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This page was generated on 2021-09-20 15:06:02 -0400 (Mon, 20 Sep 2021).

BUILD results for XBSeq on machv2

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raw results

Package 2025/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XBSeq 1.24.0  (landing page)
Yuanhang Liu
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/XBSeq
git_branch: RELEASE_3_13
git_last_commit: b28a2ce
git_last_commit_date: 2021-05-19 12:14:23 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: XBSeq
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data XBSeq
StartedAt: 2021-09-19 15:35:14 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 15:38:23 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 188.7 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 XBSeq
###
##############################################################################
##############################################################################


* checking for file ‘XBSeq/DESCRIPTION’ ... OK
* preparing ‘XBSeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘XBSeq.Rmd’ using rmarkdown
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
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

Warning: Package 'XBSeq' is deprecated and will be removed from Bioconductor
  version 3.14
Quitting from lines 167-173 (XBSeq.Rmd) 
Error: processing vignette 'XBSeq.Rmd' failed with diagnostics:
there is no package called 'DESeq'
--- failed re-building ‘XBSeq.Rmd’

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

Error: Vignette re-building failed.
Execution halted