Back to Books build report for BioC 3.13

BUILD report for OSCA.basic on malbec2

This page was generated on 2021-05-07 12:45:05 -0400 (Fri, 07 May 2021).

To the developers/maintainers of the OSCA.basic package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 4/8HostnameOS / ArchINSTALLBUILD
OSCA.basic 0.99.14  (landing page)
Aaron Lun
Snapshot Date: 2021-05-07 03:30:02 -0400 (Fri, 07 May 2021)
URL: https://git.bioconductor.org/packages/OSCA.basic
Branch: master
Last Commit: 0415b64
Last Changed Date: 2021-05-02 01:45:52 -0400 (Sun, 02 May 2021)
malbec2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  

Summary

Package: OSCA.basic
Version: 0.99.14
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.basic
StartedAt: 2021-05-07 04:02:30 -0400 (Fri, 07 May 2021)
EndedAt: 2021-05-07 05:38:49 -0400 (Fri, 07 May 2021)
EllapsedTime: 5779.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.basic
###
##############################################################################
##############################################################################


* checking for file ‘OSCA.basic/DESCRIPTION’ ... OK
* preparing ‘OSCA.basic’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'stub.utf8'
--- finished re-building ‘stub.Rmd’

"/home/biocbuild/bbs-3.13-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.basic'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"

R version 4.1.0 alpha (2021-05-01 r80254)
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> work.dir <- rebook::bookCache('OSCA.basic'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)
# 
# 
# processing file: clustering.Rmd
# 
#   |                                                                            
#   |                                                                      |   0%
#   |                                                                            
#   |.                                                                     |   1%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |..                                                                    |   3%
# label: setup (with options) 
# List of 2
#  $ echo   : logi FALSE
#  $ results: chr "asis"
# 
# 
#   |                                                                            
#   |...                                                                   |   4%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |....                                                                  |   6%
# label: unnamed-chunk-1 (with options) 
# List of 2
#  $ results: chr "asis"
#  $ echo   : logi FALSE
# 
# 
#   |                                                                            
#   |.....                                                                 |   7%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |......                                                                |   9%
# label: unnamed-chunk-2
# Loading required package: SingleCellExperiment
# 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
# Loading required package: parallel
# 
# Attaching package: 'BiocGenerics'
# 
# The following objects are masked from 'package:parallel':
# 
#     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#     clusterExport, clusterMap, parApply, parCapply, parLapply,
#     parLapplyLB, parRapply, parSapply, parSapplyLB
# 
# 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
# 
# 
#   |                                                                            
#   |.......                                                               |  10%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |........                                                              |  11%
# label: unnamed-chunk-3 (with options) 
# List of 2
#  $ echo: logi FALSE
#  $ eval: logi FALSE
# 
# 
#   |                                                                            
#   |.........                                                             |  13%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |..........                                                            |  14%
# label: unnamed-chunk-4
# Loading required package: scuttle
# 
#   |                                                                            
#   |...........                                                           |  16%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |............                                                          |  17%
# label: tsne-clust-graph (with options) 
# List of 1
#  $ fig.cap: chr "$t$-SNE plot of the 10X PBMC dataset, where each point represents a cell and is coloured according to the ident"| __truncated__
# 
# Loading required package: ggplot2
# 
#   |                                                                            
#   |.............                                                         |  19%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |..............                                                        |  20%
# label: unnamed-chunk-5
# 
#   |                                                                            
#   |...............                                                       |  21%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |................                                                      |  23%
# label: pbmc-force (with options) 
# List of 2
#  $ message: logi FALSE
#  $ fig.cap: chr "Force-directed layout for the shared nearest-neighbor graph of the PBMC dataset. Each point represents a cell a"| __truncated__
# 
# 
#   |                                                                            
#   |.................                                                     |  24%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |..................                                                    |  26%
# label: unnamed-chunk-6
# 
#   |                                                                            
#   |...................                                                   |  27%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |....................                                                  |  29%
# label: unnamed-chunk-7 (with options) 
# List of 1
#  $ echo: logi FALSE
# 
# 
#   |                                                                            
#   |.....................                                                 |  30%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |......................                                                |  31%
# label: unnamed-chunk-8
# 
#   |                                                                            
#   |.......................                                               |  33%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |........................                                              |  34%
# label: unnamed-chunk-9
# 
#   |                                                                            
#   |.........................                                             |  36%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |..........................                                            |  37%
# label: walktrap-v-others (with options) 
# List of 2
#  $ fig.asp: num 2
#  $ fig.cap: chr "Number of cells assigned to combinations of cluster labels with different community detection algorithms in the"| __truncated__
# 
# 
#   |                                                                            
#   |...........................                                           |  39%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |............................                                          |  40%
# label: unnamed-chunk-10 (with options) 
# List of 1
#  $ echo: logi FALSE
# 
# 
#   |                                                                            
#   |.............................                                         |  41%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |..............................                                        |  43%
# label: tsne-clust-kmeans (with options) 
# List of 1
#  $ fig.cap: chr "$t$-SNE plot of the 10X PBMC dataset, where each point represents a cell and is coloured according to the ident"| __truncated__
# 
# 
#   |                                                                            
#   |...............................                                       |  44%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |................................                                      |  46%
# label: tsne-clust-kmeans-best (with options) 
# List of 1
#  $ fig.cap: chr "$t$-SNE plot of the 10X PBMC dataset, where each point represents a cell and is coloured according to the ident"| __truncated__
# 
# 
#   |                                                                            
#   |.................................                                     |  47%
#    inline R code fragments
# 
# 
#   |                                                                            
#   |..................................                                    |  49%
# label: unnamed-chunk-11
# 
#   |                                                                            
#   |...................................                                   |  50%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |....................................                                  |  51%
# label: tsne-kmeans-graph-pbmc (with options) 
# List of 1
#  $ fig.cap: chr "$t$-SNE plot of the PBMC dataset, where each point represents a cell and is coloured according to the identity "| __truncated__
# 
# 
#   |                                                                            
#   |.....................................                                 |  53%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |......................................                                |  54%
# label: unnamed-chunk-12 (with options) 
# List of 2
#  $ results: chr "asis"
#  $ echo   : logi FALSE
# 
# 
#   |                                                                            
#   |.......................................                               |  56%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |........................................                              |  57%
# label: unnamed-chunk-13
# 
#   |                                                                            
#   |.........................................                             |  59%
#   ordinary text without R code
# 
# 
#   |                                                                            
#   |..........................................                            |  60%
# label: dend-416b (with options) 
# List of 1
#  $ fig.cap: chr "Hierarchy of cells in the 416B data set after hierarchical clustering, where each leaf node is a cell that is c"| __truncated__
# 
# 
# ---------------------
# Welcome to dendextend version 1.14.0
# Type citation('dendextend') for how to cite the package.
# 
# Type browseVignettes(package = 'dendextend') for the package vignette.
# The github page is: https://github.com/talgalili/dendextend/
# 
# Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
# Or contact: <tal.galili@gmail.com>
# 
# 	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
# ---------------------
# 
# 
# Attaching package: 'dendextend'
# 
# The following object is masked from 'package:stats':
# 
#     cutree
# 
# Quitting from lines 374-393 (clustering.Rmd) 
# Error in UseMethod("as.dendrogram") : 
#   no applicable method for 'as.dendrogram' applied to an object of class "list"
# Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> as.dendrogram
# 
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/OSCA.basic/0.99.14/clustering.Rmd'
Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter
Execution halted
make: *** [Makefile:4: compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted