Back to Build/check report for BioC 3.23 experimental data
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This page was generated on 2025-10-30 15:01 -0400 (Thu, 30 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4428
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 118/430HostnameOS / ArchINSTALLBUILDCHECK
estrogen 1.57.0  (landing page)
Wolfgang Huber
Snapshot Date: 2025-10-30 07:00 -0400 (Thu, 30 Oct 2025)
git_url: https://git.bioconductor.org/packages/estrogen
git_branch: devel
git_last_commit: 83848e7
git_last_commit_date: 2025-10-29 09:23:31 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped


BUILD results for estrogen on nebbiolo1

To the developers/maintainers of the estrogen 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: estrogen
Version: 1.57.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data estrogen
StartedAt: 2025-10-30 11:14:59 -0400 (Thu, 30 Oct 2025)
EndedAt: 2025-10-30 11:15:11 -0400 (Thu, 30 Oct 2025)
EllapsedTime: 11.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data estrogen
###
##############################################################################
##############################################################################


* checking for file ‘estrogen/DESCRIPTION’ ... OK
* preparing ‘estrogen’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘estrogen.Rnw’ using knitr

Quitting from estrogen.Rnw:78-80 [a.show]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unknown Bioconductor version '3.23'; see https://bioconductor.org/install
---
Backtrace:
     x
  1. \-tools::buildVignettes(dir = ".", tangle = TRUE)
  2.   +-base::tryCatch(...)
  3.   | \-base (local) tryCatchList(expr, classes, parentenv, handlers)
  4.   |   \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5.   |     \-base (local) doTryCatch(return(expr), name, parentenv, handler)
  6.   \-engine$weave(file, quiet = quiet, encoding = enc)
  7.     \-(if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", ...
  8.       \-knitr:::process_file(text, output)
  9.         +-xfun:::handle_error(...)
 10.         +-base::withCallingHandlers(...)
 11.         \-knitr:::process_group(group)
 12.           \-knitr:::call_block(x)
 13.             \-knitr:::block_exec(params)
 14.               \-knitr:::eng_r(options)
 15.                 +-knitr:::in_input_dir(...)
 16.                 | \-knitr:::in_dir(input_dir(), expr)
 17.                 \-knitr (local) evaluate(...)
 18.                   \-evaluate::evaluate(...)
 19.                     +-base::withRestarts(...)
 20.                     | \-base (local) withRestartList(expr, restarts)
 21.                     |   +-base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 22.                     |   | \-base (local) doWithOneRestart(return(expr), restart)
 23.                     |   \-base (local) withRestartList(expr, restarts[-nr])
 24.                     |     \-base (local) withOneRestart(expr, restarts[[1L]])
 25.                     |       \-base (local) doWithOneRestart(return(expr), restart)
 26.                     +-evaluate:::with_handlers(...)
 27.                     | +-base::eval(call)
 28.                     | | \-base::eval(call)
 29.                     | \-base::withCallingHandlers(...)
 30.                     \-watcher$print_value(ev$value, ev$visible, envir)
 31.                       +-base::withVisible(handle_value(handler, value, visible, envir))
 32.                       \-evaluate:::handle_value(handler, value, visible, envir)
 33.                         \-handler$value(value, visible)
 34.                           \-knitr (local) fun(x, options = options)
 35.                             +-base::withVisible(knit_print(x, ...))
 36.                             +-knitr::knit_print(x, ...)
 37.                             \-knitr:::knit_print.default(x, ...)
 38.                               \-knitr::normal_print(x)
 39.                                 +-methods::show(x)
 40.                                 \-methods::show(x)
 41.                                   +-base::cat(...)
 42.                                   +-Biobase::featureNames(object)
 43.                                   \-affy::featureNames(object)
 44.                                     \-affy::getCdfInfo(object)
 45.                                       \-affy::cdfFromBioC(cdfname, cur$where, verbose)
 46.                                         +-base::sapply(repositories(), contrib.url)
 47.                                         | \-base::lapply(X = X, FUN = FUN, ...)
 48.                                         \-BiocManager::repositories()
 49.                                           \-BiocManager:::.version_validate(version)
 50.                                             +-base::ifelse(.is_CRAN_check(), .message(txt), .stop(txt))
 51.                                             \-BiocManager:::.stop(txt)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'estrogen.Rnw' failed with diagnostics:
unknown Bioconductor version '3.23'; see https://bioconductor.org/install
--- failed re-building ‘estrogen.Rnw’

SUMMARY: processing the following file failed:
  ‘estrogen.Rnw’

Error: Vignette re-building failed.
Execution halted