| Back to Books build report for BioC 3.22 |
This page was generated on 2025-11-07 14:30 -0500 (Fri, 07 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 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 7/11 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| OSCA.intro 1.18.0 (landing page) Ludwig Geistlinger
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | |||||||||
|
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. |
| 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 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.intro
###
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* 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]
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# 4/42 [unnamed-chunk-1]
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# 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