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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mitch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings mitch_1.11.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mitch.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘mitch/DESCRIPTION’ ... OK
* this is package ‘mitch’ version ‘1.11.4’
* 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 ... 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 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 ... ERROR
Running examples in ‘mitch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mitch
> ### Title: mitch: An R package for multi-dimensional pathway enrichment
> ###   analysis
> ### Aliases: mitch
> 
> ### ** Examples
> 
> # Example workflow
> # Import some gene sets
> genesetsExample<-gmt_import(system.file('extdata/sample_genesets.gmt', 
+ package = 'mitch'))
> # Load some edgeR tables (rna, k9a, k36a). 
> data(rna,k9a,k36a)
> # Create a list of differential profiles
> myList<-list('rna'=rna,'k9a'=k9a,'k36a'=k36a)
> # Import as edgeR table 
> myImportedData<-mitch_import(myList,DEtype='edger')
Note: Mean no. genes in input = 1000
Note: no. genes in output = 1000
Note: estimated proportion of input genes in output = 1
> # Calculate enrichment using MANOVA
> resExample<-mitch_calc(myImportedData,genesetsExample,priority='effect',
+ resrows=5,cores=2)
Note: Enrichments with large effect sizes may not be 
            statistically significant.
> # Generate some high res plots in PDF format
> mitch_plots(resExample,outfile='outres.pdf')
Warning: The dot-dot notation (`..density..`) was deprecated in ggplot2 3.4.0.
ℹ Please use `after_stat(density)` instead.
ℹ The deprecated feature was likely used in the mitch package.
  Please report the issue to the authors.
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
Warning: Removed 396 rows containing missing values (`geom_tile()`).
pdf 
  2 
> #' Generate a report of the analysis in HTML format
> mitch_report(resExample,'outres.html')
Dataset saved as " /tmp/RtmpbO1r7F/outres.rds ".


processing file: mitch.Rmd
Quitting from lines 936-1272 (mitch.Rmd) 
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Calls: mitch_report ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-mitch.R’
 ERROR
Running the tests in ‘tests/test-mitch.R’ failed.
Last 13 lines of output:
              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 " /tmp/RtmpqrPcNE/3d.rds ".
  
  
  processing file: mitch.Rmd
  Quitting from lines 936-1272 (mitch.Rmd) 
  Error in xtfrm.data.frame(x) : cannot xtfrm data frames
  Calls: mitch_report ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘mitchWorkflow.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/mitch.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL mitch
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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/RtmpqrPcNE/1d.rds ".


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.17-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.17-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpqrPcNE/mitch_report.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpqrPcNE/rmarkdown-str20bfce14a0b147.html 

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


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.17-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.17-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpqrPcNE/mitch_report.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpqrPcNE/rmarkdown-str20bfce198fcfe6.html 

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


processing file: mitch.Rmd
output file: /home/biocbuild/bbs-3.17-bioc/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.17-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpqrPcNE/mitch_report.html --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpqrPcNE/rmarkdown-str20bfce5480a900.html 

Output created: /tmp/RtmpqrPcNE/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 " /tmp/RtmpqrPcNE/3d.rds ".


processing file: mitch.Rmd
Quitting from lines 936-1272 (mitch.Rmd) 
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Calls: mitch_report ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame
Execution halted