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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scRNAseq_2.23.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/scRNAseq.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.23.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scRNAseq’ 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 ... ERROR
Running examples in ‘scRNAseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: listPaths
> ### Title: List all paths for a dataset
> ### Aliases: listPaths
> 
> ### ** Examples
> 
> listPaths("he-organs-2020", "2023-12-21")
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [gypsum.artifactdb.com]:
Recv failure: Connection reset by peer
Backtrace:
    ▆
 1. └─scRNAseq::listPaths("he-organs-2020", "2023-12-21")
 2.   └─gypsum::listFiles(package, name, version, include.. = FALSE)
 3.     └─httr2::req_perform(req)
 4.       └─httr2:::handle_resp(req, resp, error_call = error_call)
 5.         └─rlang::cnd_signal(resp)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
BhaduriOrganoidData      23.772  9.202  33.078
BacherTCellData          17.443  6.168  23.734
HeOrganAtlasData         12.209  7.301  19.731
ZeiselNervousData        14.006  5.182  19.691
JessaBrainData           10.762  4.077  15.287
ErnstSpermatogenesisData 10.024  3.617  14.035
StoeckiusHashingData      9.024  1.513  11.320
ZhaoImmuneLiverData       6.686  2.905   9.680
BachMammaryData           7.502  0.728   9.411
AztekinTailData           7.090  0.641   7.760
GiladiHSCData             4.889  2.487   7.461
LunSpikeInData            5.960  0.741   7.341
NestorowaHSCData          4.502  0.598   5.404
ZilionisLungData          3.961  1.122   5.185
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ! SSL connect error [gypsum.artifactdb.com]:
  Recv failure: Connection reset by peer
  Backtrace:
      ▆
   1. └─scRNAseq::listPaths("he-organs-2020", "2023-12-21", include.metadata = TRUE) at test-listPaths.R:14:5
   2.   └─gypsum::listFiles(package, name, version, include.. = FALSE)
   3.     └─httr2::req_perform(req)
   4.       └─httr2:::handle_resp(req, resp, error_call = error_call)
   5.         └─rlang::cnd_signal(resp)
  
  [ FAIL 2 | WARN 53 | SKIP 1 | PASS 178 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  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: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scRNAseq
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scRNAseq’ ...
** this is package ‘scRNAseq’ version ‘2.23.1’
** 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 (scRNAseq)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.

> library(testthat)
> library(scRNAseq)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

> test_check("scRNAseq")
[ FAIL 2 | WARN 53 | SKIP 1 | PASS 178 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• is.null(gh_token) is TRUE (1): 'test-uploadDirectory.R:59:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-listPaths.R:4:5'): listPaths works correctly with names ────────
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `req_perform(req)`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [gypsum.artifactdb.com]:
Recv failure: Connection reset by peer
Backtrace:
    ▆
 1. └─scRNAseq::listPaths("he-organs-2020", "2023-12-21") at test-listPaths.R:4:5
 2.   └─gypsum::listFiles(package, name, version, include.. = FALSE)
 3.     └─httr2::req_perform(req)
 4.       └─httr2:::handle_resp(req, resp, error_call = error_call)
 5.         └─rlang::cnd_signal(resp)
── Error ('test-listPaths.R:14:5'): listPaths works correctly with metadata ────
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `req_perform(req)`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [gypsum.artifactdb.com]:
Recv failure: Connection reset by peer
Backtrace:
    ▆
 1. └─scRNAseq::listPaths("he-organs-2020", "2023-12-21", include.metadata = TRUE) at test-listPaths.R:14:5
 2.   └─gypsum::listFiles(package, name, version, include.. = FALSE)
 3.     └─httr2::req_perform(req)
 4.       └─httr2:::handle_resp(req, resp, error_call = error_call)
 5.         └─rlang::cnd_signal(resp)

[ FAIL 2 | WARN 53 | SKIP 1 | PASS 178 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Execution halted