Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/epimutacions

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
merida1	macOS 10.14.6 Mojave/x86_64	ERROR	skipped	skipped	skipped
nebbiolo1	Linux (Ubuntu 20.04.3 LTS)/x86_64	ERROR	skipped	skipped	skipped

merida1 Summary

[top]

Package: epimutacions

Version: 0.99.11

RVersion: 4.2

BiocVersion: 3.15

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epimutacions

BuildTime: 1 minutes 57.53 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: epimutacions_20211208161219

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: epimutacions. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

merida1 BUILD SRC output

[top]

===============================

 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(): 2021-11-24
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: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 1643 bumps.
66candidate regions were found for case sample 'GSM2562699'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 1928 bumps.
79candidate regions were found for case sample 'GSM2562700'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2039 bumps.
88candidate regions were found for case sample 'GSM2562701'
snapshotDate(): 2021-11-24
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Quitting from lines 319-321 (epimutacions.Rmd) 
Error: processing vignette 'epimutacions.Rmd' failed with diagnostics:
BiocParallel errors
  1 remote errors, element index: 1
  50 unevaluated and other errors
  first remote error:
Error in .SummarizedExperiment.charbound(j, colnames(x), fmt): <GenomicRatioSet>[,j] index out of bounds: GSM2808239

--- failed re-building ‘epimutacions.Rmd’

SUMMARY: processing the following file failed:
  ‘epimutacions.Rmd’

Error: Vignette re-building failed.
Execution halted

merida1 CHECK output

[top]

merida1 BUILD BIN output

[top]

nebbiolo1 Summary

[top]

Package: epimutacions

Version: 0.99.11

RVersion: 4.2

BiocVersion: 3.15

BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data epimutacions

BuildTime: 1 minutes 29.49 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: epimutacions_20211208161219

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: epimutacions. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

nebbiolo1 BUILD SRC output

[top]

===============================

 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(): 2021-11-24
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: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 1643 bumps.
66candidate regions were found for case sample 'GSM2562699'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 1928 bumps.
79candidate regions were found for case sample 'GSM2562700'
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.1).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2039 bumps.
88candidate regions were found for case sample 'GSM2562701'
snapshotDate(): 2021-11-24
see ?epimutacionsData and browseVignettes('epimutacionsData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Quitting from lines 319-321 (epimutacions.Rmd) 
Error: processing vignette 'epimutacions.Rmd' failed with diagnostics:
BiocParallel errors
  1 remote errors, element index: 1
  50 unevaluated and other errors
  first remote error:
Error in .SummarizedExperiment.charbound(j, colnames(x), fmt): <GenomicRatioSet>[,j] index out of bounds: GSM2808239

--- failed re-building ‘epimutacions.Rmd’

SUMMARY: processing the following file failed:
  ‘epimutacions.Rmd’

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

[top]

nebbiolo1 BUILD BIN output

[top]