Junfang Chen
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BioMM |
| Branch: master |
| Last Commit: c097a39 |
| Last Changed Date: 2019-02-14 05:21:17 -0400 (Thu, 14 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:39:13 -0400 (Tue, 09 Apr 2019).
| Package 158/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BioMM 0.99.11 Junfang Chen
| malbec2 | Linux (Ubuntu 18.04.2 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: BioMM |
| Version: 0.99.11 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioMM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioMM_0.99.11.tar.gz |
| StartedAt: 2019-04-08 23:31:49 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:33:54 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 124.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioMM.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:BioMM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioMM_0.99.11.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BioMM.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioMM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioMM’ version ‘0.99.11’
* 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 ‘BioMM’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predByCV 26.795 7.486 1.522
predByFS 8.073 3.908 0.680
BioMMstage1pca 7.027 3.657 2.662
getMetrics 3.990 2.302 1.025
getDataAfterFS 4.330 1.511 1.388
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTest.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
BioMM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BioMM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘BioMM’ ... ** R ** 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 * DONE (BioMM)
BioMM.Rcheck/tests/runTest.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.
> BiocGenerics:::testPackage("BioMM")
RUNIT TEST PROTOCOL -- Mon Apr 8 23:33:48 2019
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
BioMM RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.893 0.375 5.238
BioMM.Rcheck/BioMM-Ex.timings
| name | user | system | elapsed | |
| BioMM | 0.281 | 0.013 | 0.296 | |
| BioMMreconData | 0.411 | 0.025 | 0.437 | |
| BioMMstage1pca | 7.027 | 3.657 | 2.662 | |
| baseGLMnet | 0.721 | 0.068 | 0.790 | |
| baseModel | 0.729 | 0.080 | 0.761 | |
| baseRandForest | 0.486 | 0.055 | 0.485 | |
| baseSVM | 1.616 | 0.067 | 1.689 | |
| classifiACC | 0.323 | 0.092 | 0.818 | |
| getDataAfterFS | 4.330 | 1.511 | 1.388 | |
| getMetrics | 3.990 | 2.302 | 1.025 | |
| omics2chrlist | 0.288 | 0.067 | 0.356 | |
| omics2genelist | 0.135 | 0.004 | 0.138 | |
| omics2pathlist | 0.365 | 0.016 | 0.383 | |
| predByBS | 0.457 | 0.217 | 3.079 | |
| predByCV | 26.795 | 7.486 | 1.522 | |
| predByFS | 8.073 | 3.908 | 0.680 | |