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This page was generated on 2021-11-26 15:04:56 -0500 (Fri, 26 Nov 2021).

BUILD results for miloR on nebbiolo2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miloR.git to
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raw results

Package 1150/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miloR 1.2.0  (landing page)
Mike Morgan
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/miloR
git_branch: RELEASE_3_14
git_last_commit: 00e5e3b
git_last_commit_date: 2021-10-26 13:09:25 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: miloR
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data miloR
StartedAt: 2021-11-25 07:01:48 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 07:06:29 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 280.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data miloR
###
##############################################################################
##############################################################################


* checking for file ‘miloR/DESCRIPTION’ ... OK
* preparing ‘miloR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘milo_demo.Rmd’ using rmarkdown
Loading required package: edgeR
Loading required package: limma
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 object is masked from 'package:limma':

    plotMA

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


Attaching package: 'SingleCellExperiment'

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

    cpm

Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'scater'

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

    plotMDS


Attaching package: 'dplyr'

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 object is masked from 'package:matrixStats':

    count

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘milo_demo.Rmd’

--- re-building ‘milo_gastrulation.Rmd’ using rmarkdown
Loading required package: SpatialExperiment
snapshotDate(): 2021-10-19
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
Constructing kNN graph with k:30
Checking valid object
Checking meta.data validity
Counting cells in neighbourhoods
Using TMM normalisation
Performing spatial FDR correction withk-distance weighting
Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Converting celltype to factor...
Converting group.by to factor...
Found 345 DA neighbourhoods at FDR 10%
nhoodAdjacency found - using for nhood grouping
Converting group.by to factor...
Found 345 DA neighbourhoods at FDR 10%
nhoodAdjacency found - using for nhood grouping
Converting group.by to factor...
Quitting from lines 397-402 (milo_gastrulation.Rmd) 
Error: processing vignette 'milo_gastrulation.Rmd' failed with diagnostics:
contrasts can be applied only to factors with 2 or more levels
--- failed re-building ‘milo_gastrulation.Rmd’

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

Error: Vignette re-building failed.
Execution halted