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This page was generated on 2025-12-22 12:06 -0500 (Mon, 22 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4607
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4671
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 1345/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA2 1.20.1  (landing page)
Ricard Argelaguet
Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 2025)
git_url: https://git.bioconductor.org/packages/MOFA2
git_branch: RELEASE_3_22
git_last_commit: 2d16576
git_last_commit_date: 2025-12-17 08:41:14 -0500 (Wed, 17 Dec 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  YES
merida1macOS 12.7.6 Monterey / x86_64  OK    TIMEOUT  skippedskipped
kjohnson1macOS 13.7.5 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  

BUILD results for MOFA2 on kjohnson1

To the developers/maintainers of the MOFA2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOFA2.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: MOFA2
Version: 1.20.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MOFA2
StartedAt: 2025-12-19 04:38:40 -0500 (Fri, 19 Dec 2025)
EndedAt: 2025-12-19 05:00:06 -0500 (Fri, 19 Dec 2025)
EllapsedTime: 1286.1 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 MOFA2
###
##############################################################################
##############################################################################


* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* preparing ‘MOFA2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MEFISTO_temporal.Rmd’ using rmarkdown
2025-12-19 04:39:18.657 R[65590:324662083] XType: Using static font registry.
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.12.tar.xz...
-> https://www.python.org/ftp/python/3.12.12/Python-3.12.12.tar.xz
Installing Python-3.12.12...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 13.7.8 using python-build 2.6.17)

Inspect or clean up the working tree at /tmp/python-build.20251219043925.66418
Results logged to /tmp/python-build.20251219043925.66418.log

Last 10 log lines:
/usr/bin/install -c -m 755 Modules/select.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/select.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_socket.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_socket.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/syslog.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/syslog.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/termios.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/termios.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_posixshmem.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_posixshmem.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_multiprocessing.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_ctypes.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_ctypes.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_curses.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_curses.cpython-312-darwin.so
install: Modules/_curses.cpython-312-darwin.so: No such file or directory
make: *** [sharedinstall] Error 71

Quitting from MEFISTO_temporal.Rmd:95-98 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.12 failed
---
Backtrace:
    ▆
 1. └─MOFA2::run_mofa(sm, outfile, use_basilisk = TRUE)
 2.   └─basilisk::basiliskStart(mofa_env)
 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 'MEFISTO_temporal.Rmd' failed with diagnostics:
installation of Python 3.12.12 failed
--- failed re-building ‘MEFISTO_temporal.Rmd’

--- re-building ‘downstream_analysis.Rmd’ using rmarkdown
--- finished re-building ‘downstream_analysis.Rmd’

--- re-building ‘getting_started_R.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.12.tar.xz...
-> https://www.python.org/ftp/python/3.12.12/Python-3.12.12.tar.xz
Installing Python-3.12.12...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 13.7.8 using python-build 2.6.17)

Inspect or clean up the working tree at /tmp/python-build.20251219045000.87357
Results logged to /tmp/python-build.20251219045000.87357.log

Last 10 log lines:
/usr/bin/install -c -m 755 Modules/select.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/select.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_socket.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_socket.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/syslog.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/syslog.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/termios.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/termios.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_posixshmem.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_posixshmem.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_multiprocessing.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_ctypes.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_ctypes.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_curses.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_curses.cpython-312-darwin.so
install: Modules/_curses.cpython-312-darwin.so: No such file or directory
make: *** [sharedinstall] Error 71

Quitting from getting_started_R.Rmd:212-215 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.12 failed
---
Backtrace:
    ▆
 1. └─MOFA2::run_mofa(MOFAobject, outfile, use_basilisk = TRUE)
 2.   └─basilisk::basiliskStart(mofa_env)
 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 'getting_started_R.Rmd' failed with diagnostics:
installation of Python 3.12.12 failed
--- failed re-building ‘getting_started_R.Rmd’

SUMMARY: processing the following files failed:
  ‘MEFISTO_temporal.Rmd’ ‘getting_started_R.Rmd’

Error: Vignette re-building failed.
Execution halted