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BUILD report for HMP2Data on malbec2

This page was generated on 2020-10-15 20:45:48 -0400 (Thu, 15 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE HMP2Data PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 178/391HostnameOS / ArchINSTALLBUILDCHECK
HMP2Data 1.2.0
John Stansfield , Ekaterina Smirnova
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/HMP2Data
Branch: RELEASE_3_11
Last Commit: 313e5ae
Last Changed Date: 2020-04-27 16:43:20 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK [ ERROR ] skipped 

Summary

Package: HMP2Data
Version: 1.2.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HMP2Data
StartedAt: 2020-10-15 11:36:43 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 11:42:50 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 367.5 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HMP2Data
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* checking for file ‘HMP2Data/DESCRIPTION’ ... OK
* preparing ‘HMP2Data’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘hmp2data.Rmd’ using rmarkdown
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

Attaching package: 'IRanges'

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

    distance

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")'.


Attaching package: 'Biobase'

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

    sampleNames

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


Attaching package: 'dplyr'

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

    count

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

    combine

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

    intersect, setdiff, union

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

    intersect

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

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

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

    combine, intersect, setdiff, union

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Removed 196 rows containing non-finite values (stat_bin).
Warning: Removed 2 rows containing missing values (geom_bar).
Warning: Removed 677 rows containing non-finite values (stat_bin).
Warning: Removed 4 rows containing missing values (geom_bar).
Quitting from lines 333-341 (hmp2data.Rmd) 
Error: processing vignette 'hmp2data.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'double'
--- failed re-building ‘hmp2data.Rmd’

SUMMARY: processing the following file failed:
  ‘hmp2data.Rmd’

Error: Vignette re-building failed.
Execution halted