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This page was generated on 2024-03-28 11:32:24 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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Package 1178/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEAL 1.32.0  (landing page)
Xavier Escribà Montagut
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/MEAL
git_branch: RELEASE_3_18
git_last_commit: 4d6f89b
git_last_commit_date: 2023-10-24 10:45:36 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for MEAL on kjohnson1


To the developers/maintainers of the MEAL package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MEAL
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MEAL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MEAL_1.32.0.tar.gz
StartedAt: 2024-03-27 18:08:43 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 18:15:30 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 406.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MEAL.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MEAL.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MEAL_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MEAL.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.32.0’
* 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 ‘MEAL’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    MAJOR CHANGES
  Cannot process chunk/lines:
    o Substitute AnalysisResults and AnalysisRegionResults by ResultSet.
  Cannot process chunk/lines:
    o Substitute MethylationSet by GenomicRatioSet.
  Cannot process chunk/lines:
    USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    o Rename analysis functions.
  Cannot process chunk/lines:
    o Create wrappers for each DMR methd 
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    o Add differences of variances analysis.
  Cannot process chunk/lines:
    o Add new plot to simultaneously show all results of the same region.
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    o Add function to add matrices to MDS.
  Cannot process chunk/lines:
    o Add Methylation-SNPs correlation.
  Cannot process chunk/lines:
    USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    o Move prepareMethylationSet from MultiDataSet to MEAL.
  Cannot process chunk/lines:
    o Defunct multiCorrMethExprs.
  Cannot process chunk/lines:
    BUGS FIXES
  Cannot process chunk/lines:
    o Solve a bug in DARegion when running DMRcate.
* 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 ... WARNING
'::' or ':::' import not declared from: 'sva'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRegion: no visible global function definition for
  ‘subsetByOverlaps’
plotRegion: no visible global function definition for ‘mcols<-’
runRDA: no visible global function definition for ‘rowData’
runSVA: no visible global function definition for ‘resid’
runSVA: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  mcols<- quantile resid rowData subsetByOverlaps
Consider adding
  importFrom("stats", "quantile", "resid")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in documentation object 'getProbeResults'
  ‘robust’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'runRegionAnalysis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
exportResults 6.273  0.128   6.414
* 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: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/MEAL.Rcheck/00check.log’
for details.



Installation output

MEAL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MEAL
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘MEAL’ ...
** using staged installation
** R
** 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 (MEAL)

Tests output

MEAL.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(MEAL)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: MultiDataSet
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("MEAL")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 34.134   1.045  35.410 

Example timings

MEAL.Rcheck/MEAL-Ex.timings

nameusersystemelapsed
exportResults6.2730.1286.414
getGeneVals000
plotFeature1.0020.0591.061
plotRDA2.0030.0472.050
runDiffMeanAnalysis0.4360.0300.464
runDiffVarAnalysis0.9290.0480.983
runPipeline0.6680.0360.704
runRDA0.5620.0280.591
runRegionAnalysis0.5550.0280.583
topRDAhits0.6010.0540.655