Package: MOSim

Version: 1.0.2

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MOSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MOSim_1.0.2.tar.gz

StartedAt: 2020-04-15 04:54:12 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:07:52 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 820.2 seconds

RetCode: 0

Status:  OK

CheckDir: MOSim.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MOSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MOSim_1.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MOSim.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MOSim/DESCRIPTION' ... OK
* this is package 'MOSim' version '1.0.2'
* 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 'MOSim' 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
plotProfile        83.48   0.46   84.03
omicSettings       69.19   0.75   69.97
mosim              59.32   0.22   59.55
omicResults        59.11   0.03   59.20
experimentalDesign 48.69   0.33   49.01
omicSim             9.44   0.03    9.47
omicData            5.91   0.11    6.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotProfile        74.27   0.44   74.71
experimentalDesign 65.71   0.56   66.36
omicSettings       59.62   0.89   60.52
omicResults        47.80   0.10   47.92
mosim              45.88   0.08   45.96
omicSim             5.22   0.04    5.26
* 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://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/MOSim_1.0.2.tar.gz && rm -rf MOSim.buildbin-libdir && mkdir MOSim.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MOSim.buildbin-libdir MOSim_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MOSim_1.0.2.zip && rm MOSim_1.0.2.tar.gz MOSim_1.0.2.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 4365k  100 4365k    0     0  53.6M      0 --:--:-- --:--:-- --:--:-- 56.0M

install for i386

* installing *source* package 'MOSim' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'simulate' in package 'MOSim'
** help
*** installing help indices
  converting help for package 'MOSim'
    finding HTML links ... done
    MOSim-package                           html  
    MOSimulation-class                      html  
    MOSimulator-class                       html  
    Simulator-class                         html  
    experimentalDesign                      html  
    is.declared                             html  
    mosim                                   html  
    omicData                                html  
    omicResults                             html  
    omicSettings                            html  
    omicSim                                 html  
    plotProfile                             html  
    sampleData                              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 'MOSim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MOSim' as MOSim_1.0.2.zip
* DONE (MOSim)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MOSim' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(MOSim)
> 
> test_check("MOSim")
Simulation settings of class MOSimulation:
- Default depth: 74
- Total genes: 200
- Dif. expressed genes: 30
- Replicates: 3
- Factor levels (groups): 2
- Time vector length: 5
Simulation settings of class MOSimulation:
- Default depth: 74
- Total genes: 200
- Dif. expressed genes: 30
- Replicates: 3
- Factor levels (groups): 2
- Time vector length: 5
Simulation settings of class MOSimulation:
- Default depth: 74
- Total genes: 20
- Dif. expressed genes: 3
- Replicates: 3
- Factor levels (groups): 2
- Time vector length: 3
Simulation settings of class MOSimulation:
- Default depth: 74
- Total genes: 300
- Dif. expressed genes: 45
- Replicates: 3
- Factor levels (groups): 2
- Time vector length: 5
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  36.45    0.65   37.14 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(MOSim)
> 
> test_check("MOSim")
Simulation settings of class MOSimulation:
- Default depth: 74
- Total genes: 200
- Dif. expressed genes: 30
- Replicates: 3
- Factor levels (groups): 2
- Time vector length: 5
Simulation settings of class MOSimulation:
- Default depth: 74
- Total genes: 200
- Dif. expressed genes: 30
- Replicates: 3
- Factor levels (groups): 2
- Time vector length: 5
Simulation settings of class MOSimulation:
- Default depth: 74
- Total genes: 20
- Dif. expressed genes: 3
- Replicates: 3
- Factor levels (groups): 2
- Time vector length: 3
Simulation settings of class MOSimulation:
- Default depth: 74
- Total genes: 300
- Dif. expressed genes: 45
- Replicates: 3
- Factor levels (groups): 2
- Time vector length: 5
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  24.81    0.46   25.28