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This page was generated on 2021-11-29 15:06:01 -0500 (Mon, 29 Nov 2021).

BUILD results for miloR on machv2

To the developers/maintainers of the miloR package:
- 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: 2021-11-28 04:15:06 -0500 (Sun, 28 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    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: miloR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data miloR
StartedAt: 2021-11-28 10:15:02 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 10:21:05 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 363.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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
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
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
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
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
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
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
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
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
loading from cache
see ?MouseGastrulationData and browseVignettes('MouseGastrulationData') for documentation
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 361 DA neighbourhoods at FDR 10%
nhoodAdjacency found - using for nhood grouping
Converting group.by to factor...
Found 361 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