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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:scRNAseqApp.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings scRNAseqApp_1.13.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/scRNAseqApp.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-21 08:21:00 UTC
* checking for file ‘scRNAseqApp/DESCRIPTION’ ... OK
* this is package ‘scRNAseqApp’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 46 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘scRNAseqApp’ 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 loading without being on the library search path ... 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 ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  Error in `download.file(url0, destfile = tmp)`: cannot open URL 'https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/?format=xml&email=jou@morgridge.org&tool=scRNAseqApp&ids=10.1038/nbt.3192'
  Backtrace:
      ▆
   1. └─scRNAseqApp::createAppConfig(...) at test_createDataset.R:2:3
   2.   └─scRNAseqApp:::idConverter(doi, type = "pmid", email = email)
   3.     └─base::tryCatch(...)
   4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6.           └─value[[3L]](cond)
   7.             └─utils::download.file(url0, destfile = tmp)
  
  [ FAIL 1 | WARN 3 | SKIP 1 | PASS 4 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/scRNAseqApp.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL scRNAseqApp
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘scRNAseqApp’ ...
** this is package ‘scRNAseqApp’ version ‘1.13.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘scRNAseqApp’
** 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 (scRNAseqApp)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> require("scRNAseqApp") || stop("unable to load Package:scRNAseqApp")
Loading required package: scRNAseqApp
[1] TRUE
> require("Seurat") || stop("unable to load Package::Seurat")
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp

Attaching package: 'SeuratObject'

The following objects are masked from 'package:base':

    intersect, t

[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> require('shinytest2') || stop("unable to load shinytest2")
Loading required package: shinytest2
[1] TRUE
> test_check("scRNAseqApp")
trying URL 'https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/?format=xml&email=jou@morgridge.org&tool=scRNAseqApp&ids=10.1038/nbt.3192'
Saving _problems/test_createDataset-8.R
[ FAIL 1 | WARN 3 | SKIP 1 | PASS 4 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test_scRNAseqApp.R:18:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_createDataset.R:2:3'): createDataset works not correct ─────────
Error in `download.file(url0, destfile = tmp)`: cannot open URL 'https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/?format=xml&email=jou@morgridge.org&tool=scRNAseqApp&ids=10.1038/nbt.3192'
Backtrace:
    ▆
 1. └─scRNAseqApp::createAppConfig(...) at test_createDataset.R:2:3
 2.   └─scRNAseqApp:::idConverter(doi, type = "pmid", email = email)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
 7.             └─utils::download.file(url0, destfile = tmp)

[ FAIL 1 | WARN 3 | SKIP 1 | PASS 4 ]
Error:
! Test failures.
Execution halted