Multiple platform build/check report for BioC 3.11 - CHECK report for ceRNAnetsim on tokay2

Package: ceRNAnetsim

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ceRNAnetsim.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ceRNAnetsim_1.0.0.tar.gz

StartedAt: 2020-10-17 02:27:12 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 02:31:10 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 238.3 seconds

RetCode: 0

Status: OK

CheckDir: ceRNAnetsim.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ceRNAnetsim.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ceRNAnetsim_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ceRNAnetsim.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.0.0'
* 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 13.84   0.03   13.88
simulate_vis            8.73   0.03    8.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
find_node_perturbation 15.09   0.03   17.03
simulate_vis            7.59   0.06   10.01
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ceRNAnetsim_1.0.0.tar.gz && rm -rf ceRNAnetsim.buildbin-libdir && mkdir ceRNAnetsim.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ceRNAnetsim.buildbin-libdir ceRNAnetsim_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ceRNAnetsim_1.0.0.zip && rm ceRNAnetsim_1.0.0.tar.gz ceRNAnetsim_1.0.0.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  12.1M      0 --:--:-- --:--:-- --:--:-- 12.5M

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_1.0.0.zip
* DONE (ceRNAnetsim)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ceRNAnetsim' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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 
  44.34    0.39   44.96


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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 
  31.57    0.23   32.25

name	user	system	elapsed
calc_perturbation	2.22	0.00	2.22
find_iteration	1.88	0.00	1.87
find_node_perturbation	13.84	0.03	13.88
priming_graph	0.72	0.01	0.73
simulate	1.44	0.00	1.44
simulate_vis	8.73	0.03	8.78
update_how	1.14	0.00	1.34
update_nodes	0.36	0.02	0.38
update_variables	0.27	0.03	0.34
vis_graph	1.48	0.00	2.06

name	user	system	elapsed
calc_perturbation	2.45	0.01	2.68
find_iteration	1.92	0.02	2.46
find_node_perturbation	15.09	0.03	17.03
priming_graph	0.65	0.00	0.66
simulate	1.55	0.02	1.81
simulate_vis	7.59	0.06	10.01
update_how	1.19	0.00	1.39
update_nodes	0.52	0.00	0.52
update_variables	0.44	0.00	0.44
vis_graph	1.43	0.01	1.45

CHECK report for ceRNAnetsim on tokay2

Summary

Command output

Installation output

Tests output

Example timings