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CHECK report for ceRNAnetsim on tokay1

This page was generated on 2020-08-07 12:19:15 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ceRNAnetsim PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 251/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ceRNAnetsim 1.1.0
Selcen Ari Yuka
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/ceRNAnetsim
Branch: master
Last Commit: 8ace956
Last Changed Date: 2020-04-27 15:32:45 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ceRNAnetsim
Version: 1.1.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ceRNAnetsim.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ceRNAnetsim_1.1.0.tar.gz
StartedAt: 2020-08-07 05:57:35 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 06:01:11 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 216.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ceRNAnetsim.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ceRNAnetsim.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ceRNAnetsim_1.1.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ceRNAnetsim.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ceRNAnetsim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ceRNAnetsim' 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 'ceRNAnetsim' 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 (user + system) or elapsed time > 5s
                        user system elapsed
find_node_perturbation 12.90   0.00   12.91
simulate_vis            5.98   0.02    6.00
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
find_node_perturbation 20.76   0.01   21.20
simulate_vis            8.50   0.05    8.54
* 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

ceRNAnetsim.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ceRNAnetsim_1.1.0.tar.gz && rm -rf ceRNAnetsim.buildbin-libdir && mkdir ceRNAnetsim.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ceRNAnetsim.buildbin-libdir ceRNAnetsim_1.1.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ceRNAnetsim_1.1.0.zip && rm ceRNAnetsim_1.1.0.tar.gz ceRNAnetsim_1.1.0.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 2226k  100 2226k    0     0  6193k      0 --:--:-- --:--:-- --:--:-- 6254k

install for i386

* installing *source* package 'ceRNAnetsim' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ceRNAnetsim'
    finding HTML links ... done
    TCGA_E9_A1N5_mirnanormal                html  
    TCGA_E9_A1N5_mirnatumor                 html  
    TCGA_E9_A1N5_normal                     html  
    TCGA_E9_A1N5_tumor                      html  
    calc_perturbation                       html  
    find_iteration                          html  
    find_node_perturbation                  html  
    gene_knockdown                          html  
    huge_example                            html  
    midsamp                                 html  
    midsamp_new_counts                      html  
    minsamp                                 html  
    mirtarbasegene                          html  
    new_counts                              html  
    normalize                               html  
    prepare_rhs                             html  
    prepare_rhs_once                        html  
    priming_graph                           html  
    simulate                                html  
    simulate_vis                            html  
    update_how                              html  
    update_nodes                            html  
    update_variables                        html  
    vis_graph                               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 'ceRNAnetsim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ceRNAnetsim' as ceRNAnetsim_1.1.0.zip
* DONE (ceRNAnetsim)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ceRNAnetsim' successfully unpacked and MD5 sums checked

Tests output

ceRNAnetsim.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(ceRNAnetsim)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidygraph

Attaching package: 'tidygraph'

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

    matches

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

    filter


Attaching package: 'ceRNAnetsim'

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

    simulate

> 
> 
> test_check("ceRNAnetsim")
== testthat results  ===========================================================
[ OK: 30 | SKIPPED: 0 | WARNINGS: 36 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  30.07    0.23   30.28 

ceRNAnetsim.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(ceRNAnetsim)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidygraph

Attaching package: 'tidygraph'

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

    matches

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

    filter


Attaching package: 'ceRNAnetsim'

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

    simulate

> 
> 
> test_check("ceRNAnetsim")
== testthat results  ===========================================================
[ OK: 30 | SKIPPED: 0 | WARNINGS: 36 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  33.46    0.20   33.65 

Example timings

ceRNAnetsim.Rcheck/examples_i386/ceRNAnetsim-Ex.timings

nameusersystemelapsed
calc_perturbation1.50.01.5
find_iteration1.470.001.47
find_node_perturbation12.90 0.0012.91
priming_graph0.510.010.53
simulate1.020.001.02
simulate_vis5.980.026.00
update_how1.050.001.05
update_nodes0.310.000.31
update_variables0.320.000.31
vis_graph1.210.001.22

ceRNAnetsim.Rcheck/examples_x64/ceRNAnetsim-Ex.timings

nameusersystemelapsed
calc_perturbation2.790.002.79
find_iteration2.670.002.67
find_node_perturbation20.76 0.0121.20
priming_graph0.880.000.87
simulate1.550.021.57
simulate_vis8.500.058.54
update_how1.260.001.27
update_nodes0.480.000.49
update_variables0.450.000.45
vis_graph1.800.001.79