| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:54 -0400 (Fri, 15 Oct 2021).
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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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1805/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sojourner 1.6.0 (landing page) Sojourner Developer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: sojourner |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2021-10-15 00:14:24 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:26:37 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 733.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: sojourner.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/sojourner.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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-3.13-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 48.968 0.265 49.270
plotTrackOverlay_Dcoef-methods 37.870 0.147 38.058
fitNormDistr-methods 36.442 0.208 36.714
maskTracks-methods 13.772 0.333 14.128
Dcoef-methods 13.427 0.191 13.638
plotIndividual_Tracks-methods 10.337 0.244 10.591
plotTrack-methods 6.075 0.225 6.370
fitRT-methods 5.254 0.066 5.341
combineTrackll-methods 4.506 0.046 147.009
compare_RT_CDF-methods 4.482 0.047 147.129
* 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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/sojourner.Rcheck/00check.log’
for details.
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/4.1/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)
sojourner.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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 -- Fri Oct 15 00:26:29 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
Warning message:
multiple methods tables found for 'area'
>
> proc.time()
user system elapsed
13.348 0.539 13.875
sojourner.Rcheck/sojourner-Ex.timings
| name | user | system | elapsed | |
| Dcoef-methods | 13.427 | 0.191 | 13.638 | |
| combineTrackll-methods | 4.506 | 0.046 | 147.009 | |
| compareFolder-methods | 0.201 | 0.013 | 0.215 | |
| compare_RT_CDF-methods | 4.482 | 0.047 | 147.129 | |
| createTrackll-methods | 0.070 | 0.004 | 0.075 | |
| dispVariance-methods | 1.481 | 0.013 | 1.498 | |
| displacementCDF-methods | 3.124 | 0.145 | 3.274 | |
| dwellTime-methods | 0.594 | 0.009 | 0.604 | |
| exportTrackll-methods | 0.176 | 0.017 | 0.196 | |
| filterTrack-methods | 0.153 | 0.007 | 0.159 | |
| fitNormDistr-methods | 36.442 | 0.208 | 36.714 | |
| fitRT-methods | 5.254 | 0.066 | 5.341 | |
| linkSkippedFrames-methods | 0.190 | 0.012 | 0.203 | |
| maskTracks-methods | 13.772 | 0.333 | 14.128 | |
| mergeTracks-methods | 0.063 | 0.006 | 0.070 | |
| msd-methods | 4.522 | 0.068 | 4.594 | |
| plotIndividual_Tracks-methods | 10.337 | 0.244 | 10.591 | |
| plotLocalizations_Density-methods | 48.968 | 0.265 | 49.270 | |
| plotTrack-methods | 6.075 | 0.225 | 6.370 | |
| plotTrackOverlay_Dcoef-methods | 37.870 | 0.147 | 38.058 | |
| sojournerGUI-methods | 0.000 | 0.001 | 0.001 | |
| squareDisp-methods | 0.182 | 0.014 | 0.196 | |