Back to Books build report for BioC 3.22

This page was generated on 2025-10-15 14:30 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
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 10/11HostnameOS / ArchINSTALLBUILDCHECK
OSTA 0.99.28  (landing page)
Lukas M. Weber
Snapshot Date: 2025-10-15 06:00 -0400 (Wed, 15 Oct 2025)
git_url: https://git.bioconductor.org/packages/OSTA
git_branch: devel
git_last_commit: a4bf4b9
git_last_commit_date: 2025-10-05 16:20:23 -0400 (Sun, 05 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skipped


BUILD results for OSTA on lconway

To the developers/maintainers of the OSTA 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: OSTA
Version: 0.99.28
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
StartedAt: 2025-10-15 06:18:00 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 06:24:19 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 378.5 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 OSTA
###
##############################################################################
##############################################################################


* checking for file ‘OSTA/DESCRIPTION’ ... OK
* preparing ‘OSTA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/38] index.qmd


processing file: index.qmd
1/4 [unnamed-chunk-1]
2/4                  
3/4 [carousel]       
4/4                  
output file: index.knit.md


[ 2/38] pages/bkg-introduction.qmd

[ 3/38] pages/bkg-spatial-omics.qmd

[ 4/38] pages/bkg-infrastructure.qmd


processing file: bkg-infrastructure.qmd
1/5                        
2/5 [fig-spatialexperiment]
3/5                        
4/5 [fig-spatialdata]      
5/5                        
output file: bkg-infrastructure.knit.md


[ 5/38] pages/bkg-ecosystem.qmd


processing file: bkg-ecosystem.qmd
1/19                  
2/19 [unnamed-chunk-1]
3/19                  
4/19 [unnamed-chunk-2]
5/19                  
6/19 [unnamed-chunk-3]
7/19                  
8/19 [unnamed-chunk-4]
9/19                  
10/19 [unnamed-chunk-5]
2025-10-15 06:20:30.979 R[95216:547285669] XType: com.apple.fonts is not accessible.
2025-10-15 06:20:30.979 R[95216:547285669] XType: XTFontStaticRegistry is enabled.
11/19                  
12/19 [unnamed-chunk-6]
13/19                  
14/19 [unnamed-chunk-7]
15/19                  
16/19 [unnamed-chunk-8]
17/19                  
18/19 [unnamed-chunk-9]
19/19                  
output file: bkg-ecosystem.knit.md


[ 6/38] pages/bkg-importing-data.qmd


processing file: bkg-importing-data.qmd
1/9                  
2/9 [unnamed-chunk-1]
3/9                  
4/9 [unnamed-chunk-2]
5/9                  
6/9 [unnamed-chunk-3]
7/9                  
8/9 [unnamed-chunk-4]
9/9                  
output file: bkg-importing-data.knit.md


[ 7/38] pages/bkg-example-datasets.qmd


processing file: bkg-example-datasets.qmd
1/5                     
2/5 [list-data]         
3/5                     
4/5 [list-stexampledata]
5/5                     
output file: bkg-example-datasets.knit.md


[ 8/38] pages/bkg-python-interoperability.qmd


processing file: bkg-python-interoperability.qmd
1/31                  
2/31 [libraries]      
3/31                  
4/31 [env]            
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.11.14.tar.xz...
-> https://www.python.org/ftp/python/3.11.14/Python-3.11.14.tar.xz
Installing Python-3.11.14...
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 2.6.10-1-g8d3bba2)

Inspect or clean up the working tree at /tmp/python-build.20251015062123.96722
Results logged to /tmp/python-build.20251015062123.96722.log

Last 10 log lines:
  "_mkfifoat", referenced from:
      _os_mkfifo in lto.o
  "_mknodat", referenced from:
      _os_mknod in lto.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[4]: *** [Programs/_freeze_module] Error 1
make[3]: *** [build_all_generate_profile] Error 2
make[2]: *** [profile-gen-stamp] Error 2
make[1]: *** [profile-run-stamp] Error 2
Error: installation of Python 3.11 failed

Quitting from bkg-python-interoperability.qmd:37-47 [env]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.11 failed
---
Backtrace:
     ▆
  1. ├─reticulate::use_virtualenv(obtainEnvironmentPath(env))
  2. │ └─reticulate:::virtualenv_path(virtualenv)
  3. │   └─reticulate:::python_environment_resolve(...)
  4. │     └─envname %||% Sys.getenv("RETICULATE_PYTHON_ENV", unset = "r-reticulate")
  5. └─basilisk::obtainEnvironmentPath(env)
  6.   └─basilisk::setupBasiliskEnv(...)
  7.     ├─base::suppressMessages(install_python(version))
  8.     │ └─base::withCallingHandlers(...)
  9.     └─reticulate::install_python(version)
 10.       └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
make: *** [render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted