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CHECK report for methInheritSim on tokay1

This page was generated on 2021-05-06 12:32:12 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the methInheritSim package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1066/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methInheritSim 1.12.0  (landing page)
Pascal Belleau
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/methInheritSim
Branch: RELEASE_3_12
Last Commit: 36e0739
Last Changed Date: 2020-10-27 11:24:40 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: methInheritSim
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methInheritSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings methInheritSim_1.12.0.tar.gz
StartedAt: 2021-05-06 04:29:29 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:38:01 -0400 (Thu, 06 May 2021)
EllapsedTime: 511.5 seconds
RetCode: 0
Status:   OK   
CheckDir: methInheritSim.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:methInheritSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings methInheritSim_1.12.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/methInheritSim.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methInheritSim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methInheritSim' version '1.12.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'methInheritSim' 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
samplesForChrSynthetic 22.17   0.03   22.22
runSim                 12.39   0.18   12.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
samplesForChrSynthetic 16.99   0.01   17.00
runSim                  7.66   0.03    7.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/methInheritSim.Rcheck/00check.log'
for details.



Installation output

methInheritSim.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/methInheritSim_1.12.0.tar.gz && rm -rf methInheritSim.buildbin-libdir && mkdir methInheritSim.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methInheritSim.buildbin-libdir methInheritSim_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL methInheritSim_1.12.0.zip && rm methInheritSim_1.12.0.tar.gz methInheritSim_1.12.0.zip
###
##############################################################################
##############################################################################


  % 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  856k  100  856k    0     0  9734k      0 --:--:-- --:--:-- --:--:-- 9849k

install for i386

* installing *source* package 'methInheritSim' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methInheritSim'
    finding HTML links ... done
    calculateNbDiffCase                     html  
    createSampleID                          html  
    dataSimExample                          html  
    estBetaAlpha                            html  
    estBetaBeta                             html  
    fixSeed                                 html  
    getDiffCase                             html  
    getDiffMeth                             html  
    getSim                                  html  
    getSyntheticChr                         html  
    methInheritSim-package                  html  
    runOnEachSynCHR                         html  
    runSim                                  html  
    samplesForChrSynthetic                  html  
    saveData                                html  
    simEachGeneration                       html  
    simInheritance                          html  
    testIfAlreadyDone                       html  
    validateRunSimDoubleParameters          html  
    validateRunSimIntegerParameters         html  
    validateRunSimLogicalParameters         html  
    validateRunSimOtherParameters           html  
    validateRunSimParameters                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 'methInheritSim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methInheritSim' as methInheritSim_1.12.0.zip
* DONE (methInheritSim)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'methInheritSim' successfully unpacked and MD5 sums checked

Tests output

methInheritSim.Rcheck/tests_i386/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("methInheritSim")
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)


RUNIT TEST PROTOCOL -- Thu May 06 04:37:17 2021 
*********************************************** 
Number of test functions: 104 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
methInheritSim RUnit Tests - 104 test functions, 0 errors, 0 failures
Number of test functions: 104 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  41.57    1.71   44.18 

methInheritSim.Rcheck/tests_x64/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("methInheritSim")
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)


RUNIT TEST PROTOCOL -- Thu May 06 04:37:55 2021 
*********************************************** 
Number of test functions: 104 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
methInheritSim RUnit Tests - 104 test functions, 0 errors, 0 failures
Number of test functions: 104 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  37.01    0.71   37.79 

Example timings

methInheritSim.Rcheck/examples_i386/methInheritSim-Ex.timings

nameusersystemelapsed
calculateNbDiffCase0.000.010.02
createSampleID000
dataSimExample0.110.070.17
estBetaAlpha000
estBetaBeta0.010.000.02
fixSeed000
getDiffCase000
getDiffMeth0.190.030.22
getSim0.730.150.89
getSyntheticChr0.240.020.25
runOnEachSynCHR3.390.764.15
runSim12.39 0.1812.58
samplesForChrSynthetic22.17 0.0322.22
saveData000
simEachGeneration0.830.030.86
simInheritance1.170.011.19
testIfAlreadyDone000
validateRunSimDoubleParameters000
validateRunSimIntegerParameters0.020.000.01
validateRunSimLogicalParameters0.060.000.06
validateRunSimOtherParameters0.060.000.07
validateRunSimParameters0.060.000.06

methInheritSim.Rcheck/examples_x64/methInheritSim-Ex.timings

nameusersystemelapsed
calculateNbDiffCase000
createSampleID000
dataSimExample0.100.000.09
estBetaAlpha000
estBetaBeta000
fixSeed000
getDiffCase000
getDiffMeth0.100.000.09
getSim0.640.030.67
getSyntheticChr0.890.030.92
runOnEachSynCHR2.260.072.33
runSim7.660.037.69
samplesForChrSynthetic16.99 0.0117.00
saveData000
simEachGeneration0.650.000.65
simInheritance1.10.01.1
testIfAlreadyDone000
validateRunSimDoubleParameters000
validateRunSimIntegerParameters000
validateRunSimLogicalParameters0.060.000.06
validateRunSimOtherParameters0.040.000.05
validateRunSimParameters0.050.020.06