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This page was generated on 2025-11-20 12:05 -0500 (Thu, 20 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4615
merida1macOS 12.7.6 Montereyx86_644.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" 4610
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4598
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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

Package 2042/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sketchR 1.6.0  (landing page)
Charlotte Soneson
Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025)
git_url: https://git.bioconductor.org/packages/sketchR
git_branch: RELEASE_3_22
git_last_commit: b2a0713
git_last_commit_date: 2025-10-29 11:28:06 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.7.5 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD results for sketchR on merida1

To the developers/maintainers of the sketchR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sketchR.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: sketchR
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data sketchR
StartedAt: 2025-11-18 02:22:34 -0500 (Tue, 18 Nov 2025)
EndedAt: 2025-11-18 02:33:36 -0500 (Tue, 18 Nov 2025)
EllapsedTime: 661.6 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 sketchR
###
##############################################################################
##############################################################################


* checking for file ‘sketchR/DESCRIPTION’ ... OK
* preparing ‘sketchR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘sketchR.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.10.tar.xz...
-> https://www.python.org/ftp/python/3.12.10/Python-3.12.10.tar.xz
Installing Python-3.12.10...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12-2-g2afd173)

Inspect or clean up the working tree at /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251118022446.6412
Results logged to /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251118022446.6412.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 127.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 127.x86_64.thinlto.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[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2

Quitting from sketchR.Rmd:133-138 [geosketch]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.10 failed
---
Backtrace:
    ▆
 1. └─sketchR::geosketch(reducedDim(pbmc3k, "PCA"), N = 800, seed = 123)
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sketchR.Rmd' failed with diagnostics:
installation of Python 3.12.10 failed
--- failed re-building ‘sketchR.Rmd’

--- re-building ‘sketching_workflows.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.10.tar.xz...
-> https://www.python.org/ftp/python/3.12.10/Python-3.12.10.tar.xz
Installing Python-3.12.10...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12-2-g2afd173)

Inspect or clean up the working tree at /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251118022928.31849
Results logged to /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251118022928.31849.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 127.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 127.x86_64.thinlto.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[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2

Quitting from sketching_workflows.Rmd:60-97 [process-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.10 failed
---
Backtrace:
    ▆
 1. └─snifter::fitsne(...)
 2.   └─snifter:::.create_tsne(...)
 3.     └─basilisk::basiliskStart(python_env)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sketching_workflows.Rmd' failed with diagnostics:
installation of Python 3.12.10 failed
--- failed re-building ‘sketching_workflows.Rmd’

SUMMARY: processing the following files failed:
  ‘sketchR.Rmd’ ‘sketching_workflows.Rmd’

Error: Vignette re-building failed.
Execution halted