##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:mitch.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mitch_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitch/DESCRIPTION’ ... OK
* this is package ‘mitch’ version ‘1.19.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘mitch’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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        69.847  1.084  71.765
mitch_report 37.951  0.178  38.252
mitch_plots  29.444  0.343  29.847
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL mitch
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘mitch’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (mitch)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
Warning: program compiled against libxml 212 using older 211
> 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/tmp/RtmpZLSeNU/1d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/home/biocbuild/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/tmp/RtmpZLSeNU/mitch_report.html --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/tmp/RtmpZLSeNU/rmarkdown-str1784603c1be442.html 

Output created: /home/biocbuild/tmp/RtmpZLSeNU/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/tmp/RtmpZLSeNU/1d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/home/biocbuild/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/tmp/RtmpZLSeNU/mitch_report.html --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/tmp/RtmpZLSeNU/rmarkdown-str1784605f9a0e46.html 

Output created: /home/biocbuild/tmp/RtmpZLSeNU/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/tmp/RtmpZLSeNU/2d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/home/biocbuild/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/tmp/RtmpZLSeNU/mitch_report.html --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/tmp/RtmpZLSeNU/rmarkdown-str178460106c1ff3.html 

Output created: /home/biocbuild/tmp/RtmpZLSeNU/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/tmp/RtmpZLSeNU/3d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/home/biocbuild/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/tmp/RtmpZLSeNU/mitch_report.html --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/tmp/RtmpZLSeNU/rmarkdown-str1784604e472405.html 

Output created: /home/biocbuild/tmp/RtmpZLSeNU/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 
 93.113   1.647  94.896