Back to Books build report for BioC 3.19

This page was generated on 2024-10-18 14:30 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2/10HostnameOS / ArchINSTALLBUILDCHECK
csawBook 1.12.0  (landing page)
Aaron Lun
Snapshot Date: 2024-10-18 07:15 -0400 (Fri, 18 Oct 2024)
git_url: https://git.bioconductor.org/packages/csawBook
git_branch: RELEASE_3_19
git_last_commit: fefc393
git_last_commit_date: 2024-04-30 10:23:15 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for csawBook on nebbiolo1

To the developers/maintainers of the csawBook package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: csawBook
Version: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data csawBook
StartedAt: 2024-10-18 07:32:07 -0400 (Fri, 18 Oct 2024)
EndedAt: 2024-10-18 08:33:15 -0400 (Fri, 18 Oct 2024)
EllapsedTime: 3667.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data csawBook
###
##############################################################################
##############################################################################


* checking for file ‘csawBook/DESCRIPTION’ ... OK
* preparing ‘csawBook’:
* 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-3.19-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('csawBook'); 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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('csawBook'); 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: h3k9ac.Rmd
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# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791218dcf68_2075'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791218dcf68_2075'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791218dcf68_2075'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f79194c103c_2076'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f79194c103c_2076'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f79194c103c_2076'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f7915b61b81c_2077'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f7915b61b81c_2077'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f7915b61b81c_2077'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078'
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078'
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078'
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# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791218dcf68_2075'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f79194c103c_2076'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f7915b61b81c_2077'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078'
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
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# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791218dcf68_2075'
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# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f7915b61b81c_2077'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078'
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
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# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791218dcf68_2075'
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# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f7915b61b81c_2077'
# [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078'
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
# [W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/19f791723dfc8b_2078
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# Error:
# ! first region does not match expectations
# Backtrace:
#   1. rmarkdown::render(commandArgs(TRUE))
#   2. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
#   3. knitr:::process_file(text, output)
#   6. knitr:::process_group(group)
#   7. knitr:::call_block(x)
#      ...
#  14. base::withRestarts(...)
#  15. base (local) withRestartList(expr, restarts)
#  16. base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#  17. base (local) docall(restart$handler, restartArgs)
#  19. evaluate (local) fun(base::quote(`<smplErrr>`))
# 
# Quitting from lines 471-474 [unnamed-chunk-30] (h3k9ac.Rmd)
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/csawBook/1.12.0/h3k9ac.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