David Rasp
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BEclear |
| Branch: RELEASE_3_8 |
| Last Commit: e124e81 |
| Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:41 -0400 (Tue, 16 Apr 2019).
| Package 118/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BEclear 1.14.0 David Rasp
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BEclear |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BEclear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BEclear_1.14.0.tar.gz |
| StartedAt: 2019-04-15 22:32:52 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:34:11 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 79.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BEclear.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BEclear.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BEclear_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BEclear.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BEclear/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEclear’ version ‘1.14.0’
* 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 ‘BEclear’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BEclear-package 18.131 2.750 6.190
imputeMissingData 5.433 2.213 1.718
correctBatchEffect 4.056 2.458 1.935
clearBEgenes 3.988 1.285 0.942
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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
BEclear.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BEclear ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘BEclear’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: BEclear *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (BEclear)
BEclear.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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(testthat)
> library(BEclear)
Loading required package: BiocParallel
>
> test_check("BEclear")
INFO [2019-04-15 22:34:04] Calculating the medians for 2 batches
INFO [2019-04-15 22:34:04] Calculating the medians for 3 batches
INFO [2019-04-15 22:34:05] Calculating the p-values for 2 batches
INFO [2019-04-15 22:34:05] Calculating the p-values for 3 batches
INFO [2019-04-15 22:34:05] Calculating the p-values for 3 batches
INFO [2019-04-15 22:34:05] Adjusting p-values
INFO [2019-04-15 22:34:05] 3 wrong values found
INFO [2019-04-15 22:34:06] Replacing values below 0 or above 1:
INFO [2019-04-15 22:34:06] 3 values replaced
══ testthat results ═══════════════════════════════════════════════════════════
OK: 71 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
7.010 3.996 4.487
BEclear.Rcheck/BEclear-Ex.timings
| name | user | system | elapsed | |
| BEclear-package | 18.131 | 2.750 | 6.190 | |
| calcMedians | 0.426 | 0.413 | 0.167 | |
| calcPvalues | 2.274 | 1.242 | 0.831 | |
| calcScore | 3.469 | 1.406 | 0.997 | |
| calcSummary | 2.646 | 1.647 | 1.016 | |
| clearBEgenes | 3.988 | 1.285 | 0.942 | |
| correctBatchEffect | 4.056 | 2.458 | 1.935 | |
| countValuesToPredict | 2.871 | 2.111 | 1.040 | |
| findWrongValues | 0.471 | 0.026 | 0.498 | |
| imputeMissingData | 5.433 | 2.213 | 1.718 | |
| makeBoxplot | 2.687 | 2.066 | 1.020 | |
| replaceWrongValues | 0.593 | 0.028 | 0.624 | |