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This page was generated on 2025-11-20 12:06 -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 1085/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEEfier 1.6.0  (landing page)
Najla Abassi
Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025)
git_url: https://git.bioconductor.org/packages/iSEEfier
git_branch: RELEASE_3_22
git_last_commit: 164f3c4
git_last_commit_date: 2025-10-29 11:29:10 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for iSEEfier on kjohnson1

To the developers/maintainers of the iSEEfier package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iSEEfier.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: iSEEfier
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEfier.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEfier_1.6.0.tar.gz
StartedAt: 2025-11-18 08:05:33 -0500 (Tue, 18 Nov 2025)
EndedAt: 2025-11-18 08:07:25 -0500 (Tue, 18 Nov 2025)
EllapsedTime: 112.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: iSEEfier.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEfier.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEfier_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/iSEEfier.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEEfier/DESCRIPTION’ ... OK
* this is package ‘iSEEfier’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘iSEEfier’ 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 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 ... ERROR
Running examples in ‘iSEEfier-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glue_initials
> ### Title: Glue together initial objects into one
> ### Aliases: glue_initials
> 
> ### ** Examples
> 
> ## Load a dataset and preprocess this quickly
> sce <- scRNAseq::RichardTCellData()
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
ℹ <!DOCTYPE html> <!--[if lt IE 7]> <html class="no-js ie6 oldie" lang="en-US">
  <![endif]--> <!--[if IE 7]> <html class="no-js ie7 oldie" lang="en-US">
  <![endif]--> <!--[if IE 8]> <html class="no-js ie8 oldie" lang="en-US">
  <![endif]--> <!--[if gt IE 8]><!--> <html class="no-js" lang="en-US">
  <!--<![endif]--> <head>

<title>artifactdb.com | 500: Internal server error</title> <meta
  charset="UTF-8" /> <meta http-equiv="Content-Type" content="text/html;
  charset=UTF-8" /> <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta name="robots" content="noindex, nofollow" /> <meta name="viewport"
  content="width=device-width,initial-scale=1" /> <link rel="stylesheet"
  id="cf_styles-css" href="/cdn-cgi/styles/main.css" /> </head> <body> <div
  id="cf-wrapper"> <div id="cf-error-details" class="p-0"> <header
  class="mx-auto pt-10 lg:pt-6 lg:px-8 w-240 lg:w-full mb-8"> <h1
  class="inline-block sm:block sm:mb-2 font-light text-60 lg:text-4xl
  text-black-dark leading-tight mr-2"> <span class="inline-block">Internal
  server error</span> <span class="code-label">Error code 500</span> </h1>
  <div> Visit <a
  href="https://www.cloudflare.com/5xx-error-landing?utm_source=errorcode_500&utm_campaign=gypsum.artifactdb.com"
  target="_blank" rel="noopener noreferrer">cloudflare.com</a> for more
  information.  </div> <div class="mt-3">2025-11-18 13:07:05 UTC</div>
  </header> <div class="my-8 bg-gradient-gray"> <div class="w-240 lg:w-full
  mx-auto"> <div class="clearfix md:px-8"> <div id="cf-browser-status" class="
  relative w-1/3 md:w-full py-15 md:p-0 md:py-8 md:text-left md:border-solid
  md:border-0 md:border-b md:border-gray-400 overflow-hidden float-left
  md:float-none text-center"> <div class="relative mb-10 md:m-0">

<span class="cf-icon-browser block md:hidden h-20 bg-center
  bg-no-repeat"></span> <span class="cf-icon-ok w-12 h-12 absolute left-1/2
  md:left-auto md:right-0 md:top-0 -ml-6 -bottom-4"></span>

</div> <span class="md:block w-full truncate">You</span> <h3
  class="md:inline-block mt-3 md:mt-0 text-2xl text-gray-600 font-light
  leading-1.3">

Browser

</h3>

<span class="leading-1.3 text-2xl text-green-success">Working</span>

</div> <div id="cf-cloudflare-status" class="cf-error-source relative w-1/3
  md:w-full py-15 md:p-0 md:py-8 md:text-left md:border-solid md:border-0
  md:border-b md:border-gray-400 overflow-hidden float-left md:float-none
  text-center"> <div class="relative mb-10 md:m-0"> <a
  href="https://www.cloudflare.com/5xx-error-landing?utm_source=errorcode_500&#38;utm_campaign=gypsum.artifactdb.com"
  target="_blank" rel="noopener noreferrer"> <span class="cf-icon-cloud block
  md:hidden h-20 bg-center bg-no-repeat"></span> <span class="cf-icon-error
  w-12 h-12 absolute left-1/2 md:left-auto md:right-0 md:top-0 -ml-6
  -bottom-4"></span> </a> </div> <span class="md:block w-full
  truncate">Dublin</span> <h3 class="md:inline-block mt-3 md:mt-0 text-2xl
  text-gray-600 font-light leading-1.3"> <a
  href="https://www.cloudflare.com/5xx-error-landing?utm_source=errorcode_500&utm_campaign=gypsum.artifactdb.com"
  target="_blank" rel="noopener noreferrer"> Cloudflare </a> </h3>

