Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-15 12:06 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 188/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocHubsShiny 1.9.1  (landing page)
Marcel Ramos
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025)
git_url: https://git.bioconductor.org/packages/BiocHubsShiny
git_branch: devel
git_last_commit: 7916978
git_last_commit_date: 2025-05-21 19:32:36 -0400 (Wed, 21 May 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BiocHubsShiny on palomino8

To the developers/maintainers of the BiocHubsShiny package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocHubsShiny.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: BiocHubsShiny
Version: 1.9.1
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocHubsShiny.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings BiocHubsShiny_1.9.1.tar.gz
StartedAt: 2025-08-15 00:55:41 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 00:58:40 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 178.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocHubsShiny.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocHubsShiny.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings BiocHubsShiny_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/BiocHubsShiny.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocHubsShiny/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiocHubsShiny' version '1.9.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BiocHubsShiny' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BiocHubsShiny.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL BiocHubsShiny
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'BiocHubsShiny' ...
** this is package 'BiocHubsShiny' version '1.9.1'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocHubsShiny)

Tests output

BiocHubsShiny.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> shinytest2::test_app()
Loading required package: testthat
Loading required package: shiny
✔ | F W  S  OK | Context

⠏ |          0 | server                                                         ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpkrvjFb/file213042e8d562a". Did you mean command "preview"?

