Carlos Ruiz-Arenas
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/MEAL |
| Branch: RELEASE_3_7 |
| Last Commit: 9c3bc44 |
| Last Changed Date: 2018-05-23 09:22:15 -0400 (Wed, 23 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:28:06 -0400 (Wed, 17 Oct 2018).
| Package 854/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MEAL 1.10.1 Carlos Ruiz-Arenas
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | TIMEOUT | skipped | skipped |
| Package: MEAL |
| Version: 1.10.1 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MEAL.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MEAL_1.10.1.tar.gz |
| StartedAt: 2018-10-16 01:45:46 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 02:05:29 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 1182.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MEAL.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MEAL.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MEAL_1.10.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/MEAL.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.10.1’
* 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 ... NOTE
Missing object imported by a ':::' call: 'MultiDataSet:::nrows'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculateRelevantSNPs: no visible global function definition for
'betas'
correlationMethSNPs: no visible binding for global variable 'num_cores'
plotRegion: no visible global function definition for 'data'
plotRegion: no visible binding for global variable 'dmrcatedata'
plotRegion: no visible binding for global variable 'tx.hg19'
plotRegion: no visible binding for global variable 'tx.hg38'
plotRegion: no visible binding for global variable 'tx.mm10'
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 betas colData data dmrcatedata mcols<- num_cores resid rowData
subsetByOverlaps tx.hg19 tx.hg38 tx.mm10
Consider adding
importFrom("stats", "resid")
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'DAPipeline' 'DAProbe' 'DARegion' 'RDAset' 'filterSet'
'plotBestFeatures' 'preparePhenotype'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 or elapsed time > 5s
user system elapsed
exportResults 127.072 0.844 128.728
runRegionAnalysis 111.000 0.020 111.087
runPipeline 109.600 0.024 109.700
plotRDA 6.992 0.028 7.025
plotFeature 5.540 0.016 5.561
* 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/MEAL.Rcheck/00check.log’
for details.
MEAL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL MEAL ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘MEAL’ ... ** 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 * DONE (MEAL)
MEAL.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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)
>
> test_check("MEAL")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 62 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
537.968 1.612 540.085
MEAL.Rcheck/MEAL-Ex.timings
| name | user | system | elapsed | |
| DARegionAnalysis | 0.000 | 0.000 | 0.001 | |
| analysisRegionResults | 0.000 | 0.000 | 0.001 | |
| analysisResults | 0.000 | 0.000 | 0.001 | |
| calculateRelevantSNPs | 0.004 | 0.000 | 0.000 | |
| createRanges | 0.000 | 0.000 | 0.001 | |
| explainedVariance | 0.024 | 0.000 | 0.035 | |
| exportResults | 127.072 | 0.844 | 128.728 | |
| getGeneVals | 0 | 0 | 0 | |
| normalSNP | 0.000 | 0.000 | 0.001 | |
| plotFeature | 5.540 | 0.016 | 5.561 | |
| plotLM | 0.168 | 0.008 | 0.175 | |
| plotRDA | 6.992 | 0.028 | 7.025 | |
| prepareMethylationSet | 0.000 | 0.000 | 0.001 | |
| runDiffMeanAnalysis | 0.420 | 0.004 | 0.423 | |
| runDiffVarAnalysis | 0.388 | 0.056 | 0.445 | |
| runPipeline | 109.600 | 0.024 | 109.700 | |
| runRDA | 4.712 | 0.000 | 4.711 | |
| runRegionAnalysis | 111.000 | 0.020 | 111.087 | |
| topRDAhits | 4.860 | 0.008 | 4.872 | |