Multiple platform build/check report for BioC 3.22 - BUILD results for Pirat on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
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*

BUILD results for Pirat on lconway

To the developers/maintainers of the Pirat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pirat.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: Pirat

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat

StartedAt: 2025-08-08 18:08:04 -0400 (Fri, 08 Aug 2025)

EndedAt: 2025-08-08 18:09:00 -0400 (Fri, 08 Aug 2025)

EllapsedTime: 56.1 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 Pirat
###
##############################################################################
##############################################################################


* checking for file ‘Pirat/DESCRIPTION’ ... OK
* preparing ‘Pirat’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Pirat.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.9.5.tar.xz...
-> https://www.python.org/ftp/python/3.9.5/Python-3.9.5.tar.xz
Installing Python-3.9.5...
patching file Misc/NEWS.d/next/Build/2021-10-11-16-27-38.bpo-45405.iSfdW5.rst
patching file configure
patching file configure.ac
python-build: use readline from homebrew
python-build: use ncurses from homebrew
xcode-select: error: tool 'xcodebuild' requires Xcode, but active developer directory '/Library/Developer/CommandLineTools' is a command line tools instance

BUILD FAILED (OS X 12.7.6 using python-build 2.6.6-1-g685f281)

Inspect or clean up the working tree at /tmp/python-build.20250808180844.27786
Results logged to /tmp/python-build.20250808180844.27786.log

Last 10 log lines:
/tmp/python-build.20250808180844.27786 /private/tmp/RtmpNelB0S/Rbuild54c2723a4d4a/Pirat/vignettes
/tmp/python-build.20250808180844.27786/Python-3.9.5 /tmp/python-build.20250808180844.27786 /private/tmp/RtmpNelB0S/Rbuild54c2723a4d4a/Pirat/vignettes
python-build: use zlib from homebrew

BUILD FAILED (OS X 12.7.6 using python-build 2.6.6-1-g685f281)

Inspect or clean up the working tree at /tmp/python-build.20250808180844.27786
Results logged to /tmp/python-build.20250808180844.27786.log

Last 10 log lines:
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for --with-pydebug... no
checking for --with-trace-refs... no
checking for --with-assertions... no
checking for --enable-optimizations... yes
checking PROFILE_TASK... -m test --pgo
checking for --with-lto... yes
checking for llvm-ar... no
configure: error: llvm-ar is required for a --with-lto build with clang but could not be found.
make: *** No targets specified and no makefile found.  Stop.

Quitting from Pirat.Rmd:90-92 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.9.5 failed
---
Backtrace:
    ▆
 1. └─Pirat::my_pipeline_llkimpute(subbouyssie)
 2.   └─basilisk::basiliskStart(envPirat)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         ├─base::suppressMessages(install_python(version))
 6.         │ └─base::withCallingHandlers(...)
 7.         └─reticulate::install_python(version)
 8.           └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Pirat.Rmd' failed with diagnostics:
installation of Python 3.9.5 failed
--- failed re-building ‘Pirat.Rmd’

SUMMARY: processing the following file failed:
  ‘Pirat.Rmd’

Error: Vignette re-building failed.
Execution halted