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This page was generated on 2021-12-06 13:05:05 -0500 (Mon, 06 Dec 2021).

CHECK results for OmicsLonDA on nebbiolo2

To the developers/maintainers of the OmicsLonDA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmicsLonDA.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.

raw results

Package 1326/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmicsLonDA 1.10.0  (landing page)
Ahmed A. Metwally
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/OmicsLonDA
git_branch: RELEASE_3_14
git_last_commit: a145163
git_last_commit_date: 2021-10-26 12:51:17 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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    OK    OK  UNNEEDED, same version is already published

Summary

Package: OmicsLonDA
Version: 1.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:OmicsLonDA.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings OmicsLonDA_1.10.0.tar.gz
StartedAt: 2021-12-05 08:58:03 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 09:01:35 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 212.6 seconds
RetCode: 0
Status:   OK  
CheckDir: OmicsLonDA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:OmicsLonDA.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings OmicsLonDA_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/OmicsLonDA.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmicsLonDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmicsLonDA’ version ‘1.10.0’
* 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 ‘OmicsLonDA’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
visualizeFeatureSpline 9.868  0.156  10.025
omicslonda             9.505  0.143   9.650
testStatPermutation    8.353  0.068   8.421
permutationMC          7.141  0.068   7.209
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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


Installation output

OmicsLonDA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL OmicsLonDA
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘OmicsLonDA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (OmicsLonDA)

Tests output

OmicsLonDA.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> library(testthat)
> library(OmicsLonDA)
> 
> test_check("OmicsLonDA")
[1] "Disease" "Healthy"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 16.490   0.757  17.230 

Example timings

OmicsLonDA.Rcheck/OmicsLonDA-Ex.timings

nameusersystemelapsed
adjustBaseline3.0300.0913.122
curveFitting4.2010.2294.429
findSigInterval0.1730.0000.173
omicslonda9.5050.1439.650
permutationMC7.1410.0687.209
testStat0.2080.0040.212
testStatPermutation8.3530.0688.421
visualizeArea1.0070.0961.102
visualizeFeature3.0690.0763.144
visualizeFeatureSpline 9.868 0.15610.025
visualizeTestStatHistogram0.3940.0480.442