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CHECK report for DMRScan on tokay1

This page was generated on 2019-04-13 11:27:27 -0400 (Sat, 13 Apr 2019).

Package 423/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRScan 1.8.0
Christian M Page
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DMRScan
Branch: RELEASE_3_8
Last Commit: 28195a7
Last Changed Date: 2018-10-30 11:42:03 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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: DMRScan
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRScan.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DMRScan_1.8.0.tar.gz
StartedAt: 2019-04-13 01:51:58 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:05:10 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 792.0 seconds
RetCode: 0
Status:  OK  
CheckDir: DMRScan.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRScan.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DMRScan_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DMRScan.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DMRScan/DESCRIPTION' ... OK
* this is package 'DMRScan' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'DMRScan' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
* 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
DMRScan_slidingWindow 88.55   0.11   88.66
DMRScan_package       84.75   0.42   85.17
makeCpGregions        74.03   0.04   74.10
makeCpGgenes          51.38   0.05   51.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
DMRScan_slidingWindow 92.00   0.09   92.11
DMRScan_package       91.77   0.10   91.86
makeCpGregions        67.53   0.02   67.55
makeCpGgenes          53.09   0.06   53.16
* 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-3.8-bioc/meat/DMRScan.Rcheck/00check.log'
for details.



Installation output

DMRScan.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DMRScan_1.8.0.tar.gz && rm -rf DMRScan.buildbin-libdir && mkdir DMRScan.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRScan.buildbin-libdir DMRScan_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DMRScan_1.8.0.zip && rm DMRScan_1.8.0.tar.gz DMRScan_1.8.0.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 3202k  100 3202k    0     0  27.7M      0 --:--:-- --:--:-- --:--:-- 28.6M

install for i386

* installing *source* package 'DMRScan' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DMRScan'
    finding HTML links ... done
    DMRScan.methylationData                 html  
    DMRScan.phenotypes                      html  
    DMRScan_package                         html  
    finding level-2 HTML links ... done

    DMRScan_slidingWindow                   html  
    Rt-methods                              html  
    St-methods                              html  
    estimateThreshold                       html  
    makeCpGgenes                            html  
    makeCpGregions                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DMRScan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRScan' as DMRScan_1.8.0.zip
* DONE (DMRScan)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DMRScan' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

DMRScan.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> library(testthat)
> library(DMRScan)
> 
> test_check("DMRScan")
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.67    0.45    6.12 

DMRScan.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> library(testthat)
> library(DMRScan)
> 
> test_check("DMRScan")
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.65    0.17    3.82 

Example timings

DMRScan.Rcheck/examples_i386/DMRScan-Ex.timings

nameusersystemelapsed
DMRScan.methylationData0.580.000.58
DMRScan.phenotypes000
DMRScan_package84.75 0.4285.17
DMRScan_slidingWindow88.55 0.1188.66
Rt-methods000
St-methods000
estimateThreshold0.030.000.03
makeCpGgenes51.38 0.0551.42
makeCpGregions74.03 0.0474.10

DMRScan.Rcheck/examples_x64/DMRScan-Ex.timings

nameusersystemelapsed
DMRScan.methylationData0.500.030.53
DMRScan.phenotypes0.020.000.01
DMRScan_package91.77 0.1091.86
DMRScan_slidingWindow92.00 0.0992.11
Rt-methods000
St-methods000
estimateThreshold0.030.000.03
makeCpGgenes53.09 0.0653.16
makeCpGregions67.53 0.0267.55