Carlos Ruiz-Arenas
| Snapshot Date: 2020-02-23 16:46:07 -0500 (Sun, 23 Feb 2020) |
| URL: https://git.bioconductor.org/packages/MEAL |
| Branch: RELEASE_3_10 |
| Last Commit: 8ca2f71 |
| Last Changed Date: 2019-10-29 13:09:28 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-02-24 12:45:44 -0500 (Mon, 24 Feb 2020).
| Package 981/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MEAL 1.16.0 Carlos Ruiz-Arenas
| malbec1 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: MEAL |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MEAL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MEAL_1.16.0.tar.gz |
| StartedAt: 2020-02-24 03:49:39 -0500 (Mon, 24 Feb 2020) |
| EndedAt: 2020-02-24 03:58:50 -0500 (Mon, 24 Feb 2020) |
| EllapsedTime: 550.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MEAL.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MEAL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MEAL_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/MEAL.Rcheck’
* using R version 3.6.2 (2019-12-12)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.16.0’
* 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 ... 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
plotRegion: no visible global function definition for
'subsetByOverlaps'
plotRegion: no visible global function definition for 'mcols<-'
runBlockFinder: no visible global function definition for 'assays'
runBlockFinder: no visible global function definition for 'colData'
runRDA: no visible global function definition for 'rowData'
runSVA: no visible global function definition for 'resid'
Undefined global functions or variables:
assays colData mcols<- resid rowData subsetByOverlaps
Consider adding
importFrom("stats", "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 ... WARNING
Codoc mismatches from documentation object 'runRDA':
runRDA
Code: function(set, model, num_vars = ncol(model), range, betas =
FALSE, resultSet = TRUE, num_permutations = 10000,
...)
Docs: function(set, model, num_vars = ncol(model), range, betas =
FALSE, resultSet = TRUE, num_permutations = 10000)
Argument names in code not in docs:
...
* checking Rd \usage sections ... OK
* 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: 'calculateRelevantSNPs' is deprecated.
Warning: 'correlationMethSNPs' is deprecated.
Warning: 'explainedVariance' is deprecated.
Warning: 'normalSNP' is deprecated.
Warning: 'plotLM' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
exportResults 25.314 1.822 27.988
* 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 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/MEAL.Rcheck/00check.log’
for details.
MEAL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MEAL ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘MEAL’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' ** testing if installed package can be loaded from final location Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' ** testing if installed package keeps a record of temporary installation path * DONE (MEAL)
MEAL.Rcheck/tests/testthat.Rout
R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, 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)
Warning message:
replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
>
> test_check("MEAL")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 37 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
>
> proc.time()
user system elapsed
66.578 3.237 71.137
MEAL.Rcheck/MEAL-Ex.timings
| name | user | system | elapsed | |
| calculateRelevantSNPs | 0.000 | 0.000 | 0.001 | |
| correlationMethSNPs | 0.000 | 0.000 | 0.001 | |
| explainedVariance | 0.000 | 0.001 | 0.001 | |
| exportResults | 25.314 | 1.822 | 27.988 | |
| getGeneVals | 0.000 | 0.000 | 0.001 | |
| normalSNP | 0.001 | 0.000 | 0.001 | |
| plotFeature | 1.749 | 0.038 | 1.813 | |
| plotLM | 0.001 | 0.000 | 0.001 | |
| plotRDA | 0.804 | 0.020 | 0.834 | |
| runDiffMeanAnalysis | 0.557 | 0.043 | 0.606 | |
| runDiffVarAnalysis | 0.527 | 0.043 | 0.576 | |
| runPipeline | 1.330 | 0.045 | 1.397 | |
| runRDA | 1.191 | 0.061 | 1.263 | |
| runRegionAnalysis | 1.189 | 0.016 | 1.216 | |
| topRDAhits | 0.807 | 0.016 | 0.831 | |