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### Running command:
###
###   /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.15-data-experiment/R/library --no-vignettes --timings scRNAseq_2.9.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/scRNAseq.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.9.2’
* 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 ... WARNING
Problems with news in ‘inst/NEWS.Rd’:
  inst/NEWS.Rd:35: unexpected section header '\section'
  inst/NEWS.Rd:51: unexpected section header '\section'
  inst/NEWS.Rd:59: unexpected section header '\section'
  inst/NEWS.Rd:67: unexpected section header '\section'
  inst/NEWS.Rd:70: unexpected END_OF_INPUT '
  '
* checking R 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
HeOrganAtlasData           78.297 14.219  95.704
BhaduriOrganoidData        40.009  4.530  45.188
ZeiselNervousData          39.231  2.973  43.447
BacherTCellData            27.547  4.684  32.742
ErnstSpermatogenesisData   25.908  3.032  29.963
StoeckiusHashingData       25.875  1.453  31.743
JessaBrainData             23.268  3.818  28.467
GiladiHSCData              22.403  3.594  27.024
LunSpikeInData             18.113  1.513  22.417
LaMannoBrainData           17.408  0.928  20.479
BachMammaryData            16.499  1.325  19.203
ZhaoImmuneLiverData        15.303  1.420  17.367
BuettnerESCData            14.604  0.725  16.914
BunisHSPCData              13.659  1.352  15.862
TasicBrainData             12.828  0.941  16.578
NestorowaHSCData           12.374  1.368  15.740
ZilionisLungData           12.862  0.705  14.456
MessmerESCData             12.227  0.989  15.824
AztekinTailData            11.488  1.288  13.384
SegerstolpePancreasData    10.223  0.741  12.749
ReprocessedData             9.619  0.517  10.954
ShekharRetinaData           9.615  0.447  11.972
CampbellBrainData           9.005  0.600  10.064
KolodziejczykESCData        8.683  0.891  10.782
BaronPancreasData           8.595  0.824  10.351
KotliarovPBMCData           8.455  0.665   9.644
ZeiselBrainData             8.682  0.424  10.019
RichardTCellData            8.281  0.576  10.090
ChenBrainData               7.672  0.567   8.689
NowakowskiCortexData        7.793  0.407   9.198
HuCortexData                6.951  1.176   8.840
UsoskinBrainData            7.742  0.366   9.515
FletcherOlfactoryData       6.941  0.806   8.351
MairPBMCData                6.930  0.623   8.418
GrunPancreasData            6.735  0.395   7.868
XinPancreasData             6.827  0.192   7.870
MuraroPancreasData          5.913  0.673   8.414
MacoskoRetinaData           5.754  0.485   6.690
LedergorMyelomaData         5.596  0.304   6.345
HermannSpermatogenesisData  5.205  0.398   6.158
PaulHSCData                 4.703  0.403   5.555
* 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:
    4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
    5. └─scRNAseq::NestorowaHSCData(remove.htseq = FALSE)
    6.   └─scRNAseq:::.define_location_from_ensembl(...)
    7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
    8.       └─scRNAseq:::.AnnotationHub()
    9.         └─AnnotationHub::AnnotationHub()
   10.           └─AnnotationHub::.Hub(...)
   11.             └─AnnotationHub:::.db_create_index(hub)
   12.               └─base::readRDS(index_path)
  
  [ FAIL 1 | WARN 37 | SKIP 0 | PASS 118 ]
  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 in ‘inst/doc’ ... 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, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD INSTALL scRNAseq
###
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* installing to library ‘/home/biocbuild/bbs-3.15-data-experiment/R/library’
* installing *source* package ‘scRNAseq’ ...
** 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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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 1 | WARN 37 | SKIP 0 | PASS 118 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-loading.R:90:5): NestorowaHSCData works ─────────────────────────
Error in `readRDS(index_path)`: error reading from connection
Backtrace:
     ▆
  1. ├─scRNAseq CHECK(NestorowaHSCData(remove.htseq = FALSE)) at test-loading.R:90:4
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:4
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::NestorowaHSCData(remove.htseq = FALSE)
  6.   └─scRNAseq:::.define_location_from_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       └─scRNAseq:::.AnnotationHub()
  9.         └─AnnotationHub::AnnotationHub()
 10.           └─AnnotationHub::.Hub(...)
 11.             └─AnnotationHub:::.db_create_index(hub)
 12.               └─base::readRDS(index_path)

[ FAIL 1 | WARN 37 | SKIP 0 | PASS 118 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Execution halted