MEAL 1.16.2
Carlos Ruiz-Arenas
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MEAL |
| Branch: RELEASE_3_10 |
| Last Commit: 3232d70 |
| Last Changed Date: 2020-03-25 13:28:19 -0400 (Wed, 25 Mar 2020) |
| malbec1 | Linux (Ubuntu 18.04.4 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 | ERROR | skipped | skipped | |
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### Running command:
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### chmod a+r MEAL -R && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe 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)
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 1.5-9.4 2020-03-24
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Quitting from lines 194-196 (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 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