##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mitch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mitch_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitch/DESCRIPTION’ ... OK
* this is package ‘mitch’ version ‘1.4.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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        61.717  1.165  63.105
mitch_report 32.880  0.595  33.557
mitch_plots  24.618  0.293  24.938
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mitch
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘mitch’ ...
** using staged installation
** R
** data
** 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 (mitch)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 " /tmp/RtmpcuPeLQ/1d.rds ".


processing file: mitch.Rmd
   inline R code fragments

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

  ordinary text without R code

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.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
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  ordinary text without R code

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
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 $ 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"
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 $ 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: /Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpcuPeLQ/mitch_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/RtmpcuPeLQ/rmarkdown-str46563c92aa11.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' 

Output created: /tmp/RtmpcuPeLQ/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 " /tmp/RtmpcuPeLQ/1d.rds ".


processing file: mitch.Rmd
   inline R code fragments

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

  ordinary text without R code

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

  ordinary text without R code

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) 
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
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 $ echo   : logi FALSE

  ordinary text without R code

label: input_geneset_metrics2 (with options) 
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 $ results   : chr "asis"
 $ echo      : logi FALSE
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  ordinary text without R code

label: input_geneset_metrics3 (with options) 
List of 5
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 $ fig.height: num 7
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  ordinary text without R code

label: echart1d (with options) 
List of 6
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 $ 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"
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  ordinary text without R code

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

  ordinary text without R code

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

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label: results_table (with options) 
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 $ echo   : logi FALSE

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 $ results: chr "asis"
 $ echo   : logi FALSE

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label: detailed_geneset_reports1d (with options) 
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 $ results   : chr "asis"
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 $ 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"
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 $ 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: /Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpcuPeLQ/mitch_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/RtmpcuPeLQ/rmarkdown-str465678adeb23.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' 

Output created: /tmp/RtmpcuPeLQ/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 " /tmp/RtmpcuPeLQ/2d.rds ".


processing file: mitch.Rmd
   inline R code fragments

label: checklibraries (with options) 
List of 1
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label: peek (with options) 
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label: metrics (with options) 
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label: input_geneset_metrics1 (with options) 
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 $ echo      : logi FALSE
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  ordinary text without R code

label: input_geneset_metrics3 (with options) 
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 $ results   : chr "asis"
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.height: num 7
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  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
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 $ 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"
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label: detailed_geneset_reports1d (with options) 
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 $ results   : chr "asis"
 $ echo      : logi FALSE
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 $ 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
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 $ fig.width : num 6
 $ out.width : chr "80%"
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  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: /Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpcuPeLQ/mitch_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/RtmpcuPeLQ/rmarkdown-str46565c91e98b.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' 

Output created: /tmp/RtmpcuPeLQ/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 " /tmp/RtmpcuPeLQ/3d.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: 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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  ordinary text without R code

label: echart1d (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

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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label: heatmap (with options) 
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label: effectsize (with options) 
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 $ comment   : logi NA
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label: detailed_geneset_reports2d (with options) 
List of 7
 $ results   : chr "asis"
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 $ fig.width : num 6
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 $ comment   : logi NA
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 $ results: chr "markup"

  ordinary text without R code

output file: /Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpcuPeLQ/mitch_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/RtmpcuPeLQ/rmarkdown-str46565f32ddf8.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' 

Output created: /tmp/RtmpcuPeLQ/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 
 79.711   2.624  82.598