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This page was generated on 2022-06-27 11:10:00 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 missMethyl on nebbiolo1


To the developers/maintainers of the missMethyl package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/missMethyl.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 1203/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.30.0  (landing page)
Belinda Phipson
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/missMethyl
git_branch: RELEASE_3_15
git_last_commit: 7348466
git_last_commit_date: 2022-04-26 11:20:40 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: missMethyl
Version: 1.30.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings missMethyl_1.30.0.tar.gz
StartedAt: 2022-06-26 20:45:30 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 21:06:40 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 1270.6 seconds
RetCode: 0
Status:   OK  
CheckDir: missMethyl.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings missMethyl_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/missMethyl.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.30.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘missMethyl’ 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 ... NOTE
goregion: no visible global function definition for ‘seqlevelsStyle<-’
Undefined global functions or variables:
  seqlevelsStyle<-
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
RUVadj             24.705  1.348  26.055
topRUV             22.276  0.438  22.714
RUVfit             21.929  0.440  22.370
SWAN               21.813  0.376  22.190
getAdj             21.630  0.380  22.010
topGSA             15.911  0.285  16.195
densityByProbeType 10.254  0.115  10.369
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/missMethyl.Rcheck/00check.log’
for details.



Installation output

missMethyl.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL missMethyl
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘missMethyl’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (missMethyl)

Tests output


Example timings

missMethyl.Rcheck/missMethyl-Ex.timings

nameusersystemelapsed
RUVadj24.705 1.34826.055
RUVfit21.929 0.44022.370
SWAN21.813 0.37622.190
contrasts.varFit0.0410.0040.045
densityByProbeType10.254 0.11510.369
getAdj21.63 0.3822.01
getINCs0.1840.0040.189
getLeveneResiduals0.0080.0000.008
getMappedEntrezIDs0.0000.0000.001
gometh0.0000.0010.001
goregion0.0000.0020.001
gsameth0.0000.0010.001
gsaregion0.0000.0010.001
gsaseq0.0000.0010.001
topGSA15.911 0.28516.195
topRUV22.276 0.43822.714
topVar0.010.000.01
varFit0.0050.0040.009