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This page was generated on 2022-02-17 08:36:54 -0500 (Thu, 17 Feb 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 1362
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BUILD results for Single.mTEC.Transcriptomes on nebbiolo2


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

raw results

Package 351/406HostnameOS / ArchINSTALLBUILDCHECK
Single.mTEC.Transcriptomes 1.23.1  (landing page)
Alejandro Reyes
Snapshot Date: 2022-02-17 04:00:02 -0500 (Thu, 17 Feb 2022)
git_url: https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes
git_branch: master
git_last_commit: 9de446d
git_last_commit_date: 2021-11-22 00:26:07 -0500 (Mon, 22 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped

Summary

Package: Single.mTEC.Transcriptomes
Version: 1.23.1
Command: /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD build --keep-empty-dirs --no-resave-data Single.mTEC.Transcriptomes
StartedAt: 2022-02-17 06:19:20 -0500 (Thu, 17 Feb 2022)
EndedAt: 2022-02-17 07:03:47 -0500 (Thu, 17 Feb 2022)
EllapsedTime: 2667.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD build --keep-empty-dirs --no-resave-data Single.mTEC.Transcriptomes
###
##############################################################################
##############################################################################


* checking for file ‘Single.mTEC.Transcriptomes/DESCRIPTION’ ... OK
* preparing ‘Single.mTEC.Transcriptomes’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘mTECs.Rnw’ using knitr
Loading required package: S4Vectors
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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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

Loading required package: AnnotationDbi

Attaching package: 'genefilter'

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

    rowSds, rowVars

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

    rowSds, rowVars

gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

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

    trim

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

    combine

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

    trim

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

    startsWith, trim

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

    first, first<-

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

    combine

The following object is masked from 'package:stats4':

    nobs

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

    nobs

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

    object.size

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

    startsWith

Registered S3 method overwritten by 'gplots':
  method         from 
  reorder.factor gdata

Attaching package: 'gplots'

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

    reorder.factor

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

    space

The following object is masked from 'package:S4Vectors':

    space

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

    lowess


Attaching package: 'gridExtra'

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

    combine

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

    combine

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

    combine

    This package provides documented data and code to reproduce the 
    results and figures from the manuscript: Brennecke et al. 
    Single-cell transcriptome analysis reveals coordinated ectopic 
    gene-expression patterns in medullary thymic epithelial cells. 
    Nature Immunology 16,933-941 (2015) doi:10.1038/ni.3246 

Loading required package: lattice
Loading required package: annotate
Loading required package: XML
Warning: Removed 77 rows containing non-finite values (stat_ydensity).
Warning: Removed 77 rows containing non-finite values (stat_boxplot).
Warning: Removed 8 rows containing non-finite values (stat_ydensity).
Warning: Removed 8 rows containing non-finite values (stat_boxplot).
Warning: Removed 3 rows containing non-finite values (stat_ydensity).
Warning: Removed 3 rows containing non-finite values (stat_boxplot).
Warning: Removed 28 rows containing missing values (geom_point).
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

Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
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replace the existing scale.
Warning: Ignoring unknown parameters: fill
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replace the existing scale.
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replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Ignoring unknown parameters: fill
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.

Attaching package: 'Gviz'

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

    imageMap

Quitting from lines 2898-2933 (mTECs.Rnw) 
Error: processing vignette 'mTECs.Rnw' failed with diagnostics:
Can't add `e2` to a ggplot object.
--- failed re-building ‘mTECs.Rnw’

SUMMARY: processing the following file failed:
  ‘mTECs.Rnw’

Error: Vignette re-building failed.
Execution halted