Carlos Ruiz-Arenas
| Snapshot Date: 2018-10-21 22:32:03 -0400 (Sun, 21 Oct 2018) |
| URL: https://git.bioconductor.org/packages/MEAL |
| Branch: master |
| Last Commit: 74880a6 |
| Last Changed Date: 2018-10-02 09:37:52 -0400 (Tue, 02 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2018-10-23 02:22:06 -0400 (Tue, 23 Oct 2018).
| Package 892/1627 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MEAL 1.11.7 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 | OK | [ TIMEOUT ] | OK |
| Package: MEAL |
| Version: 1.11.7 |
| 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_1.11.7.tar.gz |
| StartedAt: 2018-10-22 15:59:14 -0400 (Mon, 22 Oct 2018) |
| EndedAt: 2018-10-22 16:39:15 -0400 (Mon, 22 Oct 2018) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: MEAL.Rcheck |
| Warnings: NA |
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### Running command:
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### /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_1.11.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MEAL.Rcheck’
* using R Under development (unstable) (2018-04-05 r74542)
* 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 ‘1.11.7’
* 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 ... WARNING
Found the following significant warnings:
Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/MEAL.Rcheck/00install.out’ for details.
* 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 '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 colData data dmrcatedata mcols<- 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 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 332.206 2.274 337.513
runRegionAnalysis 320.242 0.604 324.307
runPipeline 309.049 0.870 313.035
runRDA 14.858 0.102 15.076
plotFeature 14.177 0.127 14.465
plotRDA 12.964 0.082 13.184
topRDAhits 12.499 0.038 12.616
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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’ ... ** R ** byte-compile and prepare package for lazy loading Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found * DONE (MEAL)
MEAL.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-04-05 r74542) -- "Unsuffered Consequences"
Copyright (C) 2018 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, 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)
Warning message:
S3 method 'xts::as.xts.data.table' was declared in NAMESPACE but not found
>
> test_check("MEAL")
MEAL.Rcheck/MEAL-Ex.timings
| name | user | system | elapsed | |
| calculateRelevantSNPs | 0.007 | 0.000 | 0.006 | |
| correlationMethSNPs | 0.006 | 0.000 | 0.007 | |
| explainedVariance | 0.006 | 0.000 | 0.006 | |
| exportResults | 332.206 | 2.274 | 337.513 | |
| getGeneVals | 0.008 | 0.000 | 0.008 | |
| normalSNP | 0.006 | 0.001 | 0.007 | |
| plotFeature | 14.177 | 0.127 | 14.465 | |
| plotLM | 0.004 | 0.001 | 0.003 | |
| plotRDA | 12.964 | 0.082 | 13.184 | |
| runDiffMeanAnalysis | 0.529 | 0.088 | 0.622 | |
| runDiffVarAnalysis | 1.042 | 0.084 | 1.137 | |
| runPipeline | 309.049 | 0.870 | 313.035 | |
| runRDA | 14.858 | 0.102 | 15.076 | |
| runRegionAnalysis | 320.242 | 0.604 | 324.307 | |
| topRDAhits | 12.499 | 0.038 | 12.616 | |