Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1279/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mitch 1.19.3 (landing page) Mark Ziemann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the mitch package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mitch.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
Package: mitch |
Version: 1.19.3 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mitch.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mitch_1.19.3.tar.gz |
StartedAt: 2024-12-23 23:54:58 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-24 00:04:14 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 555.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mitch.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mitch.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mitch_1.19.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘1.19.3’ * 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 ... 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 48.682 0.930 49.519 mitch_report 27.177 0.355 27.554 mitch_plots 20.116 0.387 20.505 * 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
mitch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL mitch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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)
mitch.Rcheck/tests/test-mitch.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 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 " /tmp/RtmpiGPFBk/1d.rds ". processing file: mitch.Rmd output file: /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md /usr/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 /tmp/RtmpiGPFBk/mitch_report.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.21-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 /tmp/RtmpiGPFBk/rmarkdown-str1628e81bab0754.html Output created: /tmp/RtmpiGPFBk/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/RtmpiGPFBk/1d.rds ". processing file: mitch.Rmd output file: /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md /usr/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 /tmp/RtmpiGPFBk/mitch_report.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.21-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 /tmp/RtmpiGPFBk/rmarkdown-str1628e81aa43dbe.html Output created: /tmp/RtmpiGPFBk/mitch_report.html [1] TRUE > > test_that("1d works", { + expect_true(file.info("1d.html")$size>1000000) + }) Test passed 🌈 > > unlink("1d.html") > > > > # 2d > data(rna,k9a,genesetsExample) > x<-list("rna"=rna,"k9a"=k9a) > y<-mitch_import(x,DEtype="edgeR") Note: Mean no. genes in input = 1000 Note: no. genes in output = 1000 Note: estimated proportion of input genes in output = 1 > res<-mitch_calc(y,genesetsExample,cores=2) Note: When prioritising by significance (ie: small p-values), large effect sizes might be missed. > mitch_plots(res,outfile="2d.pdf") null device 1 > if (file.exists("2d.html")) { unlink("2d.html") } > mitch_report(res,"2d.html") Dataset saved as " /tmp/RtmpiGPFBk/2d.rds ". processing file: mitch.Rmd output file: /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md /usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiGPFBk/mitch_report.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpiGPFBk/rmarkdown-str1628e85ca0b730.html Output created: /tmp/RtmpiGPFBk/mitch_report.html [1] TRUE > > test_that("2d works", { + expect_equal( length(which(res$enrichment_result$p.adjustMANOVA<0.1)) ,1) + expect_true(file.info("2d.pdf")$size>100000) + expect_true(file.info("2d.html")$size>1000000) + }) Test passed 😸 > > unlink("2d.html") > unlink("2d.pdf") > > # 3d > data(rna,k9a,k36a,genesetsExample) > x<-list("rna"=rna,"k9a"=k9a,"k36a"=k36a) > y<-mitch_import(x,DEtype="edgeR") Note: Mean no. genes in input = 1000 Note: no. genes in output = 1000 Note: estimated proportion of input genes in output = 1 > res<-mitch_calc(y,genesetsExample,cores=2) Note: When prioritising by significance (ie: small p-values), large effect sizes might be missed. > mitch_plots(res,outfile="3d.pdf") null device 1 There were 16 warnings (use warnings() to see them) > if (file.exists("3d.html")) { unlink("3d.html") } > mitch_report(res,"3d.html") Dataset saved as " /tmp/RtmpiGPFBk/3d.rds ". processing file: mitch.Rmd output file: /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md /usr/bin/pandoc +RTS -K512m -RTS /home/biocbuild/bbs-3.21-bioc/meat/mitch.Rcheck/tests/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiGPFBk/mitch_report.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpiGPFBk/rmarkdown-str1628e8733eabd7.html Output created: /tmp/RtmpiGPFBk/mitch_report.html [1] TRUE > > test_that("3d works", { + expect_equal( length(which(res$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 65.153 2.096 67.055
mitch.Rcheck/mitch-Ex.timings
name | user | system | elapsed | |
genesetsExample | 0.007 | 0.001 | 0.007 | |
gmt_import | 0.01 | 0.00 | 0.01 | |
k36a | 0.003 | 0.001 | 0.005 | |
k9a | 0.004 | 0.000 | 0.005 | |
mitch | 48.682 | 0.930 | 49.519 | |
mitch_calc | 0.205 | 0.144 | 0.235 | |
mitch_import | 0.020 | 0.001 | 0.020 | |
mitch_plots | 20.116 | 0.387 | 20.505 | |
mitch_report | 27.177 | 0.355 | 27.554 | |
myImportedData | 0.004 | 0.000 | 0.004 | |
myList | 0.009 | 0.000 | 0.010 | |
resExample | 0.010 | 0.001 | 0.012 | |
rna | 0.004 | 0.000 | 0.005 | |