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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 Oct 2021).

BUILD results for NanoporeRNASeq on nebbiolo2

To the developers/maintainers of the NanoporeRNASeq package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 251/404HostnameOS / ArchINSTALLBUILDCHECK
NanoporeRNASeq 1.3.3  (landing page)
Ying Chen Developer
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/NanoporeRNASeq
git_branch: master
git_last_commit: bcb76fe
git_last_commit_date: 2021-10-16 06:59:56 -0400 (Sat, 16 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped

Summary

Package: NanoporeRNASeq
Version: 1.3.3
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data NanoporeRNASeq
StartedAt: 2021-10-16 11:28:28 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 11:29:29 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 61.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data NanoporeRNASeq
###
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* checking for file ‘NanoporeRNASeq/DESCRIPTION’ ... OK
* preparing ‘NanoporeRNASeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘NanoporeRNASeq.Rmd’ using rmarkdown
Loading required package: ExperimentHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2021-10-15
see ?NanoporeRNASeq and browseVignettes('NanoporeRNASeq') for documentation
loading from cache
require("Rsamtools")
see ?NanoporeRNASeq and browseVignettes('NanoporeRNASeq') for documentation
loading from cache
see ?NanoporeRNASeq and browseVignettes('NanoporeRNASeq') for documentation
loading from cache
see ?NanoporeRNASeq and browseVignettes('NanoporeRNASeq') for documentation
loading from cache
see ?NanoporeRNASeq and browseVignettes('NanoporeRNASeq') for documentation
loading from cache
see ?NanoporeRNASeq and browseVignettes('NanoporeRNASeq') for documentation
loading from cache
Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit https://lawremi.github.io/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Loading required package: BSgenome
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    hubUrl

Parsing raw coverage...
Read GAlignments from BamFile...
extracting information...
Parsing raw coverage...
Read GAlignments from BamFile...
extracting information...
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

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

    cache

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

    cache

snapshotDate(): 2021-10-15
see ?NanoporeRNASeq and browseVignettes('NanoporeRNASeq') for documentation
downloading 2 resources
retrieving 2 resources
loading from cache
Start generating read class files
iteration: 1not all chromosomes present in reference genome sequence,
            ranges are dropped

Quitting from lines 84-87 (NanoporeRNASeq.Rmd) 
Error: processing vignette 'NanoporeRNASeq.Rmd' failed with diagnostics:
BiocParallel errors
  1 remote errors, element index: 1
  5 unevaluated and other errors
  first remote error: attempt to set too many names (1) on IRanges object of length 0
--- failed re-building ‘NanoporeRNASeq.Rmd’

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

Error: Vignette re-building failed.
Execution halted