Carlos Ruiz-Arenas
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/MEAL |
| Branch: RELEASE_3_6 |
| Last Commit: 916313b |
| Last Changed Date: 2017-10-30 12:41:05 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:14:08 -0400 (Thu, 12 Apr 2018).
| Package 805/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MEAL 1.8.0 Carlos Ruiz-Arenas
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | TIMEOUT | skipped | skipped |
| Package: MEAL |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.8.0.tar.gz |
| StartedAt: 2018-04-12 00:50:58 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:57:46 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 408.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MEAL.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.8.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MEAL.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Missing or unexported object: 'Biobase::assays'
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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'DAPipeline' is deprecated.
Warning: 'DAProbe' is deprecated.
Warning: 'DARegion' is deprecated.
Warning: 'RDAset' is deprecated.
Warning: 'filterSet' is deprecated.
Warning: 'plotBestFeatures' is deprecated.
Warning: 'preparePhenotype' 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 21.992 0.676 23.745
* 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-3.6-bioc/meat/MEAL.Rcheck/00check.log’
for details.
MEAL.Rcheck/00install.out
* installing *source* package ‘MEAL’ ... ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
47.156 1.176 49.485
MEAL.Rcheck/MEAL-Ex.timings
| name | user | system | elapsed | |
| DAPipeline | 0.000 | 0.000 | 0.001 | |
| DAProbe | 0.004 | 0.000 | 0.001 | |
| DARegion | 0.000 | 0.000 | 0.001 | |
| DARegionAnalysis | 0.000 | 0.000 | 0.001 | |
| RDAset | 0 | 0 | 0 | |
| analysisRegionResults | 0 | 0 | 0 | |
| analysisResults | 0 | 0 | 0 | |
| calculateRelevantSNPs | 0.000 | 0.000 | 0.001 | |
| createRanges | 0 | 0 | 0 | |
| explainedVariance | 0.024 | 0.004 | 0.041 | |
| exportResults | 21.992 | 0.676 | 23.745 | |
| filterSet | 0.000 | 0.000 | 0.001 | |
| getGeneVals | 0 | 0 | 0 | |
| normalSNP | 0.004 | 0.000 | 0.001 | |
| plotBestFeatures | 0 | 0 | 0 | |
| plotFeature | 2.476 | 0.060 | 2.539 | |
| plotLM | 0.716 | 0.000 | 0.715 | |
| plotRDA | 1.260 | 0.008 | 1.271 | |
| prepareMethylationSet | 0.000 | 0.000 | 0.001 | |
| preparePhenotype | 0.004 | 0.000 | 0.001 | |
| runDiffMeanAnalysis | 0.676 | 0.000 | 0.675 | |
| runDiffVarAnalysis | 1.012 | 0.052 | 1.066 | |
| runPipeline | 2.236 | 0.020 | 2.257 | |
| runRDA | 1.440 | 0.028 | 1.468 | |
| runRegionAnalysis | 1.304 | 0.004 | 1.309 | |
| topRDAhits | 0.836 | 0.016 | 0.853 | |