Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-25 12:06:51 -0400 (Wed, 25 May 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" 4155
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 MethylMix on palomino3


To the developers/maintainers of the MethylMix package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethylMix.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 1153/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethylMix 2.26.0  (landing page)
Olivier Gevaert
Snapshot Date: 2022-05-24 13:55:11 -0400 (Tue, 24 May 2022)
git_url: https://git.bioconductor.org/packages/MethylMix
git_branch: RELEASE_3_15
git_last_commit: ed5443f
git_last_commit_date: 2022-04-26 11:21:15 -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  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MethylMix
Version: 2.26.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MethylMix.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MethylMix_2.26.0.tar.gz
StartedAt: 2022-05-25 01:30:52 -0400 (Wed, 25 May 2022)
EndedAt: 2022-05-25 01:33:37 -0400 (Wed, 25 May 2022)
EllapsedTime: 164.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MethylMix.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:MethylMix.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MethylMix_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/MethylMix.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 'MethylMix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylMix' version '2.26.0'
* 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 whether package 'MethylMix' 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 ... NOTE
Namespace in Imports field not imported from: 'digest'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MethylMix: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
MethylMix_PlotModel 31.23   0.25   31.50
MethylMix_Predict   24.07   0.04   24.11
MethylMix           23.69   0.02   23.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/MethylMix.Rcheck/00check.log'
for details.



Installation output

MethylMix.Rcheck/00install.out

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


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MethylMix' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (MethylMix)

Tests output

MethylMix.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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(MethylMix)
> 
> test_check("MethylMix")
Found 251 samples with both methylation and expression data.
Correlating methylation data with gene expression...

Found 9 transcriptionally predictive genes.

Starting Beta mixture modeling.
Running Beta mixture model on 9 genes and on 251 samples.
ERBB2 :  2  components are best.
FAAH :  2  components are best.
FOXD1 :  2  components are best.
ME1 :  2  components are best.
MGMT :  2  components are best.
OAS1 :  2  components are best.
SOX10 :  2  components are best.
TRAF6 :  2  components are best.
ZNF217 :  2  components are best.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
  25.68    0.29   25.96 

Example timings

MethylMix.Rcheck/MethylMix-Ex.timings

nameusersystemelapsed
ClusterProbes000
Download_DNAmethylation000
Download_GeneExpression000
GetData000
MethylMix23.69 0.0223.72
MethylMix_ModelGeneExpression0.060.000.06
MethylMix_PlotModel31.23 0.2531.50
MethylMix_Predict24.07 0.0424.11
Preprocess_DNAmethylation000
Preprocess_GeneExpression000