MEAL 1.17.1
Carlos Ruiz-Arenas
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/MEAL |
| Branch: master |
| Last Commit: fd3ffd7 |
| Last Changed Date: 2020-01-06 10:07:51 -0500 (Mon, 06 Jan 2020) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | [ ERROR ] | skipped | skipped | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MEAL
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* checking for file ‘MEAL/DESCRIPTION’ ... OK
* preparing ‘MEAL’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MEAL.Rmd’ using rmarkdown
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: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
Warning: Package 'MEAL' is deprecated and will be removed from Bioconductor
version 3.12
Loading required package: minfi
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following object is masked from 'package:MultiDataSet':
rowRanges
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: rngtools
Loading required package: pkgmaker
Loading required package: registry
Attaching package: 'pkgmaker'
The following object is masked from 'package:S4Vectors':
new2
The following object is masked from 'package:base':
isFALSE
Warning in if (datatype == "array") { :
the condition has length > 1 and only the first element will be used
Your contrast returned 6561 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Fitting chr15...
Fitting chr9...
Fitting chr1...
Fitting chr14...
Fitting chr6...
Fitting chr3...
Fitting chr13...
Fitting chr4...
Fitting chrX...
Fitting chr20...
Fitting chr11...
Fitting chr16...
Fitting chr10...
Fitting chr2...
Fitting chr17...
Fitting chr7...
Fitting chr19...
Fitting chr22...
Fitting chr21...
Fitting chr8...
Fitting chr12...
Fitting chr5...
Fitting chrY...
Fitting chr18...
Demarcating regions...
Done!
snapshotDate(): 2020-01-08
see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation
loading from cache
Warning in has_utility("convert", "ImageMagick") :
ImageMagick not installed or not in PATH
Quitting from lines 197-199 (MEAL.Rmd)
Error: processing vignette 'MEAL.Rmd' failed with diagnostics:
argument 2 is not a vector
--- failed re-building ‘MEAL.Rmd’
--- re-building ‘caseExample.Rmd’ using rmarkdown
Warning in has_utility("convert", "ImageMagick") :
ImageMagick not installed or not in PATH
Warning in createModel(set, model) :
There are some missing values in the samples data. Only complete cases will be used.
Warning in add_eset(object, gexpSet, dataset.type = "expression", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
Warning in add_rse(object, methySet, dataset.type = "methylation") :
No id column found in colData. The id will be equal to the sampleNames
Computing residuals
Computing correlation Methylation-Expression
--- finished re-building ‘caseExample.Rmd’
SUMMARY: processing the following file failed:
‘MEAL.Rmd’
Error: Vignette re-building failed.
Execution halted