Irene Zeng
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/sparsenetgls |
| Branch: RELEASE_3_8 |
| Last Commit: 1eec6fe |
| Last Changed Date: 2019-01-04 13:51:14 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:12:29 -0400 (Tue, 16 Apr 2019).
| Package 1482/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sparsenetgls 1.0.1 Irene Zeng
| 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: sparsenetgls |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sparsenetgls.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sparsenetgls_1.0.1.tar.gz |
| StartedAt: 2019-04-16 02:55:20 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:57:03 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 103.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sparsenetgls.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:sparsenetgls.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sparsenetgls_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/sparsenetgls.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 ‘sparsenetgls/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparsenetgls’ version ‘1.0.1’
* 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 ‘sparsenetgls’ 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 or elapsed time > 5s
user system elapsed
sparsenetgls 15.47 1.454 17.07
* 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
sparsenetgls.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sparsenetgls ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘sparsenetgls’ ... ** R ** data *** moving datasets to lazyload DB ** 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 (sparsenetgls)
sparsenetgls.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(lme4)
Loading required package: Matrix
> library(Matrix)
> library(MASS)
> library(sparsenetgls)
>
> test_check("sparsenetgls")
The input is identified as the covariance matrix.
Conducting the graphical lasso (glasso) wtih lossless screening....in progress: 19%
Conducting the graphical lasso (glasso) wtih lossless screening....in progress: 40%
Conducting the graphical lasso (glasso) wtih lossless screening....in progress: 60%
Conducting the graphical lasso (glasso)....done.
The input is identified as the covariance matrix.
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 9%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 19%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 30%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 40%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 50%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 60%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 70%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 80%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 90%
Conducting the graphical lasso (glasso)....done.
══ testthat results ═══════════════════════════════════════════════════════════
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
15.561 4.390 20.070
sparsenetgls.Rcheck/sparsenetgls-Ex.timings
| name | user | system | elapsed | |
| assess_direct | 0.000 | 0.000 | 0.001 | |
| bandprec | 0.021 | 0.004 | 0.025 | |
| convertbeta | 0.338 | 0.007 | 0.347 | |
| glassonet2 | 0.618 | 0.002 | 0.626 | |
| lassoglmnet | 0.022 | 0.000 | 0.023 | |
| path_result_for_roc | 0.002 | 0.000 | 0.002 | |
| plot_roc | 0.005 | 0.000 | 0.006 | |
| plotsngls | 3.378 | 0.040 | 3.452 | |
| sparsenetgls | 15.470 | 1.454 | 17.070 | |