Back to Books build report for BioC 3.15

This page was generated on 2022-10-19 14:00:04 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
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BUILD results for OSCA.intro on nebbiolo1


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

raw results

Package 5/8HostnameOS / ArchINSTALLBUILD
OSCA.intro 1.4.1  (landing page)
Aaron Lun
Snapshot Date: 2022-10-19 06:45:01 -0400 (Wed, 19 Oct 2022)
git_url: https://git.bioconductor.org/packages/OSCA.intro
git_branch: RELEASE_3_15
git_last_commit: 3687787
git_last_commit_date: 2022-05-18 14:54:11 -0400 (Wed, 18 May 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  

Summary

Package: OSCA.intro
Version: 1.4.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.intro
StartedAt: 2022-10-19 07:01:08 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 07:03:28 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 140.7 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 OSCA.intro
###
##############################################################################
##############################################################################


* checking for file ‘OSCA.intro/DESCRIPTION’ ... OK
* preparing ‘OSCA.intro’:
* 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.knit'
--- finished re-building ‘stub.Rmd’

"/home/biocbuild/bbs-3.15-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.intro'); 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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.intro'); 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: sce-class.Rmd
# 
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#   ordinary text without R code
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# label: setup (with options) 
# List of 2
#  $ echo   : logi FALSE
#  $ results: chr "asis"
# 
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#    inline R code fragments
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# label: sce-structure (with options) 
# List of 3
#  $ fig.wide: logi TRUE
#  $ echo    : logi FALSE
#  $ fig.cap : chr "Overview of the structure of the `SingleCellExperiment` class. Each row of the assays corresponds to a row of t"| __truncated__
# 
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#    inline R code fragments
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#    inline R code fragments
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# label: unnamed-chunk-2 (with options) 
# List of 1
#  $ message: logi FALSE
# 
# 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
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# The following objects are masked from 'package:matrixStats':
# 
#     anyMissing, rowMedians
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#   ordinary text without R code
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# label: unnamed-chunk-3 (with options) 
# List of 1
#  $ eval: logi FALSE
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# label: unnamed-chunk-4 (with options) 
# List of 2
#  $ echo   : logi FALSE
#  $ results: chr "asis"
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#   ordinary text without R code
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# label: unnamed-chunk-5
# Loading required package: dbplyr
# adding rname 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip'
# Quitting from lines 61-66 (sce-class.Rmd) 
# Error in bfcrpath(bfc, file.path("https://www.ebi.ac.uk/arrayexpress/files",  : 
#   not all 'rnames' found or unique.
# Calls: <Anonymous> ... eval_with_user_handlers -> eval -> eval -> bfcrpath -> bfcrpath
# In addition: Warning messages:
# 1: download failed
#   web resource path: 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip'
#   local file path: 'raw_data/2aad922bd39fbd_E-MTAB-5522.processed.1.zip'
#   reason: Not Found (HTTP 404). 
# 2: bfcadd() failed; resource removed
#   rid: BFC2
#   fpath: 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip'
#   reason: download failed 
# 3: In value[[3L]](cond) : 
# trying to add rname 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip' produced error:
#   bfcadd() failed; see warnings()
# 
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/OSCA.intro/1.4.1/sce-class.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