===============================
R CMD BUILD
===============================
* checking for file ‘epimutacions/DESCRIPTION’ ... OK
* preparing ‘epimutacions’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epimutacions.Rmd’ using rmarkdown
Loading required package: epimutacionsData
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2022-03-29
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
require("minfi")
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
Selected epimutation detection method 'manova'
Selected method 'manova' required of 'bumphunter'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.2).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
Warning in regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, :
NAs found and removed. ind changed.
[bumphunterEngine] Found 1643 bumps.
66 candidate regions were found for case sample 'GSM2562699'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.2).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
Warning in regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, :
NAs found and removed. ind changed.
[bumphunterEngine] Found 1928 bumps.
79 candidate regions were found for case sample 'GSM2562700'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.2).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
Warning in regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, :
NAs found and removed. ind changed.
[bumphunterEngine] Found 2039 bumps.
88 candidate regions were found for case sample 'GSM2562701'
snapshotDate(): 2022-03-29
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
Quitting from lines 438-441 (epimutacions.Rmd)
Error: processing vignette 'epimutacions.Rmd' failed with diagnostics:
could not find function "as_tibble"
--- failed re-building ‘epimutacions.Rmd’
SUMMARY: processing the following file failed:
‘epimutacions.Rmd’
Error: Vignette re-building failed.
Execution halted
===============================
R CMD BUILD
===============================
* checking for file ‘epimutacions/DESCRIPTION’ ... OK
* preparing ‘epimutacions’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epimutacions.Rmd’ using rmarkdown
Loading required package: epimutacionsData
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2022-03-29
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
require("minfi")
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
Selected epimutation detection method 'manova'
Selected method 'manova' required of 'bumphunter'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.2).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
Warning in regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, :
NAs found and removed. ind changed.
[bumphunterEngine] Found 1643 bumps.
66 candidate regions were found for case sample 'GSM2562699'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.2).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
Warning in regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, :
NAs found and removed. ind changed.
[bumphunterEngine] Found 1928 bumps.
79 candidate regions were found for case sample 'GSM2562700'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.2).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
Warning in regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, :
NAs found and removed. ind changed.
[bumphunterEngine] Found 2039 bumps.
88 candidate regions were found for case sample 'GSM2562701'
snapshotDate(): 2022-03-29
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
loading from cache
Quitting from lines 438-441 (epimutacions.Rmd)
Error: processing vignette 'epimutacions.Rmd' failed with diagnostics:
could not find function "as_tibble"
--- failed re-building ‘epimutacions.Rmd’
SUMMARY: processing the following file failed:
‘epimutacions.Rmd’
Error: Vignette re-building failed.
Execution halted