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 20.04.4 LTS)/x86_64	ERROR	skipped	skipped	skipped

merida1 Summary

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Package: epimutacions

Version: 0.99.23

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: 4 minutes 37.02 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: epimutacions_20220331091635

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

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

 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
Warning in knitr::include_graphics(file.path(getwd(), "fig/implementation.png")) :
  It is highly recommended to use relative paths for images. You had absolute paths: "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/Rtmp1lj5wi/Rbuilde765263b1b53/epimutacions/vignettes/fig/implementation.png"
Loading required package: epimutacionsData
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Warning in knitr::include_graphics(file.path(getwd(), "fig/workflow.png")) :
  It is highly recommended to use relative paths for images. You had absolute paths: "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/Rtmp1lj5wi/Rbuilde765263b1b53/epimutacions/vignettes/fig/workflow.png"
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
Loading DB
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19
Annotating:
GencodeBasicV12_NAME
Regulatory_Feature_Group
Relation_to_Island
- Extracting and annotating OMIMs
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Ensembl site unresponsive, trying uswest mirror
Ensembl site unresponsive, trying uswest mirror
Ensembl site unresponsive, trying useast mirror
Ensembl site unresponsive, trying uswest mirror
Ensembl site unresponsive, trying asia mirror
Quitting from lines 584-585 (epimutacions.Rmd) 
Error: processing vignette 'epimutacions.Rmd' failed with diagnostics:
invalid 'text' argument
--- failed re-building ‘epimutacions.Rmd’

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

Error: Vignette re-building failed.
Execution halted

merida1 CHECK output

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merida1 BUILD BIN output

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nebbiolo1 Summary

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Package: epimutacions

Version: 0.99.23

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 57.04 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: epimutacions_20220331091635

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

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

 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
Warning in knitr::include_graphics(file.path(getwd(), "fig/implementation.png")) :
  It is highly recommended to use relative paths for images. You had absolute paths: "/tmp/RtmpBsmgqw/Rbuilde259bd54e5e6/epimutacions/vignettes/fig/implementation.png"
Loading required package: epimutacionsData
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Warning in knitr::include_graphics(file.path(getwd(), "fig/workflow.png")) :
  It is highly recommended to use relative paths for images. You had absolute paths: "/tmp/RtmpBsmgqw/Rbuilde259bd54e5e6/epimutacions/vignettes/fig/workflow.png"
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
Loading DB
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19
Annotating:
GencodeBasicV12_NAME
Regulatory_Feature_Group
Relation_to_Island
- Extracting and annotating OMIMs
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Ensembl site unresponsive, trying useast mirror
Ensembl site unresponsive, trying asia mirror
Quitting from lines 584-585 (epimutacions.Rmd) 
Error: processing vignette 'epimutacions.Rmd' failed with diagnostics:
invalid 'text' argument
--- failed re-building ‘epimutacions.Rmd’

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

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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