Multiple platform build/check report for BioC 3.9 - CHECK report for methInheritSim on tokay2

Package: methInheritSim

Version: 1.5.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methInheritSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methInheritSim_1.5.1.tar.gz

StartedAt: 2019-04-09 04:08:36 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:15:25 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 408.4 seconds

RetCode: 0

Status: OK

CheckDir: methInheritSim.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methInheritSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methInheritSim_1.5.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/methInheritSim.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.5.1'
* 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 or elapsed time > 5s
                       user system elapsed
samplesForChrSynthetic 9.36   0.04    9.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
samplesForChrSynthetic 13.92   0.03   13.95
runSim                  6.80   0.03    6.83
* 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-3.9-bioc/meat/methInheritSim.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/methInheritSim_1.5.1.tar.gz && rm -rf methInheritSim.buildbin-libdir && mkdir methInheritSim.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methInheritSim.buildbin-libdir methInheritSim_1.5.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL methInheritSim_1.5.1.zip && rm methInheritSim_1.5.1.tar.gz methInheritSim_1.5.1.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  857k  100  857k    0     0  8408k      0 --:--:-- --:--:-- --:--:-- 8934k

install for i386

* installing *source* package 'methInheritSim' ...
** 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_1.5.1.zip
* DONE (methInheritSim)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'methInheritSim' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)


RUNIT TEST PROTOCOL -- Tue Apr 09 04:14:47 2019 
*********************************************** 
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 
  26.03    2.32   27.85


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)


RUNIT TEST PROTOCOL -- Tue Apr 09 04:15:19 2019 
*********************************************** 
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 
  30.96    0.96   31.95

name	user	system	elapsed
calculateNbDiffCase	0	0	0
createSampleID	0.00	0.02	0.02
dataSimExample	0.02	0.00	0.01
estBetaAlpha	0	0	0
estBetaBeta	0	0	0
fixSeed	0	0	0
getDiffCase	0	0	0
getDiffMeth	0.00	0.01	0.02
getSim	1.17	0.11	1.28
getSyntheticChr	0.19	0.08	0.26
runOnEachSynCHR	1.45	0.31	1.77
runSim	4.69	0.10	4.78
samplesForChrSynthetic	9.36	0.04	9.41
saveData	0	0	0
simEachGeneration	0.47	0.02	0.48
simInheritance	0.67	0.00	0.67
testIfAlreadyDone	0	0	0
validateRunSimDoubleParameters	0	0	0
validateRunSimIntegerParameters	0	0	0
validateRunSimLogicalParameters	0.04	0.00	0.05
validateRunSimOtherParameters	0.05	0.02	0.06
validateRunSimParameters	0.05	0.00	0.05

name	user	system	elapsed
calculateNbDiffCase	0	0	0
createSampleID	0	0	0
dataSimExample	0.00	0.02	0.01
estBetaAlpha	0	0	0
estBetaBeta	0	0	0
fixSeed	0	0	0
getDiffCase	0	0	0
getDiffMeth	0.00	0.02	0.02
getSim	0.49	0.01	0.50
getSyntheticChr	0.86	0.00	0.86
runOnEachSynCHR	1.76	0.05	1.84
runSim	6.80	0.03	6.83
samplesForChrSynthetic	13.92	0.03	13.95
saveData	0	0	0
simEachGeneration	0.71	0.03	0.74
simInheritance	0.75	0.02	0.76
testIfAlreadyDone	0	0	0
validateRunSimDoubleParameters	0	0	0
validateRunSimIntegerParameters	0	0	0
validateRunSimLogicalParameters	0.09	0.00	0.09
validateRunSimOtherParameters	0.07	0.01	0.08
validateRunSimParameters	0.04	0.03	0.08

CHECK report for methInheritSim on tokay2

Summary

Command output

Installation output

Tests output

Example timings