Back to Workflows build report for BioC 3.15

This page was generated on 2022-10-18 14:00:09 -0400 (Tue, 18 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for rnaseqGene on nebbiolo1


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

raw results

Package 23/29HostnameOS / ArchINSTALLBUILD
rnaseqGene 1.20.0  (landing page)
Michael Love
Snapshot Date: 2022-10-18 07:45:02 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/rnaseqGene
git_branch: RELEASE_3_15
git_last_commit: 5d6595d
git_last_commit_date: 2022-04-26 12:40:53 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK  

Summary

Package: rnaseqGene
Version: 1.20.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rnaseqGene
StartedAt: 2022-10-18 08:02:21 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 08:03:18 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 56.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rnaseqGene
###
##############################################################################
##############################################################################


* checking for file ‘rnaseqGene/DESCRIPTION’ ... OK
* preparing ‘rnaseqGene’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘rnaseqGene.Rmd’ using rmarkdown

Attaching package: 'rmarkdown'

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

    html_document, md_document, pdf_document

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: GenomicRanges
Loading required package: stats4
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: 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: 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

Quitting from lines 359-361 (rnaseqGene.Rmd) 
Error: processing vignette 'rnaseqGene.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘rnaseqGene.Rmd’

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

Error: Vignette re-building failed.
Execution halted