Multiple platform build/check report for BioC 3.13 - CHECK results for mitch on tokay2


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 " C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2/1d.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) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: scatterplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
 $ warning   : logi FALSE

  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
 $ message   : logi FALSE

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: C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoca414cd357a0.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2\rmarkdown-stra414712247ef.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2/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 " C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2/1d.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) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: scatterplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
 $ warning   : logi FALSE

  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
 $ message   : logi FALSE

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: C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoca41422f8315.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2\rmarkdown-stra414dc61740.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2/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 " C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2/2d.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) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: scatterplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
 $ warning   : logi FALSE

  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
 $ message   : logi FALSE

  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: C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoca414175fffe.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2\rmarkdown-stra414136a1bf5.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2/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 " C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2/3d.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) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: scatterplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
 $ warning   : logi FALSE

  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
 $ message   : logi FALSE

  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

No significant enrichments found.
  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: C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_i386/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoca41459b425a3.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2\rmarkdown-stra41447525e61.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpG03oh2/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 
  54.23    5.34   65.23


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 " C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi/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) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: scatterplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
 $ warning   : logi FALSE

  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
 $ message   : logi FALSE

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: C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandocba1876547ff2.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi\rmarkdown-strba1847517a7b.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi/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 " C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi/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) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: scatterplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
 $ warning   : logi FALSE

  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
 $ message   : logi FALSE

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: C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandocba185b2a6e46.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi\rmarkdown-strba1830e85ee5.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi/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 " C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi/2d.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) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: scatterplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
 $ warning   : logi FALSE

  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
 $ message   : logi FALSE

  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: C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandocba184591353c.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi\rmarkdown-strba1865035191.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi/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 " C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi/3d.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) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: scatterplot (with options) 
List of 5
 $ echo      : logi FALSE
 $ fig.height: num 6
 $ fig.width : num 6.5
 $ message   : logi FALSE
 $ warning   : logi FALSE

  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
 $ message   : logi FALSE

  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

No significant enrichments found.
  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: C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "C:/Users/biocbuild/bbs-3.13-bioc/meat/mitch.Rcheck/tests_x64/mitch.knit.md" --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandocba186f721e6a.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi\rmarkdown-strba1871ac5ded.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQLKVMi/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 
  56.23    4.75   66.00

CHECK results for mitch on tokay2

Summary

Command output

Installation output

Tests output

Example timings