##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mitch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mitch_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/mitch.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 'mitch/DESCRIPTION' ... OK
* this is package 'mitch' version '1.7.0'
* 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 'mitch' 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
mitch        40.55   3.06   45.82
mitch_report 19.30   2.16   23.31
mitch_plots  15.50   0.29   15.80
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-mitch.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

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mitch
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mitch' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mitch'
    finding HTML links ... done
    genesetsExample                         html  
    gmt_import                              html  
    k36a                                    html  
    k9a                                     html  
    mitch                                   html  
    mitch_calc                              html  
    mitch_import                            html  
    mitch_plots                             html  
    mitch_report                            html  
    myImportedData                          html  
    myList                                  html  
    resExample                              html  
    rna                                     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 (mitch)
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("mitch")
> library("testthat")
> 
> test_that("multiplication works", {
+     expect_equal(2 * 2, 4)
+ })
Test passed 
> 
> # 1d
> data(rna,genesetsExample)
> y<-mitch_import(rna,DEtype="edgeR")
The input is a single dataframe; one contrast only. Converting
        it to a list for you.
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small
            p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="1d.pdf") 
null device 
          1 
> if (file.exists("1d.html")) { unlink("1d.html") } 
> mitch_report(res,"1d.html")
Dataset saved as " D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMduTCs/1d.rds ".


processing file: mitch.Rmd
   inline R code fragments

label: checklibraries (with options) 
List of 1
 $ echo: logi FALSE

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label: peek (with options) 
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label: metrics (with options) 
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label: scatterplot (with options) 
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 $ fig.width : num 6.5
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label: contourplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ warning   : logi FALSE
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Contour plot does not apply to unidimensional analysis.
  ordinary text without R code

label: input_geneset_metrics1 (with options) 
List of 2
 $ results: chr "asis"
 $ echo   : logi FALSE

  ordinary text without R code

label: input_geneset_metrics2 (with options) 
List of 5
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"

  ordinary text without R code

label: input_geneset_metrics3 (with options) 
List of 5
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7

  ordinary text without R code

label: echart1d (with options) 
List of 6
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

label: echart2d (with options) 
List of 6
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

  ordinary text without R code

label: heatmap (with options) 
List of 6
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 10
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

  ordinary text without R code

label: effectsize (with options) 
List of 6
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

  ordinary text without R code

label: results_table (with options) 
List of 2
 $ results: chr "asis"
 $ echo   : logi FALSE

  ordinary text without R code

label: results_table_complete (with options) 
List of 2
 $ results: chr "asis"
 $ echo   : logi FALSE

  ordinary text without R code

label: detailed_geneset_reports1d (with options) 
List of 7
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6
 $ out.width : chr "80%"
 $ comment   : logi NA
 $ message   : logi FALSE

  ordinary text without R code

label: detailed_geneset_reports2d (with options) 
List of 7
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 5
 $ fig.width : num 6
 $ out.width : chr "80%"
 $ comment   : logi NA
 $ message   : logi FALSE

  ordinary text without R code

label: session_info (with options) 
List of 3
 $ include: logi TRUE
 $ echo   : logi TRUE
 $ results: chr "markup"

  ordinary text without R code

output file: D:/biocbuild/bbs-3.15-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "D:/biocbuild/bbs-3.15-bioc/meat/mitch.Rcheck/tests/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc28d8875684210.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 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --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\RtmpMduTCs\rmarkdown-str28d88181b4318.html" 

Output created: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMduTCs/mitch_report.html
[1] TRUE
> 
> test_that("1d works", {
+     expect_equal(  length(which(res$enrichment_result$p.adjustANOVA<0.1)) ,1)
+     expect_true(file.info("1d.pdf")$size>10000)
+     expect_true(file.info("1d.html")$size>1000000)
+ })
Test passed 
> 
> unlink("1d.html")
> unlink("1d.pdf")
> 
> 
> # 1d part 2 to make sure that saving files at a different location works
> MYPATH=paste(getwd(),"/1d.html",sep="")
> if (file.exists("1d.html")) { unlink("1d.html") }
> mitch_report(res,MYPATH)
Dataset saved as " D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMduTCs/1d.rds ".


processing file: mitch.Rmd
   inline R code fragments

label: checklibraries (with options) 
List of 1
 $ echo: logi FALSE

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label: peek (with options) 
List of 1
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label: metrics (with options) 
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label: scatterplot (with options) 
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 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
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  ordinary text without R code

label: contourplot (with options) 
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 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ warning   : logi FALSE
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Contour plot does not apply to unidimensional analysis.
  ordinary text without R code

label: input_geneset_metrics1 (with options) 
List of 2
 $ results: chr "asis"
 $ echo   : logi FALSE

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label: input_geneset_metrics2 (with options) 
List of 5
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"

  ordinary text without R code

label: input_geneset_metrics3 (with options) 
List of 5
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7

  ordinary text without R code

label: echart1d (with options) 
List of 6
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

label: echart2d (with options) 
List of 6
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

  ordinary text without R code

label: heatmap (with options) 
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 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 10
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

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label: effectsize (with options) 
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 $ results   : chr "asis"
 $ echo      : logi FALSE
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 $ message   : logi FALSE

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label: results_table (with options) 
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label: results_table_complete (with options) 
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 $ results: chr "asis"
 $ echo   : logi FALSE

