Mark Ziemann
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/mitch |
| Branch: master |
| Last Commit: 2493c0d |
| Last Changed Date: 2019-12-16 23:41:09 -0500 (Mon, 16 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:56:10 -0500 (Thu, 16 Jan 2020).
| Package 1062/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mitch 0.99.26 Mark Ziemann
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: mitch |
| Version: 0.99.26 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mitch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mitch_0.99.26.tar.gz |
| StartedAt: 2020-01-16 06:36:21 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 06:43:36 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 435.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mitch.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mitch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mitch_0.99.26.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/mitch.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mitch/DESCRIPTION’ ... OK
* this is package ‘mitch’ version ‘0.99.26’
* 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 102.695 4.833 109.639
mitch_report 62.730 3.716 67.985
mitch_plots 34.230 1.006 35.307
* 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
mitch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mitch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)
mitch.Rcheck/tests/test-mitch.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
+ })
>
> # 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/Rtmpr8486N/1d.RData ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
Contour plot does not apply to unidimensional analysis.
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: /Users/biocbuild/bbs-3.11-bioc/meat/mitch.Rcheck/tests/mitch.knit.md
/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.11-bioc/meat/mitch.Rcheck/tests/mitch.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output /tmp/Rtmpr8486N/mitch_report.html --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /tmp/Rtmpr8486N/rmarkdown-str8c545143ea9c.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/lua/latex-div.lua
Output created: /tmp/Rtmpr8486N/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>4000000)
+ })
>
> unlink("1d.html")
> unlink("1d.pdf")
>
>
> # 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/Rtmpr8486N/2d.RData ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: /Users/biocbuild/bbs-3.11-bioc/meat/mitch.Rcheck/tests/mitch.knit.md
/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.11-bioc/meat/mitch.Rcheck/tests/mitch.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output /tmp/Rtmpr8486N/mitch_report.html --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /tmp/Rtmpr8486N/rmarkdown-str8c546ea440ab.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/lua/latex-div.lua
Output created: /tmp/Rtmpr8486N/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)
+ })
>
> 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
> if (file.exists("3d.html")) { unlink("3d.html") }
> mitch_report(res,"3d.html")
Dataset saved as " /tmp/Rtmpr8486N/3d.RData ".
processing file: mitch.Rmd
inline R code fragments
label: checklibraries (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: peek (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: metrics (with options)
List of 1
$ echo: logi FALSE
ordinary text without R code
label: scatterplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ message : logi FALSE
$ warning : logi FALSE
ordinary text without R code
label: contourplot (with options)
List of 5
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6.5
$ warning : logi FALSE
$ message : logi FALSE
ordinary text without R code
label: input_geneset_metrics1 (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: input_geneset_metrics2 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
ordinary text without R code
label: input_geneset_metrics3 (with options)
List of 5
$ results : chr "asis"
$ echo : logi FALSE
$ message : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
ordinary text without R code
label: echart1d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
label: echart2d (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
No significant enrichments found.
ordinary text without R code
label: heatmap (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 10
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: effectsize (with options)
List of 6
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 7
$ fig.width : num 7
$ fig.show : chr "all"
$ message : logi FALSE
ordinary text without R code
label: results_table (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: results_table_complete (with options)
List of 2
$ results: chr "asis"
$ echo : logi FALSE
ordinary text without R code
label: detailed_geneset_reports1d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 6
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: detailed_geneset_reports2d (with options)
List of 7
$ results : chr "asis"
$ echo : logi FALSE
$ fig.height: num 5
$ fig.width : num 6
$ out.width : chr "80%"
$ comment : logi NA
$ message : logi FALSE
ordinary text without R code
label: session_info (with options)
List of 3
$ include: logi TRUE
$ echo : logi TRUE
$ results: chr "markup"
ordinary text without R code
output file: /Users/biocbuild/bbs-3.11-bioc/meat/mitch.Rcheck/tests/mitch.knit.md
/usr/local/bin/pandoc +RTS -K512m -RTS /Users/biocbuild/bbs-3.11-bioc/meat/mitch.Rcheck/tests/mitch.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output /tmp/Rtmpr8486N/mitch_report.html --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /tmp/Rtmpr8486N/rmarkdown-str8c5470ce14d4.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown/rmd/lua/latex-div.lua
Output created: /tmp/Rtmpr8486N/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)
+ })
>
> unlink("3d.html")
> unlink("3d.pdf")
>
>
>
> proc.time()
user system elapsed
136.692 9.830 147.833
mitch.Rcheck/mitch-Ex.timings
| name | user | system | elapsed | |
| genesetsExample | 0.014 | 0.005 | 0.020 | |
| gmt_import | 0.037 | 0.003 | 0.041 | |
| k36a | 0.004 | 0.005 | 0.009 | |
| k9a | 0.006 | 0.006 | 0.011 | |
| mitch | 102.695 | 4.833 | 109.639 | |
| mitch_calc | 0.600 | 0.427 | 0.677 | |
| mitch_import | 0.042 | 0.019 | 0.060 | |
| mitch_plots | 34.230 | 1.006 | 35.307 | |
| mitch_report | 62.730 | 3.716 | 67.985 | |
| myImportedData | 0.007 | 0.005 | 0.012 | |
| myList | 0.013 | 0.005 | 0.018 | |
| resExample | 0.020 | 0.006 | 0.026 | |
| rna | 0.006 | 0.005 | 0.011 | |