Multiple platform build/check report for BioC 3.22 - BUILD results for Ibex on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4615
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4610
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 Ibex on merida1

To the developers/maintainers of the Ibex package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Ibex.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: Ibex

Version: 1.0.0

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

StartedAt: 2025-11-17 23:16:48 -0500 (Mon, 17 Nov 2025)

EndedAt: 2025-11-17 23:40:28 -0500 (Mon, 17 Nov 2025)

EllapsedTime: 1419.9 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 Ibex
###
##############################################################################
##############################################################################


* checking for file ‘Ibex/DESCRIPTION’ ... OK
* preparing ‘Ibex’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Ibex.Rmd’ using knitr
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.9.25.tar.xz...
-> https://www.python.org/ftp/python/3.9.25/Python-3.9.25.tar.xz
Installing Python-3.9.25...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk
Installed Python-3.9.25 to /Users/biocbuild/.pyenv/versions/3.9.25
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.22.0/Ibex/1.0.0/IbexEnv/lib/python3.9/site-packages (23.0.1)
Collecting pip
  Downloading pip-25.3-py3-none-any.whl (1.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 20.4 MB/s eta 0:00:00
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.22.0/Ibex/1.0.0/IbexEnv/lib/python3.9/site-packages (79.0.1)
Collecting setuptools
  Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 15.3 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 79.0.1
    Uninstalling setuptools-79.0.1:
      Successfully uninstalled setuptools-79.0.1
  Attempting uninstall: pip
    Found existing installation: pip 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Collecting keras==3.6.*
  Using cached keras-3.6.0-py3-none-any.whl.metadata (5.8 kB)
ERROR: Ignored the following versions that require a different python version: 3.11.0 Requires-Python >=3.10; 3.11.1 Requires-Python >=3.10; 3.11.2 Requires-Python >=3.10; 3.11.3 Requires-Python >=3.10; 3.12.0 Requires-Python >=3.10
ERROR: Could not find a version that satisfies the requirement tensorflow==2.18.* (from versions: 2.5.0, 2.5.1, 2.5.2, 2.5.3, 2.6.0rc0, 2.6.0rc1, 2.6.0rc2, 2.6.0, 2.6.1, 2.6.2, 2.6.3, 2.6.4, 2.6.5, 2.7.0rc0, 2.7.0rc1, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.8.0rc0, 2.8.0rc1, 2.8.0, 2.8.1, 2.8.2, 2.8.3, 2.8.4, 2.9.0rc0, 2.9.0rc1, 2.9.0rc2, 2.9.0, 2.9.1, 2.9.2, 2.9.3, 2.10.0rc0, 2.10.0rc1, 2.10.0rc2, 2.10.0rc3, 2.10.0, 2.10.1, 2.11.0rc0, 2.11.0rc1, 2.11.0rc2, 2.11.0, 2.11.1, 2.12.0rc0, 2.12.0rc1, 2.12.0, 2.12.1, 2.13.0rc0, 2.13.0rc1, 2.13.0rc2, 2.13.0, 2.13.1, 2.14.0rc0, 2.14.0rc1, 2.14.0, 2.14.1, 2.15.0rc0, 2.15.0rc1, 2.15.0, 2.15.1, 2.16.0rc0, 2.16.1, 2.16.2)
ERROR: No matching distribution found for tensorflow==2.18.*

Quitting from Ibex.Rmd:207-229 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'keras==3.6.*'", "'tensorflow==2.18.*'", "'h5py==3.13'", "'numpy==1.26'"
---
Backtrace:
    ▆
 1. └─Ibex::Ibex_matrix(...)
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::virtualenv_create(...)
 7.             └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Ibex.Rmd' failed with diagnostics:
Error installing package(s): "'keras==3.6.*'", "'tensorflow==2.18.*'", "'h5py==3.13'", "'numpy==1.26'"
--- failed re-building ‘Ibex.Rmd’

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

Error: Vignette re-building failed.
Execution halted