⠋ |   1      0 | server                                                         
⠙ |   1      1 | server                                                         
⠹ |   1      2 | server                                                         
✔ |   1      2 | server [28.2s]
────────────────────────────────────────────────────────────────────────────────
Warning ('test-server.R:4:9'): (code run outside of `test_that()`)
running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpkrvjFb/file213042e8d562a -V' had status 1
Backtrace:
      ▆
   1. ├─shiny::testServer(...) at test-server.R:1:1
   2. │ ├─shiny:::withMockContext(...)
   3. │ │ ├─shiny::isolate(...)
   4. │ │ │ ├─shiny::..stacktraceoff..(...)
   5. │ │ │ └─ctx$run(...)
   6. │ │ │   ├─promises::with_promise_domain(...)
   7. │ │ │   │ └─domain$wrapSync(expr)
   8. │ │ │   ├─shiny::withReactiveDomain(...)
   9. │ │ │   │ └─promises::with_promise_domain(...)
  10. │ │ │   │   └─domain$wrapSync(expr)
  11. │ │ │   │     └─base::force(expr)
  12. │ │ │   ├─shiny::captureStackTraces(...)
  13. │ │ │   │ └─promises::with_promise_domain(...)
  14. │ │ │   │   └─domain$wrapSync(expr)
  15. │ │ │   │     └─base::withCallingHandlers(expr, error = doCaptureStack)
  16. │ │ │   └─env$runWith(self, func)
  17. │ │ │     └─shiny (local) contextFunc()
  18. │ │ │       └─shiny::..stacktraceon..(expr)
  19. │ │ ├─shiny::withReactiveDomain(...)
  20. │ │ │ └─promises::with_promise_domain(...)
  21. │ │ │   └─domain$wrapSync(expr)
  22. │ │ │     └─base::force(expr)
  23. │ │ └─withr::with_options(...)
  24. │ │   └─base::force(code)
  25. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
  26. └─session$setInputs(hub = "AnnotationHub") at test-server.R:4:9
  27.   └─private$flush()
  28.     └─shiny:::flushReact()
  29.       └─.getReactiveEnvironment()$flush()
  30.         └─ctx$executeFlushCallbacks()
  31.           └─base::lapply(...)
  32.             └─shiny (local) FUN(X[[i]], ...)
  33.               └─shiny (local) flushCallback()
  34.                 ├─shiny:::hybrid_chain(...)
  35.                 │ └─shiny (local) do()
  36.                 │   ├─base::tryCatch(...)
  37.                 │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  38.                 │   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  39.                 │   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  40.                 │   ├─shiny::captureStackTraces(...)
  41.                 │   │ └─promises::with_promise_domain(...)
  42.                 │   │   └─domain$wrapSync(expr)
  43.                 │   │     └─base::withCallingHandlers(expr, error = doCaptureStack)
  44.                 │   ├─base::withVisible(force(expr))
  45.                 │   └─base::force(expr)
  46.                 ├─shiny:::shinyCallingHandlers(run())
  47.                 │ ├─base::withCallingHandlers(...)
  48.                 │ └─shiny::captureStackTraces(expr)
  49.                 │   └─promises::with_promise_domain(...)
  50.                 │     └─domain$wrapSync(expr)
  51.                 │       └─base::withCallingHandlers(expr, error = doCaptureStack)
  52.                 └─shiny (local) run()
  53.                   └─ctx$run(.func)
  54.                     ├─promises::with_promise_domain(...)
  55.                     │ └─domain$wrapSync(expr)
  56.                     ├─shiny::withReactiveDomain(...)
  57.                     │ └─promises::with_promise_domain(...)
  58.                     │   └─domain$wrapSync(expr)
  59.                     │     └─base::force(expr)
  60.                     ├─shiny::captureStackTraces(...)
  61.                     │ └─promises::with_promise_domain(...)
  62.                     │   └─domain$wrapSync(expr)
  63.                     │     └─base::withCallingHandlers(expr, error = doCaptureStack)
  64.                     └─env$runWith(self, func)
  65.                       └─shiny (local) contextFunc()
  66.                         ├─shiny::..stacktraceon..(`<observer>`(...))
  67.                         └─shiny (local) `<observer>`(...)
  68.                           └─shiny::observe()
  69.                             ├─base::tryCatch(...)
  70.                             │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  71.                             │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  72.                             │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  73.                             ├─private$withCurrentOutput(name, func(self, name))
  74.                             │ └─promises::with_promise_domain(...)
  75.                             │   └─domain$wrapSync(expr)
  76.                             │     └─base::force(expr)
  77.                             └─shiny (local) func(self, name)
  78.                               └─shiny (local) renderFunc(...)
  79.                                 ├─shiny:::hybrid_chain(...)
  80.                                 │ └─shiny (local) do()
  81.                                 │   ├─base::tryCatch(...)
  82.                                 │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  83.                                 │   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  84.                                 │   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  85.                                 │   ├─shiny::captureStackTraces(...)
  86.                                 │   │ └─promises::with_promise_domain(...)
  87.                                 │   │   └─domain$wrapSync(expr)
  88.                                 │   │     └─base::withCallingHandlers(expr, error = doCaptureStack)
  89.                                 │   ├─base::withVisible(force(expr))
  90.                                 │   └─base::force(expr)
  91.                                 ├─promises::with_promise_domain(domain, func())
  92.                                 │ └─domain$wrapSync(expr)
  93.                                 │   └─base::force(expr)
  94.                                 └─shiny (local) func()
  95.                                   └─BiocHubsShiny (local) renderPrint()
  96.                                     ├─utils::capture.output(sessioninfo::session_info())
  97.                                     │ └─base::withVisible(...elt(i))
  98.                                     └─sessioninfo::session_info()
  99.                                       ├─base::structure(...)
 100.                                       ├─sessioninfo:::drop_null(...)
 101.                                       └─sessioninfo::platform_info()
 102.                                         ├─sessioninfo:::as_platform_info(...)
 103.                                         │ └─base::stopifnot(is.list(x))
 104.                                         ├─sessioninfo:::drop_null(...)
 105.                                         └─sessioninfo:::get_quarto_version()
 106.                                           └─base::system2(...)
────────────────────────────────────────────────────────────────────────────────

⠏ |          0 | shinytest2                                                     
⠙ |      2   0 | shinytest2                                                     
✔ |      3   0 | shinytest2

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 28.6 s

── Skipped tests (3) ───────────────────────────────────────────────────────────
• On CRAN (3): 'test-shinytest2.R:6:5', 'test-shinytest2.R:19:5',
  'test-shinytest2.R:31:5'

[ FAIL 0 | WARN 1 | SKIP 3 | PASS 2 ]
Deleting unused snapshots:
• linux-4.3/shinytest2/BiocHubsShiny-EH-001.png
• linux-4.3/shinytest2/BiocHubsShiny-about-001.png
• linux-4.3/shinytest2/BiocHubsShiny-selection-001.png
> 
> proc.time()
   user  system elapsed 
  20.26    2.14   30.95

Example timings

BiocHubsShiny.Rcheck/BiocHubsShiny-Ex.timings

nameusersystemelapsed
BiocHubsShiny000