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CHECK report for RandomWalkRestartMH on tokay1

This page was generated on 2019-04-13 11:29:16 -0400 (Sat, 13 Apr 2019).

Package 1247/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RandomWalkRestartMH 1.2.0
Alberto Valdeolivas Urbelz
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/RandomWalkRestartMH
Branch: RELEASE_3_8
Last Commit: f360f5c
Last Changed Date: 2018-10-30 11:42:09 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: RandomWalkRestartMH
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RandomWalkRestartMH.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RandomWalkRestartMH_1.2.0.tar.gz
StartedAt: 2019-04-13 04:51:09 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:53:28 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 139.5 seconds
RetCode: 0
Status:  OK  
CheckDir: RandomWalkRestartMH.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RandomWalkRestartMH.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RandomWalkRestartMH_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RandomWalkRestartMH.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RandomWalkRestartMH/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RandomWalkRestartMH' version '1.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'RandomWalkRestartMH' 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
** running examples for arch 'x64' ... OK
* 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

RandomWalkRestartMH.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RandomWalkRestartMH_1.2.0.tar.gz && rm -rf RandomWalkRestartMH.buildbin-libdir && mkdir RandomWalkRestartMH.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RandomWalkRestartMH.buildbin-libdir RandomWalkRestartMH_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RandomWalkRestartMH_1.2.0.zip && rm RandomWalkRestartMH_1.2.0.tar.gz RandomWalkRestartMH_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  394k  100  394k    0     0  10.0M      0 --:--:-- --:--:-- --:--:-- 11.0M

install for i386

* installing *source* package 'RandomWalkRestartMH' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RandomWalkRestartMH'
    finding HTML links ... done
    Disease_Network                         html  
    GeneDiseaseRelations                    html  
    PPI_Network                             html  
    Pathway_Network                         html  
    Random.Walk.Restart.Multiplex           html  
    Random.Walk.Restart.MultiplexHet        html  
    compute.adjacency.matrix                html  
    compute.transition.matrix               html  
    create.multiplex                        html  
    create.multiplexHet                     html  
    create.multiplexHetNetwork.topResults   html  
    create.multiplexNetwork.topResults      html  
    isMultiplex                             html  
    isMultiplexHet                          html  
    isRWRMH_Results                         html  
    isRWRM_Results                          html  
    normalize.multiplex.adjacency           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RandomWalkRestartMH' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RandomWalkRestartMH' as RandomWalkRestartMH_1.2.0.zip
* DONE (RandomWalkRestartMH)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RandomWalkRestartMH' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

RandomWalkRestartMH.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(RandomWalkRestartMH)
> 
> test_check("RandomWalkRestartMH")
== testthat results  ===========================================================
OK: 10 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.53    0.15    2.67

RandomWalkRestartMH.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(RandomWalkRestartMH)
> 
> test_check("RandomWalkRestartMH")
== testthat results  ===========================================================
OK: 10 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.68    0.14    2.81

Example timings

RandomWalkRestartMH.Rcheck/examples_i386/RandomWalkRestartMH-Ex.timings

nameusersystemelapsed
Random.Walk.Restart.Multiplex0.210.000.21
Random.Walk.Restart.MultiplexHet0.20.00.2
compute.adjacency.matrix0.030.000.03
compute.transition.matrix0.080.000.08
create.multiplex0.010.000.01
create.multiplexHet0.050.000.05
create.multiplexHetNetwork.topResults0.190.000.19
create.multiplexNetwork.topResults0.060.000.06
isMultiplex0.020.000.02
isMultiplexHet0.040.000.04
isRWRMH_Results0.110.000.11
isRWRM_Results0.250.000.25
normalize.multiplex.adjacency0.030.000.03

RandomWalkRestartMH.Rcheck/examples_x64/RandomWalkRestartMH-Ex.timings

nameusersystemelapsed
Random.Walk.Restart.Multiplex0.220.000.22
Random.Walk.Restart.MultiplexHet0.220.000.22
compute.adjacency.matrix0.030.000.04
compute.transition.matrix0.160.000.15
create.multiplex0.010.000.02
create.multiplexHet0.050.000.04
create.multiplexHetNetwork.topResults0.120.000.13
create.multiplexNetwork.topResults0.080.000.08
isMultiplex0.020.000.01
isMultiplexHet0.040.000.05
isRWRMH_Results0.110.000.11
isRWRM_Results0.250.000.25
normalize.multiplex.adjacency0.030.000.03