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CHECK report for MOSim on malbec1

This page was generated on 2020-04-15 12:16:06 -0400 (Wed, 15 Apr 2020).

Package 1084/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOSim 1.0.2
Carlos Martínez
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/MOSim
Branch: RELEASE_3_10
Last Commit: 753625b
Last Changed Date: 2020-04-03 12:12:15 -0400 (Fri, 03 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 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MOSim
Version: 1.0.2
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MOSim.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MOSim_1.0.2.tar.gz
StartedAt: 2020-04-15 06:49:39 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:58:17 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 518.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MOSim.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MOSim.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MOSim_1.0.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MOSim.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotProfile        81.556  0.172  81.953
omicSettings       75.416  0.268  76.087
omicResults        70.728  0.096  70.978
experimentalDesign 69.096  0.244  69.505
mosim              65.140  0.108  65.393
omicSim             7.632  0.048   7.769
omicData            5.540  0.084   5.654
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

MOSim.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MOSim
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* 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
** 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
* DONE (MOSim)

Tests output

MOSim.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 34.184   0.532  34.844 

Example timings

MOSim.Rcheck/MOSim-Ex.timings

nameusersystemelapsed
experimentalDesign69.096 0.24469.505
mosim65.140 0.10865.393
omicData5.5400.0845.654
omicResults70.728 0.09670.978
omicSettings75.416 0.26876.087
omicSim7.6320.0487.769
plotProfile81.556 0.17281.953