<span class="leading-1.3 text-2xl text-red-error">Error</span>

</div> <div id="cf-host-status" class=" relative w-1/3 md:w-full py-15 md:p-0
  md:py-8 md:text-left md:border-solid md:border-0 md:border-b
  md:border-gray-400 overflow-hidden float-left md:float-none text-center">
  <div class="relative mb-10 md:m-0">

<span class="cf-icon-server block md:hidden h-20 bg-center
  bg-no-repeat"></span> <span class="cf-icon-ok w-12 h-12 absolute left-1/2
  md:left-auto md:right-0 md:top-0 -ml-6 -bottom-4"></span>

</div> <span class="md:block w-full truncate">gypsum.artifactdb.com</span> <h3
  class="md:inline-block mt-3 md:mt-0 text-2xl text-gray-600 font-light
  leading-1.3">

Host

</h3>

<span class="leading-1.3 text-2xl text-green-success">Working</span>

</div> </div> </div> </div>

<div class="w-240 lg:w-full mx-auto mb-8 lg:px-8"> <div class="clearfix"> <div
  class="w-1/2 md:w-full float-left pr-6 md:pb-10 md:pr-0 leading-relaxed"> <h2
  class="text-3xl font-normal leading-1.3 mb-4">What happened?</h2> <p>There is
  an internal server error on Cloudflare's network.</p> </div> <div
  class="w-1/2 md:w-full float-left leading-relaxed"> <h2 class="text-3xl
  font-normal leading-1.3 mb-4">What can I do?</h2> <p class="mb-6">Please try
  again in a few minutes.</p> </div> </div> </div>

<div class="cf-error-footer cf-wrapper w-240 lg:w-full py-10 sm:py-4 sm:px-8
  mx-auto text-center sm:text-left border-solid border-0 border-t
  border-gray-300"> <p class="text-13"> <span class="cf-footer-item sm:block
  sm:mb-1">Cloudflare Ray ID: <strong
  class="font-semibold">9a07b0554a8dc20e</strong></span> <span
  class="cf-footer-separator sm:hidden">&bull;</span> <span
  id="cf-footer-item-ip" class="cf-footer-item hidden sm:block sm:mb-1"> Your
  IP: <button type="button" id="cf-footer-ip-reveal"
  class="cf-footer-ip-reveal-btn">Click to reveal</button> <span class="hidden"
  id="cf-footer-ip">207.254.102.128</span> <span class="cf-footer-separator
  sm:hidden">&bull;</span> </span> <span class="cf-footer-item sm:block
  sm:mb-1"><span>Performance &amp; security by</span> <a rel="noopener
  noreferrer"
  href="https://www.cloudflare.com/5xx-error-landing?utm_source=errorcode_500&#38;utm_campaign=gypsum.artifactdb.com"
  id="brand_link" target="_blank">Cloudflare</a></span>

</p> <script>(function(){function d(){var
  b=a.getElementById("cf-footer-item-ip"),c=a.getElementById("cf-footer-ip-reveal");b&&"classList"in
  b&&(b.classList.remove("hidden"),c.addEventListener("click",function(){c.classList.add("hidden");a.getElementById("cf-footer-ip").classList.remove("hidden")}))}var
  a=document;document.addEventListener&&a.addEventListener("DOMContentLoaded",d)})();</script>
  </div><!-- /.error-footer -->

</div> </div> </body> </html>
Backtrace:
     ▆
  1. └─scRNAseq::RichardTCellData()
  2.   └─scRNAseq::fetchDataset("richard-tcell-2018", "2023-12-19", realize.assays = TRUE)
  3.     └─gypsum::saveVersion(package, name, version, cache = cache, overwrite = overwrite)
  4.       └─gypsum::listFiles(project, asset, version, url = url)
  5.         └─httr2::req_perform(req)
  6.           └─httr2:::handle_resp(req, resp, error_call = error_call)
  7.             └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
  8.               ├─rlang::catch_cnd(...)
  9.               │ ├─rlang::eval_bare(...)
 10.               │ ├─base::tryCatch(...)
 11.               │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.               │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.               │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 14.               │ └─base::force(expr)
 15.               └─rlang::abort(...)
Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/iSEEfier.Rcheck/00check.log’
for details.

Installation output

iSEEfier.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iSEEfier
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘iSEEfier’ ...
** this is package ‘iSEEfier’ version ‘1.6.0’
** 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 (iSEEfier)

Tests output

iSEEfier.Rcheck/tests/testthat.Rout


R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(iSEEfier)
> 
> test_check("iSEEfier")
--- Loading packages...
- Done!
--- Preparing datasets...
- Done!!


Some names of the panels were specified by the same name, but this situation can be handled at runtime by iSEE
(This is just a non-critical message)

Returning an `initial` configuration including 20 different panels. Enjoy!
If you want to obtain a preview of the panels configuration, you can call `view_initial_tiles()` on the output of this function
Merging together 2 `initial` configuration objects...
Combining sets of 10, 11 different panels.

Some names of the panels were specified by the same name, but this situation can be handled at runtime by iSEE
(This is just a non-critical message)
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 67 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 67 ]
> 
> proc.time()
   user  system elapsed 
 12.839   0.604  14.721

Example timings

iSEEfier.Rcheck/iSEEfier-Ex.timings

nameusersystemelapsed