Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for sparsenetgls on merida1

This page was generated on 2019-04-16 12:12:29 -0400 (Tue, 16 Apr 2019).

Package 1482/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparsenetgls 1.0.1
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)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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


Installation output

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)

Tests output

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 

Example timings

sparsenetgls.Rcheck/sparsenetgls-Ex.timings

nameusersystemelapsed
assess_direct0.0000.0000.001
bandprec0.0210.0040.025
convertbeta0.3380.0070.347
glassonet20.6180.0020.626
lassoglmnet0.0220.0000.023
path_result_for_roc0.0020.0000.002
plot_roc0.0050.0000.006
plotsngls3.3780.0403.452
sparsenetgls15.470 1.45417.070