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This page was generated on 2021-09-13 15:06:23 -0400 (Mon, 13 Sep 2021).

CHECK results for dmrseq on tokay2

To the developers/maintainers of the dmrseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dmrseq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 520/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dmrseq 1.12.0  (landing page)
Keegan Korthauer
Snapshot Date: 2021-09-12 04:50:10 -0400 (Sun, 12 Sep 2021)
git_url: https://git.bioconductor.org/packages/dmrseq
git_branch: RELEASE_3_13
git_last_commit: e8485f3
git_last_commit_date: 2021-05-19 12:33:43 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: dmrseq
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dmrseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dmrseq_1.12.0.tar.gz
StartedAt: 2021-09-12 21:49:25 -0400 (Sun, 12 Sep 2021)
EndedAt: 2021-09-12 22:04:04 -0400 (Sun, 12 Sep 2021)
EllapsedTime: 878.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: dmrseq.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dmrseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dmrseq_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/dmrseq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dmrseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dmrseq' version '1.12.0'
* 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 'dmrseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
* 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 LazyData ... WARNING
  LazyData DB of 8.8 MB without LazyDataCompression set
  See ยง1.1.6 of 'Writing R Extensions'
* 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
getAnnot 17.13   1.94   28.51
dmrseq   11.91   3.03  205.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
getAnnot 17.55   0.90   19.74
dmrseq   12.66   2.13  209.85
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/dmrseq.Rcheck/00check.log'
for details.



Installation output

dmrseq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/dmrseq_1.12.0.tar.gz && rm -rf dmrseq.buildbin-libdir && mkdir dmrseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dmrseq.buildbin-libdir dmrseq_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL dmrseq_1.12.0.zip && rm dmrseq_1.12.0.tar.gz dmrseq_1.12.0.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
 84 2288k   84 1935k    0     0  2369k      0 --:--:-- --:--:-- --:--:-- 2368k
100 2288k  100 2288k    0     0  2552k      0 --:--:-- --:--:-- --:--:-- 2553k

install for i386

* installing *source* package 'dmrseq' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
** help
*** installing help indices
  converting help for package 'dmrseq'
    finding HTML links ... done
    BS.chr21                                html  
    annot.chr21                             html  
    dmrPlotAnnotations                      html  
    dmrs.ex                                 html  
    dmrseq                                  html  
    getAnnot                                html  
    meanDiff                                html  
    plotDMRs                                html  
    plotEmpiricalDistribution               html  
    simDMRs                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'dmrseq' ...
** testing if installed package can be loaded
Warning: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr'
* MD5 sums
packaged installation of 'dmrseq' as dmrseq_1.12.0.zip
* DONE (dmrseq)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'dmrseq' successfully unpacked and MD5 sums checked

Tests output


Example timings

dmrseq.Rcheck/examples_i386/dmrseq-Ex.timings

nameusersystemelapsed
BS.chr211.860.051.91
annot.chr21000
dmrs.ex000
dmrseq 11.91 3.03205.78
getAnnot17.13 1.9428.51
meanDiff1.210.071.30
plotDMRs1.660.131.78
plotEmpiricalDistribution4.490.504.99
simDMRs2.810.082.89

dmrseq.Rcheck/examples_x64/dmrseq-Ex.timings

nameusersystemelapsed
BS.chr211.110.031.14
annot.chr21000
dmrs.ex000
dmrseq 12.66 2.13209.85
getAnnot17.55 0.9019.74
meanDiff0.330.080.41
plotDMRs1.080.051.13
plotEmpiricalDistribution3.380.483.86
simDMRs3.150.073.22