Back to Books build report for BioC 3.22

This page was generated on 2025-11-07 14:30 -0500 (Fri, 07 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4902
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4692
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4638
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 7/11HostnameOS / ArchINSTALLBUILDCHECK
OSCA.intro 1.18.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2025-11-07 06:30 -0500 (Fri, 07 Nov 2025)
git_url: https://git.bioconductor.org/packages/OSCA.intro
git_branch: RELEASE_3_22
git_last_commit: eb57eb4
git_last_commit_date: 2025-10-29 10:12:56 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skipped


BUILD results for OSCA.intro on lconway

To the developers/maintainers of the OSCA.intro 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: OSCA.intro
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.intro
StartedAt: 2025-11-07 06:47:13 -0500 (Fri, 07 Nov 2025)
EndedAt: 2025-11-07 06:50:52 -0500 (Fri, 07 Nov 2025)
EllapsedTime: 219.8 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 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’

"/Library/Frameworks/R.framework/Resources/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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: getting-datasets.Rmd
# 1/42                   
# 2/42 [setup]           
# 3/42                   
# 4/42 [unnamed-chunk-1] 
# 5/42                   
# 6/42 [unnamed-chunk-2] 
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# 19/42                   
# 20/42 [unnamed-chunk-9] 
# 21/42                   
# 22/42 [unnamed-chunk-10]
# 23/42                   
# 24/42 [unnamed-chunk-11]
# 25/42                   
# 26/42 [unnamed-chunk-12]
# 27/42                   
# 28/42 [unnamed-chunk-13]
# 29/42                   
# 30/42 [unnamed-chunk-14]
# 31/42                   
# 32/42 [unnamed-chunk-15]
# 33/42                   
# 34/42 [unnamed-chunk-16]
# 35/42                   
# 36/42 [unnamed-chunk-17]
# 37/42                   
# 38/42 [unnamed-chunk-18]
# python-build: use openssl@3 from homebrew
# python-build: use readline from homebrew
# Downloading Python-3.14.0.tar.xz...
# -> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
# Installing Python-3.14.0...
# python-build: use readline from homebrew
# python-build: use ncurses from homebrew
# python-build: use zlib from xcode sdk
# 
# BUILD FAILED (OS X 12.7.6 using python-build 2.6.12-1-g032022d)
# 
# Inspect or clean up the working tree at /tmp/python-build.20251107064857.92142
# Results logged to /tmp/python-build.20251107064857.92142.log
# 
# Last 10 log lines:
# Undefined symbols for architecture x86_64:
#   "_mkfifoat", referenced from:
#       _os_mkfifo in 158.x86_64.thinlto.o
#   "_mknodat", referenced from:
#       _os_mknod in 158.x86_64.thinlto.o
# ld: symbol(s) not found for architecture x86_64
# clang: error: linker command failed with exit code 1 (use -v to see invocation)
# make[3]: *** [Programs/_freeze_module] Error 1
# make[2]: *** [profile-gen-stamp] Error 2
# make[1]: *** [profile-run-stamp] Error 2
# Error: installation of Python 3.14.0 failed
# 
# Quitting from getting-datasets.Rmd:231-236 [unnamed-chunk-18]
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# <error/rlang_error>
# Error:
# ! installation of Python 3.14.0 failed
# ---
# Backtrace:
#     ▆
#  1. └─zellkonverter::readH5AD(demo)
#  2.   └─basilisk::basiliskRun(...)
#  3.     └─basilisk::basiliskStart(...)
#  4.       └─basilisk::obtainEnvironmentPath(env)
#  5.         └─basilisk::setupBasiliskEnv(...)
#  6.           ├─base::suppressMessages(install_python(version))
#  7.           │ └─base::withCallingHandlers(...)
#  8.           └─reticulate::install_python(version)
#  9.             └─reticulate:::stopf("installation of Python %s failed", version)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/Library/Caches/rebook/OSCA.intro/1.18.0/getting-datasets.Rmd'
Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter
Execution halted
make: *** [compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted