##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hypeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings hypeR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/hypeR.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 'hypeR/DESCRIPTION' ... OK
* this is package 'hypeR' version '1.11.0'
* 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 whether package 'hypeR' 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 ... NOTE
.dots_multi_plot : <anonymous>: no visible binding for global variable
  'pval'
.dots_multi_plot : <anonymous>: no visible binding for global variable
  'fdr'
.dots_multi_plot : <anonymous>: no visible binding for global variable
  'label'
.dots_multi_plot: no visible global function definition for 'head'
.dots_multi_plot: no visible binding for global variable 'significance'
.dots_multi_plot: no visible binding for global variable 'signature'
.dots_multi_plot: no visible binding for global variable 'label'
.dots_multi_plot: no visible binding for global variable 'size'
.dots_plot: no visible binding for global variable 'pval'
.dots_plot: no visible binding for global variable 'fdr'
.dots_plot: no visible binding for global variable 'significance'
.dots_plot: no visible binding for global variable 'size'
.enrichment_map: no visible binding for global variable 'pval'
.enrichment_map: no visible binding for global variable 'fdr'
.find_members: no visible binding for global variable 'from'
.find_members: no visible binding for global variable 'to'
.hiearchy_map: no visible binding for global variable 'pval'
.hiearchy_map: no visible binding for global variable 'fdr'
.hiearchy_map : <anonymous>: no visible binding for global variable
  'label'
.hyper_enrichment: no visible global function definition for 'is'
.ks_enrichment: no visible global function definition for 'is'
enrichr_available: no visible binding for global variable '.'
ggvenn: no visible binding for global variable 'x'
ggvenn: no visible binding for global variable 'y'
hyp_dots: no visible global function definition for 'is'
hyp_emap: no visible global function definition for 'is'
hyp_hmap: no visible global function definition for 'is'
hyp_show: no visible global function definition for 'is'
hyp_to_excel: no visible global function definition for 'is'
hyp_to_graph: no visible global function definition for 'is'
hyp_to_rmd: no visible global function definition for 'is'
hyp_to_rmd : <anonymous>: no visible global function definition for
  'is'
hyp_to_table: no visible global function definition for 'is'
hyp_to_table: no visible global function definition for 'write.table'
hypeR: no visible global function definition for 'is'
hypeR: no visible global function definition for 'packageVersion'
hypeR: no visible global function definition for 'head'
msigdb_available: no visible binding for global variable 'gs_cat'
msigdb_available: no visible binding for global variable 'gs_subcat'
msigdb_download: no visible binding for global variable 'gs_name'
msigdb_download: no visible binding for global variable 'gene_symbol'
msigdb_version: no visible global function definition for
  'packageVersion'
rctbl_build: no visible global function definition for 'is'
Undefined global functions or variables:
  . fdr from gene_symbol gs_cat gs_name gs_subcat head is label
  packageVersion pval signature significance size to write.table x y
Consider adding
  importFrom("methods", "is", "signature")
  importFrom("utils", "head", "packageVersion", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
msigdb_available 14.65   2.21   16.98
hyp_hmap          6.14   0.11    6.90
enrichr_download  0.03   0.04   10.61
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/hypeR.Rcheck/00check.log'
for details.

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'hypeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hypeR'
    finding HTML links ... done
    clean_genesets                          html  
    dot-check_overlap                       html  
    dot-dots_multi_plot                     html  
    dot-dots_plot                           html  
    dot-enrichment_map                      html  
    dot-find_members                        html  
    dot-format_str                          html  
    dot-github_rds                          html  
    dot-hexa                                html  
    dot-hiearchy_map                        html  
    dot-hyper_enrichment                    html  
    dot-hyperdb_url                         html  
    dot-jaccard_similarity                  html  
    dot-ks_enrichment                       html  
    dot-kstest                              html  
    dot-overlap_similarity                  html  
    dot-reverselog_trans                    html  
    dot-string_args                         html  
    enrichr_available                       html  
    enrichr_connect                         html  
    enrichr_download                        html  
    enrichr_gsets                           html  
    enrichr_urls                            html  
    genesets_Server                         html  
    genesets_UI                             html  
    ggempty                                 html  
    ggeplot                                 html  
    ggvenn                                  html  
    gsets                                   html  
    hyp                                     html  
    hyp_dots                                html  
    hyp_emap                                html  
    hyp_hmap                                html  
    hyp_show                                html  
    hyp_to_excel                            html  
    hyp_to_graph                            html  
    hyp_to_rmd                              html  
    hyp_to_table                            html  
    hypeR                                   html  
    hyperdb_available                       html  
    hyperdb_gsets                           html  
    hyperdb_rgsets                          html  
    limma                                   html  
    msigdb_available                        html  
    msigdb_check_species                    html  
    msigdb_download                         html  
    msigdb_gsets                            html  
    msigdb_info                             html  
    msigdb_species                          html  
    msigdb_version                          html  
    multihyp                                html  
    pvector                                 html  
    rctbl_build                             html  
    rctbl_hyp                               html  
    rctbl_mhyp                              html  
    rgsets                                  html  
    wgcna                                   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 (hypeR)
Making 'packages.html' ... done

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(magrittr)

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> library(hypeR)
> 
> test_check("hypeR")
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS hyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.1.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str26805e2b3709.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS multihyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.1.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str2680100b3d6d.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 4 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 5 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 6 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 7 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 8 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 9 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS lmultihyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.1.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str26805ad939e0.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS hyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.2.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str268040b95297.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS multihyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.2.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str268067c565a2.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 4 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 5 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 6 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 7 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 8 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 9 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS lmultihyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.2.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str2680680a312b.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 4 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 5 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 6 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 7 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 8 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 9 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS lmultihyp.3.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.3.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str26803fe01a1c.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS hyp.4.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.4.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str2680306018e.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS multihyp.4.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.4.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str268030932f4f.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 4 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS combo.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.1.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str268094e550a.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 4 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS combo.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.2.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str2680695e3527.html" --variable code_folding=hide --variable code_menu=1 
   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 2 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 3 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: 4 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

label: unnamed-chunk-1
  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS combo.3.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.3.html --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEtih41\rmarkdown-str26803cf16794.html" --variable code_folding=hide --variable code_menu=1 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 409 ]
> 
> proc.time()
   user  system elapsed 
  50.75    2.95   75.76