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This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1255/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitch 1.12.0  (landing page)
Mark Ziemann
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/mitch
git_branch: RELEASE_3_17
git_last_commit: 6e6a434
git_last_commit_date: 2023-04-25 11:14:23 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for mitch on kjohnson2


To the developers/maintainers of the mitch package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: mitch
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mitch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mitch_1.12.0.tar.gz
StartedAt: 2023-10-18 08:15:32 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 08:22:13 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 400.5 seconds
RetCode: 0
Status:   OK  
CheckDir: mitch.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mitch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mitch_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitch/DESCRIPTION’ ... OK
* this is package ‘mitch’ version ‘1.12.0’
* 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 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        57.694  1.637  93.956
mitch_report 33.343  0.672  52.081
mitch_plots  23.091  0.433  35.944
* 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: OK


Installation output

mitch.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output

mitch.Rcheck/tests/test-mitch.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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/Rtmp2XIhvG/1d.rds ".


processing file: mitch.Rmd
output file: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp2XIhvG/mitch_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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/Rtmp2XIhvG/rmarkdown-str70376fe17161.html 

Output created: /tmp/Rtmp2XIhvG/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/Rtmp2XIhvG/1d.rds ".


processing file: mitch.Rmd
output file: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp2XIhvG/mitch_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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/Rtmp2XIhvG/rmarkdown-str70374877e81d.html 

Output created: /tmp/Rtmp2XIhvG/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/Rtmp2XIhvG/2d.rds ".


processing file: mitch.Rmd
output file: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp2XIhvG/mitch_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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/Rtmp2XIhvG/rmarkdown-str70371a45b09e.html 

Output created: /tmp/Rtmp2XIhvG/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/Rtmp2XIhvG/3d.rds ".


processing file: mitch.Rmd
output file: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck/tests/mitch.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp2XIhvG/mitch_report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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/Rtmp2XIhvG/rmarkdown-str70374d61a1b8.html 

Output created: /tmp/Rtmp2XIhvG/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 
 78.082   3.033 126.625 

Example timings

mitch.Rcheck/mitch-Ex.timings

nameusersystemelapsed
genesetsExample0.0090.0020.014
gmt_import0.0130.0020.022
k36a0.0050.0020.010
k9a0.0050.0020.010
mitch57.694 1.63793.956
mitch_calc0.2620.1540.491
mitch_import0.0250.0060.045
mitch_plots23.091 0.43335.944
mitch_report33.343 0.67252.081
myImportedData0.0050.0030.012
myList0.0110.0030.021
resExample0.0130.0030.026
rna0.0050.0030.011