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This page was generated on 2022-01-20 11:07:55 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
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 OmicsLonDA on riesling1


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 1322/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmicsLonDA 1.11.1  (landing page)
Ahmed A. Metwally
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/OmicsLonDA
git_branch: master
git_last_commit: 67af5e0
git_last_commit_date: 2021-11-21 00:39:43 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: OmicsLonDA
Version: 1.11.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmicsLonDA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OmicsLonDA_1.11.1.tar.gz
StartedAt: 2022-01-19 19:34:46 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 19:37:55 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 189.3 seconds
RetCode: 0
Status:   OK  
CheckDir: OmicsLonDA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmicsLonDA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OmicsLonDA_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/OmicsLonDA.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmicsLonDA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmicsLonDA' version '1.11.1'
* 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 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 9.28   0.33    9.61
testStatPermutation    8.42   0.25    8.67
omicslonda             7.74   0.33    8.06
permutationMC          6.75   0.53    7.28
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL OmicsLonDA
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'OmicsLonDA'
    finding HTML links ... done
    adjustBaseline                          html  
    curveFitting                            html  
    findSigInterval                         html  
    omicslonda                              html  
    omicslonda_data_example                 html  
    permutationMC                           html  
    testStat                                html  
    testStatPermutation                     html  
    visualizeArea                           html  
    visualizeFeature                        html  
    visualizeFeatureSpline                  html  
    visualizeTestStatHistogram              html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'iasva' is missing or broken
 done

Tests output

OmicsLonDA.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  11.78    1.40   13.17 

Example timings

OmicsLonDA.Rcheck/OmicsLonDA-Ex.timings

nameusersystemelapsed
adjustBaseline1.890.041.94
curveFitting2.790.082.86
findSigInterval0.070.030.11
omicslonda7.740.338.06
permutationMC6.750.537.28
testStat0.240.020.25
testStatPermutation8.420.258.67
visualizeArea1.160.161.31
visualizeFeature3.310.123.44
visualizeFeatureSpline9.280.339.61
visualizeTestStatHistogram0.280.240.63