Back to Books build report for BioC 3.22 |
This page was generated on 2025-10-15 14:30 -0400 (Wed, 15 Oct 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" | 4867 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4655 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 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 10/11 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
OSTA 0.99.28 (landing page) Lukas M. Weber
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||
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 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. |
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 |
############################################################################## ############################################################################## ### ### 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/ [1m[34m [ 1/38] index.qmd[39m[22m [31m processing file: index.qmd [39m1/4 [unnamed-chunk-1] 2/4 3/4 [carousel] 4/4 [31moutput file: index.knit.md [39m[1m[34m [ 2/38] pages/bkg-introduction.qmd[39m[22m [1m[34m [ 3/38] pages/bkg-spatial-omics.qmd[39m[22m [1m[34m [ 4/38] pages/bkg-infrastructure.qmd[39m[22m [31m processing file: bkg-infrastructure.qmd [39m1/5 2/5 [fig-spatialexperiment] 3/5 4/5 [fig-spatialdata] 5/5 [31moutput file: bkg-infrastructure.knit.md [39m[1m[34m [ 5/38] pages/bkg-ecosystem.qmd[39m[22m [31m processing file: bkg-ecosystem.qmd [39m1/19 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] [31m2025-10-15 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. [39m11/19 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 [31moutput file: bkg-ecosystem.knit.md [39m[1m[34m [ 6/38] pages/bkg-importing-data.qmd[39m[22m [31m processing file: bkg-importing-data.qmd [39m1/9 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 [31moutput file: bkg-importing-data.knit.md [39m[1m[34m [ 7/38] pages/bkg-example-datasets.qmd[39m[22m [31m processing file: bkg-example-datasets.qmd [39m1/5 2/5 [list-data] 3/5 4/5 [list-stexampledata] 5/5 [31moutput file: bkg-example-datasets.knit.md [39m[1m[34m [ 8/38] pages/bkg-python-interoperability.qmd[39m[22m [31m processing file: bkg-python-interoperability.qmd [39m1/31 2/31 [libraries] 3/31 4/31 [env] python-build: use openssl@3 from homebrew python-build: use readline from homebrew [31mDownloading Python-3.11.14.tar.xz... [39m[31m-> https://www.python.org/ftp/python/3.11.14/Python-3.11.14.tar.xz [39m[31mInstalling Python-3.11.14... [39mpython-build: use readline from homebrew python-build: use ncurses from homebrew python-build: use zlib from xcode sdk [31m [39m[31mBUILD FAILED[39m[31m (OS X 12.7.6 using python-build 2.6.10-1-g8d3bba2) [39m[31m [39m[31mInspect or clean up the working tree at /tmp/python-build.20251015062123.96722 [39m[31mResults logged to /tmp/python-build.20251015062123.96722.log [39m[31mLast 10 log lines: [39m[31m "_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 [39m[31mError: installation of Python 3.11 failed [39m[31m 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) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [39m[31mExecution halted [39mmake: *** [render] Error 1 Error in tools::buildVignettes(dir = ".", tangle = TRUE) : running 'make' failed Execution halted