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This page was generated on 2021-12-06 12:31:58 -0500 (Mon, 06 Dec 2021).

BUILD results for IsoformSwitchAnalyzeR on nebbiolo1

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IsoformSwitchAnalyzeR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 956/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoformSwitchAnalyzeR 1.17.0  (landing page)
Kristoffer Vitting-Seerup
Snapshot Date: 2021-12-05 13:55:08 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
git_branch: master
git_last_commit: 3312ab4
git_last_commit_date: 2021-10-26 12:35:46 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    ERROR  skipped

Summary

Package: IsoformSwitchAnalyzeR
Version: 1.17.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data IsoformSwitchAnalyzeR
StartedAt: 2021-12-05 16:31:57 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 16:33:13 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 76.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data IsoformSwitchAnalyzeR
###
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* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* preparing ‘IsoformSwitchAnalyzeR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘IsoformSwitchAnalyzeR.Rmd’ using rmarkdown
Loading required package: limma
Loading required package: DEXSeq
Loading required package: BiocParallel
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    plotMA

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

Welcome to Bioconductor

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

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

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: DESeq2
Loading required package: AnnotationDbi
Loading required package: RColorBrewer
Loading required package: ggplot2
Step 1 of 3 : Detecting isoform switches...
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE) :
  some variables in design formula are characters, converting to factors
Quitting from lines 484-490 (IsoformSwitchAnalyzeR.Rmd) 
Error: processing vignette 'IsoformSwitchAnalyzeR.Rmd' failed with diagnostics:
0 rows in value to replace 12rows
--- failed re-building ‘IsoformSwitchAnalyzeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted