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BUILD report for chimera on tokay1

This page was generated on 2021-05-05 12:11:30 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the chimera package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 280/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.32.0  (landing page)
Raffaele A Calogero
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/chimera
Branch: RELEASE_3_12
Last Commit: a3c6b1f
Last Changed Date: 2020-10-27 10:49:26 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: chimera
Version: 1.32.0
Command: chmod a+r chimera -R && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data chimera
StartedAt: 2021-05-04 20:11:26 -0400 (Tue, 04 May 2021)
EndedAt: 2021-05-04 20:12:49 -0400 (Tue, 04 May 2021)
EllapsedTime: 83.0 seconds
RetCode: 1
Status:   ERROR   
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   chmod a+r chimera -R && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data chimera
###
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* checking for file 'chimera/DESCRIPTION' ... OK
* preparing 'chimera':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'chimera.Rnw' using Sweave
Loading required package: Biobase
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

Welcome to Bioconductor

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

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

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: GenomicAlignments
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: AnnotationDbi
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
Loading required package: Homo.sapiens
Loading required package: OrganismDbi
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Warning: Package 'chimera' is deprecated and will be removed from Bioconductor
  version 3.13
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:1 mapping between keys and columns
Loading required package: Rsubread

Error: processing vignette 'chimera.Rnw' failed with diagnostics:
 chunk 6 
Error in bowtie_build(references = ebwt, outdir = getwd(), prefix = chimera.db,  : 
  could not find function "bowtie_build"

--- failed re-building 'chimera.Rnw'

SUMMARY: processing the following file failed:
  'chimera.Rnw'

Error: Vignette re-building failed.
Execution halted