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This page was generated on 2021-09-24 15:06:39 -0400 (Fri, 24 Sep 2021).

BUILD results for DMRcate on machv2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DMRcate.git to
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raw results

Package 517/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DMRcate 2.6.0  (landing page)
Tim Peters
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/DMRcate
git_branch: RELEASE_3_13
git_last_commit: d7de4ca
git_last_commit_date: 2021-05-19 12:03:06 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: DMRcate
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DMRcate
StartedAt: 2021-09-23 11:44:53 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 11:55:40 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 647.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DMRcate
###
##############################################################################
##############################################################################


* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* preparing ‘DMRcate’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DMRcate.Rnw’ using knitr
Loading required package: minfi
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.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

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
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'

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

snapshotDate(): 2021-05-18
Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'FlowSorted.Blood.EPIC'
installing the source package 'FlowSorted.Blood.EPIC'

trying URL 'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/FlowSorted.Blood.EPIC_1.10.1.tar.gz'
Content type 'application/x-gzip' length 86944 bytes (84 KB)
==================================================
downloaded 84 KB

* installing *source* package ‘FlowSorted.Blood.EPIC’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FlowSorted.Blood.EPIC)

The downloaded source packages are in
	'/private/tmp/Rtmpint8Tm/downloaded_packages'
Old packages: 'rgeos'
see ?FlowSorted.Blood.EPIC and browseVignettes('FlowSorted.Blood.EPIC') for documentation
loading from cache
snapshotDate(): 2021-05-18
Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'DMRcatedata'
installing the source package 'DMRcatedata'

trying URL 'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/DMRcatedata_2.10.0.tar.gz'
Content type 'application/x-gzip' length 102152 bytes (99 KB)
==================================================
downloaded 99 KB

* installing *source* package ‘DMRcatedata’ ...
** using staged installation
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DMRcatedata)

The downloaded source packages are in
	'/private/tmp/Rtmpint8Tm/downloaded_packages'
Old packages: 'rgeos'
see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation
loading from cache
see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation
loading from cache
Your contrast returned 31793 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
snapshotDate(): 2021-05-18
see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation
loading from cache
snapshotDate(): 2021-05-18
see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation
loading from cache
Quitting from lines 125-131 (DMRcate.Rnw) 
Error: processing vignette 'DMRcate.Rnw' failed with diagnostics:
Could not resolve host: api.genome.ucsc.edu
--- failed re-building ‘DMRcate.Rnw’

SUMMARY: processing the following file failed:
  ‘DMRcate.Rnw’

Error: Vignette re-building failed.
Execution halted