##############################################################################
##############################################################################
###
### 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_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/scRNAseq.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘2.24.0’
* 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
BhaduriOrganoidData      23.471  7.855  31.598
BacherTCellData          17.758  4.183  22.308
ZeiselNervousData        13.717  4.439  18.689
HeOrganAtlasData         11.768  5.927  17.839
JessaBrainData            9.223  3.648  13.262
ErnstSpermatogenesisData  9.873  2.690  12.952
StoeckiusHashingData      8.826  0.689  10.379
ZhaoImmuneLiverData       6.144  2.095   8.361
BachMammaryData           7.311  0.683   9.664
AztekinTailData           6.747  0.752   7.531
GiladiHSCData             4.760  1.875   6.748
LunSpikeInData            5.952  0.287   6.955
ZilionisLungData          4.024  0.794   5.097
KolodziejczykESCData      4.020  0.791   5.066
* 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:
    6.   └─scRNAseq:::.convert_to_ensembl(...)
    7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
    8.       └─AnnotationHub::AnnotationHub()
    9.         └─AnnotationHub::.Hub(...)
   10.           └─base::tryCatch(...)
   11.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   12.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13.                 └─value[[3L]](cond)
  
  [ FAIL 5 | WARN 30 | SKIP 1 | PASS 171 ]
  Error:
  ! Test failures.
  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: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scRNAseq’ ...
** this is package ‘scRNAseq’ version ‘2.24.0’
** 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 (scRNAseq)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
Saving _problems/test-loading-11.R
Saving _problems/test-loading-16.R
Saving _problems/test-loading-29.R
Saving _problems/test-loading-33.R
Saving _problems/test-loading-37.R
[ FAIL 5 | WARN 30 | SKIP 1 | PASS 171 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-loading.R:11:5'): BaronPancreasData works ──────────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(BaronPancreasData(ensembl = TRUE)) at test-loading.R:11:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label)
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::BaronPancreasData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       └─AnnotationHub::AnnotationHub()
  9.         └─AnnotationHub::.Hub(...)
 10.           └─base::tryCatch(...)
 11.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                 └─value[[3L]](cond)
── Error ('test-loading.R:16:5'): BuettnerESCData works ────────────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─scRNAseq::BuettnerESCData() at test-loading.R:16:5
 2.   └─scRNAseq:::.define_location_from_ensembl(...)
 3.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
 4.       └─AnnotationHub::AnnotationHub()
 5.         └─AnnotationHub::.Hub(...)
 6.           └─base::tryCatch(...)
 7.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.                 └─value[[3L]](cond)
── Error ('test-loading.R:29:5'): CampbellBrainData works ──────────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(CampbellBrainData(ensembl = TRUE)) at test-loading.R:29:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label)
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::CampbellBrainData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       └─AnnotationHub::AnnotationHub()
  9.         └─AnnotationHub::.Hub(...)
 10.           └─base::tryCatch(...)
 11.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                 └─value[[3L]](cond)
── Error ('test-loading.R:33:5'): ChenBrainData works ──────────────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(ChenBrainData(ensembl = TRUE)) at test-loading.R:33:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label)
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::ChenBrainData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       └─AnnotationHub::AnnotationHub()
  9.         └─AnnotationHub::.Hub(...)
 10.           └─base::tryCatch(...)
 11.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                 └─value[[3L]](cond)
── Error ('test-loading.R:37:5'): GrunHSCData works ────────────────────────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(GrunHSCData(ensembl = TRUE)) at test-loading.R:37:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label)
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::GrunHSCData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       └─AnnotationHub::AnnotationHub()
  9.         └─AnnotationHub::.Hub(...)
 10.           └─base::tryCatch(...)
 11.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                 └─value[[3L]](cond)

[ FAIL 5 | WARN 30 | SKIP 1 | PASS 171 ]
Error:
! Test failures.
Warning message:
call dbDisconnect() when finished working with a connection 
Execution halted