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CHECK report for sights on malbec1

This page was generated on 2021-05-06 12:29:08 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the sights package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1705/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sights 1.16.0  (landing page)
Elika Garg
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/sights
Branch: RELEASE_3_12
Last Commit: 90d3300
Last Changed Date: 2020-10-27 11:15:24 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: sights
Version: 1.16.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:sights.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings sights_1.16.0.tar.gz
StartedAt: 2021-05-06 06:02:51 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:04:37 -0400 (Thu, 06 May 2021)
EllapsedTime: 105.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sights.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:sights.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings sights_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/sights.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sights/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sights’ version ‘1.16.0’
* 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 ‘sights’ 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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

sights.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL sights
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘sights’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (sights)

Tests output

sights.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(sights)
> test_check("sights") 
alpha= 2.527861 beta= 2.054019 
alpha= 2.162155 beta= 2.810248 
alpha= 2.162155 beta= 2.810248 
alpha= 2.162155 beta= 2.810248 
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
 52.936   0.184  53.215 

Example timings

sights.Rcheck/sights-Ex.timings

nameusersystemelapsed
ex_dataMatrix0.0320.0000.034
inglese0.0880.0040.090
normLoess0.2160.0040.220
normMedFil0.1040.0000.104
normR0.0560.0000.054
normRobZ0.0040.0000.005
normSPAWN0.0680.0040.074
normSights0.0080.0000.005
normZ0.0040.0000.003
plot3d0.6920.0000.691
plotAutoco2.6120.0242.637
plotBox0.8240.0000.824
plotHeatmap1.5000.0081.509
plotHist0.3520.0040.359
plotIGFit0.1800.0000.178
plotScatter2.7440.0842.831
plotSights1.5560.0001.557
statFDR0.0440.0000.043
statRVM0.0120.0000.011
statSights0.0160.0000.015
statT0.0320.0000.033