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BUILD report for scfind on malbec2

This page was generated on 2020-10-17 11:55:41 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE scfind PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1593/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scfind 1.10.0
Vladimir Kiselev
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/scfind
Branch: RELEASE_3_11
Last Commit: 0b9a68c
Last Changed Date: 2020-04-27 15:10:39 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
machv2 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: scfind
Version: 1.10.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scfind
StartedAt: 2020-10-16 21:37:46 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 21:38:45 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 58.2 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scfind
###
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* checking for file ‘scfind/DESCRIPTION’ ... OK
* preparing ‘scfind’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘scfind.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Warning: Package 'scfind' is deprecated and will be removed from Bioconductor
  version 3.12
Quitting from lines 44-55 (scfind.Rmd) 
Error: processing vignette 'scfind.Rmd' failed with diagnostics:
could not find function "isSpike<-"
--- failed re-building ‘scfind.Rmd’

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

Error: Vignette re-building failed.
Execution halted