Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:05:55 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for DMRcate on palomino3


To the developers/maintainers of the DMRcate package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DMRcate.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 547/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcate 2.10.0  (landing page)
Tim Peters
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/DMRcate
git_branch: RELEASE_3_15
git_last_commit: 81e8370
git_last_commit_date: 2022-04-26 11:18:02 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DSS' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    TIMEOUT    OK  

Summary

Package: DMRcate
Version: 2.10.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DMRcate.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DMRcate_2.10.0.tar.gz
StartedAt: 2022-06-24 00:33:56 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 01:52:34 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 4718.0 seconds
RetCode: 0
Status:   OK  
CheckDir: DMRcate.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DMRcate.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DMRcate_2.10.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/DMRcate.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DMRcate/DESCRIPTION' ... OK
* this is package 'DMRcate' version '2.10.0'
* 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 'DMRcate' 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
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
DMR.plot            221.33  12.03  588.00
DMRcate-package     169.68   6.19  176.56
cpg.annotate        139.67  12.61  517.05
dmrcate             135.03   6.16  141.58
extractRanges       133.20   6.03  139.92
rmSNPandCH          127.36   4.90  132.64
changeFDR            58.79   9.51  901.89
sequencing.annotate  53.55  12.60 1725.49
* 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: OK


Installation output

DMRcate.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DMRcate
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'DMRcate' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS'
Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS'
Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS'
Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS'
** testing if installed package keeps a record of temporary installation path
* DONE (DMRcate)

Tests output


Example timings

DMRcate.Rcheck/DMRcate-Ex.timings

nameusersystemelapsed
DMR.plot221.33 12.03588.00
DMRcate-package169.68 6.19176.56
changeFDR 58.79 9.51901.89
cpg.annotate139.67 12.61517.05
dmrcate135.03 6.16141.58
extractRanges133.20 6.03139.92
rmSNPandCH127.36 4.90132.64
sequencing.annotate 53.55 12.601725.49