##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mitch.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mitch_1.18.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mitch/DESCRIPTION’ ... OK
* this is package ‘mitch’ version ‘1.18.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 code 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 loading without being on the library search path ... 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        43.649  0.615  44.176
mitch_report 24.271  0.170  24.461
mitch_plots  17.900  0.286  18.186
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-mitch.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL mitch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 " /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/1d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/mitch_report.html --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.20-bioc/R/site-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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/rmarkdown-str3997f86644e52c.html 

Output created: /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/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 " /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/1d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/mitch_report.html --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.20-bioc/R/site-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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/rmarkdown-str3997f83b2ef2bd.html 

Output created: /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/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 " /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/2d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/mitch_report.html --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.20-bioc/R/site-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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/rmarkdown-str3997f823c63119.html 

Output created: /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/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 
There were 16 warnings (use warnings() to see them)
> if (file.exists("3d.html")) { unlink("3d.html") }
> mitch_report(res,"3d.html")
Dataset saved as " /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/3d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.20-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/mitch_report.html --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.20-bioc/R/site-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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/rmarkdown-str3997f837508148.html 

Output created: /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpBYhPer/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 
 60.900   1.539  62.267