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BioC 3.5: CHECK report for MethylMix on tokay2

This page was generated on 2017-10-18 14:23:51 -0400 (Wed, 18 Oct 2017).

Package 806/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethylMix 2.4.0
Olivier Gevaert
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/MethylMix
Branch: RELEASE_3_5
Last Commit: 4f19b00
Last Changed Date: 2017-05-29 19:42:08 -0400 (Mon, 29 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MethylMix
Version: 2.4.0
Command: rm -rf MethylMix.buildbin-libdir MethylMix.Rcheck && mkdir MethylMix.buildbin-libdir MethylMix.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylMix.buildbin-libdir MethylMix_2.4.0.tar.gz >MethylMix.Rcheck\00install.out 2>&1 && cp MethylMix.Rcheck\00install.out MethylMix-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MethylMix.buildbin-libdir --install="check:MethylMix-install.out" --force-multiarch --no-vignettes --timings MethylMix_2.4.0.tar.gz
StartedAt: 2017-10-18 01:17:32 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:22:25 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 293.5 seconds
RetCode: 0
Status:  OK  
CheckDir: MethylMix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MethylMix.buildbin-libdir MethylMix.Rcheck && mkdir MethylMix.buildbin-libdir MethylMix.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylMix.buildbin-libdir MethylMix_2.4.0.tar.gz >MethylMix.Rcheck\00install.out 2>&1 && cp MethylMix.Rcheck\00install.out MethylMix-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MethylMix.buildbin-libdir --install="check:MethylMix-install.out" --force-multiarch --no-vignettes --timings MethylMix_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MethylMix.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethylMix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylMix' version '2.4.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'MethylMix' 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 ... NOTE
Namespace in Imports field not imported from: 'digest'
  All declared Imports should be used.
* 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
MethylMix_PlotModel 32.28   0.03   32.31
MethylMix_Predict   29.86   0.00   29.86
MethylMix           26.09   0.01   26.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
MethylMix_PlotModel 34.61   0.06   34.67
MethylMix           27.73   0.01   27.75
MethylMix_Predict   27.05   0.00   27.04
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MethylMix.Rcheck/00check.log'
for details.


MethylMix.Rcheck/00install.out:


install for i386

* installing *source* package 'MethylMix' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'MethylMix' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethylMix' as MethylMix_2.4.0.zip
* DONE (MethylMix)

MethylMix.Rcheck/examples_i386/MethylMix-Ex.timings:

nameusersystemelapsed
Download_DNAmethylation000
Download_GeneExpression000
GetData000
MethylMix26.09 0.0126.17
MethylMix_ModelGeneExpression0.050.000.05
MethylMix_PlotModel32.28 0.0332.31
MethylMix_Predict29.86 0.0029.86
Preprocess_DNAmethylation000
Preprocess_GeneExpression0.020.000.02

MethylMix.Rcheck/examples_x64/MethylMix-Ex.timings:

nameusersystemelapsed
Download_DNAmethylation0.010.000.02
Download_GeneExpression000
GetData000
MethylMix27.73 0.0127.75
MethylMix_ModelGeneExpression0.110.020.13
MethylMix_PlotModel34.61 0.0634.67
MethylMix_Predict27.05 0.0027.04
Preprocess_DNAmethylation000
Preprocess_GeneExpression000