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label: detailed_geneset_reports1d (with options) 
List of 7
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6
 $ out.width : chr "80%"
 $ comment   : logi NA
 $ message   : logi FALSE

  ordinary text without R code

label: detailed_geneset_reports2d (with options) 
List of 7
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 5
 $ fig.width : num 6
 $ out.width : chr "80%"
 $ comment   : logi NA
 $ message   : logi FALSE

  ordinary text without R code

label: session_info (with options) 
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 $ include: logi TRUE
 $ echo   : logi TRUE
 $ results: chr "markup"

  ordinary text without R code

output file: D:/biocbuild/bbs-3.15-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "D:/biocbuild/bbs-3.15-bioc/meat/mitch.Rcheck/tests/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc28d88131116c8.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 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --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\RtmpMduTCs\rmarkdown-str28d885e1f18a0.html" 

Output created: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMduTCs/mitch_report.html
[1] TRUE
> 
> test_that("1d works", {
+     expect_true(file.info("1d.html")$size>1000000)
+ })
Test passed 
> 
> unlink("1d.html")
> 
> 
> 
> # 2d
> data(rna,k9a,genesetsExample)
> x<-list("rna"=rna,"k9a"=k9a)
> y<-mitch_import(x,DEtype="edgeR")
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small 
            p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="2d.pdf")
null device 
          1 
> if (file.exists("2d.html")) { unlink("2d.html") }
> mitch_report(res,"2d.html")
Dataset saved as " D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMduTCs/2d.rds ".


processing file: mitch.Rmd
   inline R code fragments

label: checklibraries (with options) 
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label: peek (with options) 
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label: contourplot (with options) 
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label: input_geneset_metrics1 (with options) 
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label: input_geneset_metrics3 (with options) 
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 $ results   : chr "asis"
 $ echo      : logi FALSE
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 $ fig.height: num 7
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label: echart1d (with options) 
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 $ results   : chr "asis"
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 $ message   : logi FALSE

label: echart2d (with options) 
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 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

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label: heatmap (with options) 
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 $ results   : chr "asis"
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label: effectsize (with options) 
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label: detailed_geneset_reports1d (with options) 
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 $ out.width : chr "80%"
 $ comment   : logi NA
 $ message   : logi FALSE

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label: detailed_geneset_reports2d (with options) 
List of 7
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 5
 $ fig.width : num 6
 $ out.width : chr "80%"
 $ comment   : logi NA
 $ message   : logi FALSE

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label: session_info (with options) 
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 $ include: logi TRUE
 $ echo   : logi TRUE
 $ results: chr "markup"

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output file: D:/biocbuild/bbs-3.15-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "D:/biocbuild/bbs-3.15-bioc/meat/mitch.Rcheck/tests/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc28d88151c2720.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 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --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\RtmpMduTCs\rmarkdown-str28d881b032211.html" 

Output created: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMduTCs/mitch_report.html
[1] TRUE
> 
> test_that("2d works", {
+     expect_equal(  length(which(res$enrichment_result$p.adjustMANOVA<0.1)) ,1)
+     expect_true(file.info("2d.pdf")$size>100000)
+     expect_true(file.info("2d.html")$size>1000000)
+ })
Test passed 
> 
> unlink("2d.html")
> unlink("2d.pdf")
> 
> # 3d
> data(rna,k9a,k36a,genesetsExample)
> x<-list("rna"=rna,"k9a"=k9a,"k36a"=k36a)
> y<-mitch_import(x,DEtype="edgeR")
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> res<-mitch_calc(y,genesetsExample,cores=2)
Note: When prioritising by significance (ie: small 
            p-values), large effect sizes might be missed.
> mitch_plots(res,outfile="3d.pdf")
null device 
          1 
> if (file.exists("3d.html")) { unlink("3d.html") }
> mitch_report(res,"3d.html")
Dataset saved as " D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMduTCs/3d.rds ".


processing file: mitch.Rmd
   inline R code fragments

label: checklibraries (with options) 
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label: contourplot (with options) 
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label: input_geneset_metrics1 (with options) 
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 $ results   : chr "asis"
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label: input_geneset_metrics3 (with options) 
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 $ results   : chr "asis"
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 $ fig.height: num 7
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label: echart1d (with options) 
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 $ results   : chr "asis"
 $ echo      : logi FALSE
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 $ fig.show  : chr "all"
 $ message   : logi FALSE

label: echart2d (with options) 
List of 6
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 7
 $ fig.width : num 7
 $ fig.show  : chr "all"
 $ message   : logi FALSE

No significant enrichments found.
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 $ echo   : logi FALSE

  ordinary text without R code

label: detailed_geneset_reports1d (with options) 
List of 7
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6
 $ out.width : chr "80%"
 $ comment   : logi NA
 $ message   : logi FALSE

  ordinary text without R code

label: detailed_geneset_reports2d (with options) 
List of 7
 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ fig.height: num 5
 $ fig.width : num 6
 $ out.width : chr "80%"
 $ comment   : logi NA
 $ message   : logi FALSE

  ordinary text without R code

label: session_info (with options) 
List of 3
 $ include: logi TRUE
 $ echo   : logi TRUE
 $ results: chr "markup"

  ordinary text without R code

output file: D:/biocbuild/bbs-3.15-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "D:/biocbuild/bbs-3.15-bioc/meat/mitch.Rcheck/tests/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc28d886db6ada.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 --template "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --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\RtmpMduTCs\rmarkdown-str28d886d56267a.html" 

Output created: D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpMduTCs/mitch_report.html
[1] TRUE
> 
> test_that("3d works", {
+     expect_equal(  length(which(res$enrichment_result$p.adjustMANOVA<0.1)) ,1)
+     expect_true(file.info("3d.pdf")$size>100000)
+     expect_true(file.info("3d.html")$size>1000000)
+ })
Test passed 
> 
> unlink("3d.html")
> unlink("3d.pdf")
> 
> 
> 
> proc.time()
   user  system elapsed 
  45.79    5.50   60.60