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CHECK report for DASC on tokay2

This page was generated on 2018-01-15 07:24:42 -0500 (Mon, 15 Jan 2018).

Package 332/1478HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DASC 1.1.0
Haidong Yi
Snapshot Date: 2018-01-14 17:00:54 -0500 (Sun, 14 Jan 2018)
URL: https://git.bioconductor.org/packages/DASC
Branch: master
Last Commit: 173a443
Last Changed Date: 2017-10-30 12:54:31 -0500 (Mon, 30 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: DASC
Version: 1.1.0
Command: rm -rf DASC.buildbin-libdir DASC.Rcheck && mkdir DASC.buildbin-libdir DASC.Rcheck && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DASC.buildbin-libdir DASC_1.1.0.tar.gz >DASC.Rcheck\00install.out 2>&1 && cp DASC.Rcheck\00install.out DASC-install.out && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --library=DASC.buildbin-libdir --install="check:DASC-install.out" --force-multiarch --no-vignettes --timings DASC_1.1.0.tar.gz
StartedAt: 2018-01-14 23:24:50 -0500 (Sun, 14 Jan 2018)
EndedAt: 2018-01-14 23:27:36 -0500 (Sun, 14 Jan 2018)
EllapsedTime: 165.6 seconds
RetCode: 0
Status:  OK  
CheckDir: DASC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DASC.buildbin-libdir DASC.Rcheck && mkdir DASC.buildbin-libdir DASC.Rcheck && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DASC.buildbin-libdir DASC_1.1.0.tar.gz >DASC.Rcheck\00install.out 2>&1 && cp DASC.Rcheck\00install.out DASC-install.out  &&  C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --library=DASC.buildbin-libdir --install="check:DASC-install.out" --force-multiarch --no-vignettes --timings DASC_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DASC.Rcheck'
* using R Under development (unstable) (2018-01-02 r74023)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DASC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DASC' version '1.1.0'
* 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 'DASC' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
DASC 1.52   0.15   14.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
DASC 1.62   0.07   19.54
* 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

DASC.Rcheck/00install.out


install for i386

* installing *source* package 'DASC' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DASC'
    finding HTML links ... done
    DASC                                    html  
    Ini_SemiNMF                             html  
    Loss_Fro                                html  
    Semi_NMF                                html  
    Sptree                                  html  
    adj2vector                              html  
    get_father                              html  
    merge                                   html  
    stanfordData                            html  
    trans_ADJ                               html  
    trans_Laplace                           html  
    update_G                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DASC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DASC' as DASC_1.1.0.zip
* DONE (DASC)
In R CMD INSTALL
In R CMD INSTALL

Tests output

DASC.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2018-01-02 r74023) -- "Unsuffered Consequences"
Copyright (C) 2018 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(DASC)
> library(NMF)
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following objects are masked from 'package:base':

    isFALSE, isNamespaceLoaded

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 19/20

Attaching package: 'NMF'

The following object is masked from 'package:testthat':

    compare

> library(Biobase)
> library(cvxclustr)
Loading required package: Matrix
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:NMF':

    algorithm, compare

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("DASC")
== testthat results  ===========================================================
OK: 0 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.15    0.15    4.28 

DASC.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2018-01-02 r74023) -- "Unsuffered Consequences"
Copyright (C) 2018 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(DASC)
> library(NMF)
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following objects are masked from 'package:base':

    isFALSE, isNamespaceLoaded

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 19/20

Attaching package: 'NMF'

The following object is masked from 'package:testthat':

    compare

> library(Biobase)
> library(cvxclustr)
Loading required package: Matrix
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:NMF':

    algorithm, compare

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("DASC")
== testthat results  ===========================================================
OK: 0 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.09    0.15    5.23 

Example timings

DASC.Rcheck/examples_i386/DASC-Ex.timings

nameusersystemelapsed
DASC 1.52 0.1514.94
Sptree0.010.000.02
adj2vector000
get_father000
trans_ADJ0.010.000.02
trans_Laplace000
update_G000

DASC.Rcheck/examples_x64/DASC-Ex.timings

nameusersystemelapsed
DASC 1.62 0.0719.54
Sptree0.010.000.01
adj2vector000
get_father0.010.000.01
trans_ADJ0.040.000.04
trans_Laplace000
update_G000