maintainers of the sojourner package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sojourner.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1834/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sojourner 1.8.0  (landing page)
Sojourner Developer
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/sojourner
git_branch: RELEASE_3_14
git_last_commit: 64477c4
git_last_commit_date: 2021-10-26 12:53:41 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: sojourner
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sojourner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sojourner_1.8.0.tar.gz
StartedAt: 2022-04-12 18:47:29 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:02:30 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 900.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: sojourner.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sojourner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sojourner_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/sojourner.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.8.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘area’
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/sojourner.Rcheck/00install.out’ for details.
* 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 70.922  0.532  71.508
plotTrackOverlay_Dcoef-methods    46.273  0.155  46.460
fitNormDistr-methods              45.511  0.250  45.797
maskTracks-methods                16.600  0.384  17.009
Dcoef-methods                     16.726  0.222  16.966
plotIndividual_Tracks-methods     14.125  0.418  14.552
plotTrack-methods                  6.971  0.221   7.251
fitRT-methods                      6.494  0.038   6.536
msd-methods                        6.158  0.042   6.210
compare_RT_CDF-methods             5.179  0.048 179.224
combineTrackll-methods             5.040  0.048 174.538
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/sojourner.Rcheck/00check.log’
for details.



Installation output

sojourner.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sojourner
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘sojourner’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: multiple methods tables found for ‘area’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘area’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘area’
** testing if installed package keeps a record of temporary installation path
* DONE (sojourner)

Tests output

sojourner.Rcheck/tests/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Tue Apr 12 19:02:20 2022 
*********************************************** 
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 
Warning message:
multiple methods tables found for 'area' 
> 
> proc.time()
   user  system elapsed 
 16.899   0.645  17.536 

Example timings

sojourner.Rcheck/sojourner-Ex.timings

nameusersystemelapsed
Dcoef-methods16.726 0.22216.966
combineTrackll-methods 5.040 0.048174.538
compareFolder-methods0.1950.0120.211
compare_RT_CDF-methods 5.179 0.048179.224
createTrackll-methods0.0650.0070.074
dispVariance-methods1.7760.0151.793
displacementCDF-methods3.5810.1803.790
dwellTime-methods0.5170.0080.527
exportTrackll-methods0.1550.0190.177
filterTrack-methods0.1470.0070.155
fitNormDistr-methods45.511 0.25045.797
fitRT-methods6.4940.0386.536
linkSkippedFrames-methods0.1970.0140.217
maskTracks-methods16.600 0.38417.009
mergeTracks-methods0.0860.0080.093
msd-methods6.1580.0426.210
plotIndividual_Tracks-methods14.125 0.41814.552
plotLocalizations_Density-methods70.922 0.53271.508
plotTrack-methods6.9710.2217.251
plotTrackOverlay_Dcoef-methods46.273 0.15546.460
sojournerGUI-methods0.0010.0000.001
squareDisp-methods0.2430.0130.258