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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DiscoRhythm.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DiscoRhythm_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DiscoRhythm.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DiscoRhythm/DESCRIPTION’ ... OK
* this is package ‘DiscoRhythm’ version ‘1.15.0’
* 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 ‘DiscoRhythm’ 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 ... NOTE
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
discoApp: no visible binding for global variable ‘.discorhythm_ncores’
discoApp: no visible binding for global variable ‘.discorhythm_local’
discoBatch: no visible binding for global variable ‘discoODAres’
Undefined global functions or variables:
  .discorhythm_local .discorhythm_ncores discoODAres
* checking Rd files ... NOTE
checkRd: (-1) discoParseMeta.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) discoParseMeta.Rd:29: Escaped LaTeX specials: \_
* 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 ... ERROR
Running examples in ‘DiscoRhythm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: discoBatch
> ### Title: Core DiscoRhythm Workflow
> ### Aliases: discoBatch
> 
> ### ** Examples
> 
> indata <- discoGetSimu()
> 
> # Batch execute (on demo data) to generate a DiscoRhythm_report.html report.
> # Returns the results of discoODAs
> discoODAres <- discoBatch(indata,
+ report="DiscoRhythm_report.html",
+ osc_method="CS")
[WARNING] Could not parse YAML metadata at line 14 column 1: Duplicate key in mapping: Scalar (Pos {posByteOffset = 207, posCharOffset = 207, posLine = 11, posColumn = 0}) (SUnknown Nothing "date")


processing file: DiscoRhythm_report.Rmd
output file: /home/biocbuild/bbs-3.17-bioc/meat/DiscoRhythm.Rcheck/DiscoRhythm_report.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.17-bioc/meat/DiscoRhythm.Rcheck/DiscoRhythm_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/bbs-3.17-bioc/meat/DiscoRhythm.Rcheck/DiscoRhythm_report.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --wrap preserve --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /tmp/RtmpCIyoYx/BiocStyle/template.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css /home/biocbuild/bbs-3.17-bioc/R/library/BiocStyle/resources/html/bioconductor.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpCIyoYx/rmarkdown-str3f6cd04720517d.html --variable source_embed=DiscoRhythm_report.Rmd --include-after-body /tmp/RtmpCIyoYx/file3f6cd02242394a.html --variable code_menu=1 
Killed
* 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 ...
  ‘disco_workflow_vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/DiscoRhythm.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DiscoRhythm
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘DiscoRhythm’ ...
** 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 (DiscoRhythm)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(DiscoRhythm)
> 
> test_check("DiscoRhythm")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 10.503   1.362  15.024