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CHECK report for DMRScan on tokay2

This page was generated on 2020-10-17 11:56:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DMRScan PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 491/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRScan 1.10.0
Christian M Page
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DMRScan
Branch: RELEASE_3_11
Last Commit: 419c30e
Last Changed Date: 2020-04-27 15:04:43 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DMRScan
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRScan.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DMRScan_1.10.0.tar.gz
StartedAt: 2020-10-17 03:28:26 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:41:26 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 779.9 seconds
RetCode: 0
Status:  OK  
CheckDir: DMRScan.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DMRScan.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DMRScan_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DMRScan.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.10.0'
* 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 '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 (user + system) or elapsed time > 5s
                       user system elapsed
DMRScan_package       89.84   0.94   90.78
DMRScan_slidingWindow 75.61   0.12   75.95
makeCpGregions        65.67   0.04   65.72
makeCpGgenes          51.38   0.07   51.43
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
DMRScan_package       102.35   0.20  102.57
DMRScan_slidingWindow  94.97   0.10   95.06
makeCpGregions         85.68   0.03   85.87
makeCpGgenes           58.12   0.06   58.19
* 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-3.11-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://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DMRScan_1.10.0.tar.gz && rm -rf DMRScan.buildbin-libdir && mkdir DMRScan.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DMRScan.buildbin-libdir DMRScan_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DMRScan_1.10.0.zip && rm DMRScan_1.10.0.tar.gz DMRScan_1.10.0.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  28.9M      0 --:--:-- --:--:-- --:--:-- 30.9M

install for i386

* installing *source* package 'DMRScan' ...
** using staged installation
** 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 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 'DMRScan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRScan' as DMRScan_1.10.0.zip
* DONE (DMRScan)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DMRScan' successfully unpacked and MD5 sums checked

Tests output


Example timings

DMRScan.Rcheck/examples_i386/DMRScan-Ex.timings

nameusersystemelapsed
DMRScan.methylationData0.700.030.74
DMRScan.phenotypes0.000.020.01
DMRScan_package89.84 0.9490.78
DMRScan_slidingWindow75.61 0.1275.95
Rt-methods000
St-methods000
estimateThreshold0.060.000.07
makeCpGgenes51.38 0.0751.43
makeCpGregions65.67 0.0465.72

DMRScan.Rcheck/examples_x64/DMRScan-Ex.timings

nameusersystemelapsed
DMRScan.methylationData0.810.000.81
DMRScan.phenotypes000
DMRScan_package102.35 0.20102.57
DMRScan_slidingWindow94.97 0.1095.06
Rt-methods000
St-methods000
estimateThreshold0.030.000.03
makeCpGgenes58.12 0.0658.19
makeCpGregions85.68 0.0385.87