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This page was generated on 2025-10-31 12:04 -0400 (Fri, 31 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 1773/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.10.0  (landing page)
Qian Liu
Snapshot Date: 2025-10-30 13:45 -0400 (Thu, 30 Oct 2025)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: RELEASE_3_22
git_last_commit: 2d4066b
git_last_commit_date: 2025-10-29 11:20:44 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for ReUseData on lconway

To the developers/maintainers of the ReUseData package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.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: ReUseData
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReUseData
StartedAt: 2025-10-30 18:19:08 -0400 (Thu, 30 Oct 2025)
EndedAt: 2025-10-30 18:36:29 -0400 (Thu, 30 Oct 2025)
EllapsedTime: 1041.1 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 ReUseData
###
##############################################################################
##############################################################################


* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* preparing ‘ReUseData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ReUseData_data.Rmd’ using rmarkdown
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 2.6.11-2-g1b7d2f0)

Inspect or clean up the working tree at /tmp/python-build.20251030182132.34858
Results logged to /tmp/python-build.20251030182132.34858.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[3]: *** [Programs/_freeze_module] Error 1
make[2]: *** [build_all_generate_profile] Error 2
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2

Quitting from ReUseData_data.Rmd:95-97 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.11 failed
---
Backtrace:
    ▆
 1. └─Rcwl::install_cwltool()
 2.   └─basilisk::basiliskStart(env_Rcwl)
 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 'ReUseData_data.Rmd' failed with diagnostics:
installation of Python 3.11 failed
--- failed re-building ‘ReUseData_data.Rmd’

--- re-building ‘ReUseData_quickStart.Rmd’ using rmarkdown
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 2.6.11-2-g1b7d2f0)

Inspect or clean up the working tree at /tmp/python-build.20251030182623.96868
Results logged to /tmp/python-build.20251030182623.96868.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[3]: *** [Programs/_freeze_module] Error 1
make[2]: *** [build_all_generate_profile] Error 2
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2

Quitting from ReUseData_quickStart.Rmd:74-76 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.11 failed
---
Backtrace:
    ▆
 1. └─Rcwl::install_cwltool()
 2.   └─basilisk::basiliskStart(env_Rcwl)
 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 'ReUseData_quickStart.Rmd' failed with diagnostics:
installation of Python 3.11 failed
--- failed re-building ‘ReUseData_quickStart.Rmd’

--- re-building ‘ReUseData_recipe.Rmd’ using rmarkdown
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 2.6.11-2-g1b7d2f0)

Inspect or clean up the working tree at /tmp/python-build.20251030183137.33807
Results logged to /tmp/python-build.20251030183137.33807.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[3]: *** [Programs/_freeze_module] Error 1
make[2]: *** [build_all_generate_profile] Error 2
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2

Quitting from ReUseData_recipe.Rmd:166-168 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.11 failed
---
Backtrace:
    ▆
 1. └─Rcwl::install_cwltool()
 2.   └─basilisk::basiliskStart(env_Rcwl)
 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 'ReUseData_recipe.Rmd' failed with diagnostics:
installation of Python 3.11 failed
--- failed re-building ‘ReUseData_recipe.Rmd’

SUMMARY: processing the following files failed:
  ‘ReUseData_data.Rmd’ ‘ReUseData_quickStart.Rmd’
  ‘ReUseData_recipe.Rmd’

Error: Vignette re-building failed.
Execution halted