BioC 3.6: CHECK report for methInheritSim on tokay1

Package: methInheritSim

Version: 0.99.11

Command: rm -rf methInheritSim.buildbin-libdir methInheritSim.Rcheck && mkdir methInheritSim.buildbin-libdir methInheritSim.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methInheritSim.buildbin-libdir methInheritSim_0.99.11.tar.gz >methInheritSim.Rcheck\00install.out 2>&1 && cp methInheritSim.Rcheck\00install.out methInheritSim-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=methInheritSim.buildbin-libdir --install="check:methInheritSim-install.out" --force-multiarch --no-vignettes --timings methInheritSim_0.99.11.tar.gz

StartedAt: 2017-08-16 00:46:01 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:53:54 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 472.7 seconds

RetCode: 0

Status:  OK

CheckDir: methInheritSim.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf methInheritSim.buildbin-libdir methInheritSim.Rcheck && mkdir methInheritSim.buildbin-libdir methInheritSim.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methInheritSim.buildbin-libdir methInheritSim_0.99.11.tar.gz >methInheritSim.Rcheck\00install.out 2>&1 && cp methInheritSim.Rcheck\00install.out methInheritSim-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=methInheritSim.buildbin-libdir --install="check:methInheritSim-install.out" --force-multiarch --no-vignettes --timings methInheritSim_0.99.11.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/methInheritSim.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '0.99.11'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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 7.47   0.05    7.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
samplesForChrSynthetic 8.41      0     8.4
* 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-3.6-bioc/meat/methInheritSim.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'methInheritSim' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'methInheritSim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methInheritSim' as methInheritSim_0.99.11.zip
* DONE (methInheritSim)

name	user	system	elapsed
calculateNbDiffCase	0	0	0
createSampleID	0	0	0
dataSimExample	0.03	0.00	0.03
estBetaAlpha	0	0	0
estBetaBeta	0	0	0
fixSeed	0	0	0
getDiffCase	0.03	0.00	0.03
getDiffMeth	0.03	0.00	0.03
getSim	1.50	0.03	1.53
getSyntheticChr	0.61	0.03	0.64
runOnEachSynCHR	1.59	0.08	1.69
runSim	3.13	0.07	3.20
samplesForChrSynthetic	7.47	0.05	7.52
saveData	0	0	0
simEachGeneration	0.55	0.03	0.58
simInheritance	0.9	0.0	0.9
testIfAlreadyDone	0	0	0
validateRunSimDoubleParameters	0	0	0
validateRunSimIntegerParameters	0	0	0
validateRunSimLogicalParameters	0.03	0.02	0.05
validateRunSimOtherParameters	0.03	0.01	0.05
validateRunSimParameters	0.05	0.00	0.04

name	user	system	elapsed
calculateNbDiffCase	0	0	0
createSampleID	0.01	0.00	0.02
dataSimExample	0.02	0.00	0.01
estBetaAlpha	0	0	0
estBetaBeta	0	0	0
fixSeed	0	0	0
getDiffCase	0.02	0.01	0.03
getDiffMeth	0.04	0.00	0.04
getSim	1.85	0.06	1.91
getSyntheticChr	0.36	0.02	0.37
runOnEachSynCHR	2.77	0.01	2.78
runSim	4.09	0.00	4.10
samplesForChrSynthetic	8.41	0.00	8.40
saveData	0	0	0
simEachGeneration	0.42	0.00	0.42
simInheritance	0.75	0.00	0.75
testIfAlreadyDone	0	0	0
validateRunSimDoubleParameters	0	0	0
validateRunSimIntegerParameters	0	0	0
validateRunSimLogicalParameters	0.03	0.00	0.04
validateRunSimOtherParameters	0.05	0.00	0.04
validateRunSimParameters	0.03	0.00	0.03