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CHECK report for sparsenetgls on tokay2

This page was generated on 2019-10-16 12:42:23 -0400 (Wed, 16 Oct 2019).

Package 1558/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparsenetgls 1.2.0
Irene Zeng
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/sparsenetgls
Branch: RELEASE_3_9
Last Commit: f936663
Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sparsenetgls
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sparsenetgls.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings sparsenetgls_1.2.0.tar.gz
StartedAt: 2019-10-16 07:15:23 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:17:52 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 148.8 seconds
RetCode: 0
Status:  OK  
CheckDir: sparsenetgls.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sparsenetgls.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings sparsenetgls_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/sparsenetgls.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sparsenetgls/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sparsenetgls' version '1.2.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
sparsenetgls 12.38   1.81   14.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
sparsenetgls 12.96   2.03   14.99
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/sparsenetgls_1.2.0.tar.gz && rm -rf sparsenetgls.buildbin-libdir && mkdir sparsenetgls.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sparsenetgls.buildbin-libdir sparsenetgls_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL sparsenetgls_1.2.0.zip && rm sparsenetgls_1.2.0.tar.gz sparsenetgls_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 19516  100 19516    0     0   129k      0 --:--:-- --:--:-- --:--:--  135k

install for i386

* installing *source* package 'sparsenetgls' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sparsenetgls'
    finding HTML links ... done
    assess_direct                           html  
    bandprec                                html  
    convertbeta                             html  
    glassonet2                              html  
    lassoglmnet                             html  
    path_result_for_roc                     html  
    plot_roc                                html  
    plotsngls                               html  
    sparsenetgls                            html  
** 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

install for x64

* installing *source* package 'sparsenetgls' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sparsenetgls' as sparsenetgls_1.2.0.zip
* DONE (sparsenetgls)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'sparsenetgls' successfully unpacked and MD5 sums checked

Tests output

sparsenetgls.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 20%
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: 10%
Conducting the graphical lasso (glasso) wtih lossy screening....in progress: 20%
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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.39    3.43   15.79 

sparsenetgls.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.23    2.71   14.93 

Example timings

sparsenetgls.Rcheck/examples_i386/sparsenetgls-Ex.timings

nameusersystemelapsed
assess_direct000
bandprec0.010.000.01
convertbeta0.290.000.30
glassonet20.820.000.92
lassoglmnet0.030.000.03
path_result_for_roc000
plot_roc0.010.000.01
plotsngls2.470.112.58
sparsenetgls12.38 1.8114.19

sparsenetgls.Rcheck/examples_x64/sparsenetgls-Ex.timings

nameusersystemelapsed
assess_direct000
bandprec0.030.000.03
convertbeta0.270.020.28
glassonet20.840.000.93
lassoglmnet0.020.000.01
path_result_for_roc000
plot_roc0.010.000.02
plotsngls2.890.092.98
sparsenetgls12.96 2.0314.99