##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scRNAseq_2.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/scRNAseq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.19.1’
* 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: BachMammaryData
> ### Title: Obtain the Bach mammary data
> ### Aliases: BachMammaryData
> 
> ### ** Examples
> 
> sce <- BachMammaryData(samples="NP_1")
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
loading from cache
require("ensembldb")
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Execution halted
* 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:
    7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
    8.       ├─AnnotationHub()[[ahub.id]]
    9.       └─AnnotationHub()[[ahub.id]]
   10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
   11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
   12.             └─base::tryCatch(...)
   13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   15.                   └─value[[3L]](cond)
  
  [ FAIL 28 | WARN 10 | SKIP 1 | PASS 67 ]
  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-3.20-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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: 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 28 | WARN 10 | SKIP 1 | PASS 67 ]

══ 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: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
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, arg = "object")
  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()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:16:5'): BuettnerESCData works ────────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
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()[[ahub.id]]
  5.       └─AnnotationHub()[[ahub.id]]
  6.         └─AnnotationHub (local) .local(x, i, j = j, ...)
  7.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  8.             └─base::tryCatch(...)
  9.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                   └─value[[3L]](cond)
── Error ('test-loading.R:29:5'): CampbellBrainData works ──────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
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, arg = "object")
  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()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:33:5'): ChenBrainData works ──────────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
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, arg = "object")
  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()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:37:5'): GrunHSCData works ────────────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
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, arg = "object")
  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()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:41:5'): GrunPancreasData works ───────────────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(GrunPancreasData(ensembl = TRUE)) at test-loading.R:41:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::GrunPancreasData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:49:5'): KolodziejczykESCData works ───────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. └─scRNAseq::KolodziejczykESCData() at test-loading.R:49:5
  2.   └─scRNAseq:::.define_location_from_ensembl(...)
  3.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  4.       ├─AnnotationHub()[[ahub.id]]
  5.       └─AnnotationHub()[[ahub.id]]
  6.         └─AnnotationHub (local) .local(x, i, j = j, ...)
  7.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  8.             └─base::tryCatch(...)
  9.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                   └─value[[3L]](cond)
── Error ('test-loading.R:58:5'): LaMannoBrainData works ───────────────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(LaMannoBrainData(ensembl = TRUE, "human-es")) at test-loading.R:58:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::LaMannoBrainData(ensembl = TRUE, "human-es")
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:66:5'): LunSpikeInData works ─────────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. └─scRNAseq::LunSpikeInData() at test-loading.R:66:5
  2.   └─scRNAseq:::.define_location_from_ensembl(...)
  3.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  4.       ├─AnnotationHub()[[ahub.id]]
  5.       └─AnnotationHub()[[ahub.id]]
  6.         └─AnnotationHub (local) .local(x, i, j = j, ...)
  7.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  8.             └─base::tryCatch(...)
  9.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                   └─value[[3L]](cond)
── Error ('test-loading.R:78:5'): MacoskoRetinaData works ──────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(MacoskoRetinaData(ensembl = TRUE)) at test-loading.R:78:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::MacoskoRetinaData(ensembl = TRUE)
  6.   ├─AnnotationHub()[[tag]]
  7.   └─AnnotationHub()[[tag]]
  8.     └─AnnotationHub (local) .local(x, i, j = j, ...)
  9.       └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 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:82:5'): MarquesBrainData works ───────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(MarquesBrainData(ensembl = TRUE)) at test-loading.R:82:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::MarquesBrainData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:86:5'): MuraroPancreasData works ─────────────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(MuraroPancreasData(ensembl = TRUE)) at test-loading.R:86:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::MuraroPancreasData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:90:5'): NestorowaHSCData works ───────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(NestorowaHSCData(remove.htseq = FALSE)) at test-loading.R:90:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  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.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:94:5'): PaulHSCData works ────────────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(PaulHSCData(ensembl = TRUE)) at test-loading.R:94:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::PaulHSCData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:99:5'): Reprocessed*Data works ───────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(ReprocessedAllenData(assays = "tophat_counts", ensembl = TRUE)) at test-loading.R:99:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::ReprocessedAllenData(assays = "tophat_counts", ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:105:5'): RomanovBrainData works ──────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(RomanovBrainData(ensembl = TRUE)) at test-loading.R:105:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::RomanovBrainData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:109:5'): SegerstolpePancreasData works ───────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(SegerstolpePancreasData(ensembl = TRUE)) at test-loading.R:109:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::SegerstolpePancreasData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:113:5'): ShekharRetinaData works ─────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(ShekharRetinaData(ensembl = TRUE)) at test-loading.R:113:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::ShekharRetinaData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:117:5'): TasicBrainData works ────────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(TasicBrainData(ensembl = TRUE)) at test-loading.R:117:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::TasicBrainData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:121:5'): UsoskinBrainData works ──────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(UsoskinBrainData(ensembl = TRUE)) at test-loading.R:121:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::UsoskinBrainData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:125:5'): XinPancreasData works ───────────────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(XinPancreasData(ensembl = TRUE)) at test-loading.R:125:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::XinPancreasData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:129:5'): ZeiselBrainData works ───────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(ZeiselBrainData(ensembl = TRUE)) at test-loading.R:129:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::ZeiselBrainData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:133:5'): ZilionisBrianData works ─────────────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(ZilionisLungData(ensembl = TRUE)) at test-loading.R:133:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::ZilionisLungData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:143:5'): StoeckiusHashingData works ──────────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(StoeckiusHashingData(ensembl = TRUE)) at test-loading.R:143:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::StoeckiusHashingData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:166:5'): MairPBMCData works ──────────────────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(MairPBMCData(mode = c("adt", "rna"), ensembl = TRUE)) at test-loading.R:166:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::MairPBMCData(mode = c("adt", "rna"), ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:174:5'): KotliarovPBMCData works ─────────────────────
Error: failed to load resource
  name: AH73881
  title: Ensembl 97 EnsDb for Homo sapiens
  reason: file is not a database
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(KotliarovPBMCData(mode = c("adt", "rna"), ensembl = TRUE)) at test-loading.R:174:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::KotliarovPBMCData(mode = c("adt", "rna"), ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:182:5'): HuCortexData works ──────────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(HuCortexData(ensembl = TRUE)) at test-loading.R:182:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::HuCortexData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)
── Error ('test-loading.R:190:5'): WuKidneyData works ──────────────────────────
Error: failed to load resource
  name: AH73905
  title: Ensembl 97 EnsDb for Mus musculus
  reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database!
Backtrace:
     ▆
  1. ├─scRNAseq (local) CHECK(WuKidneyData(ensembl = TRUE)) at test-loading.R:190:5
  2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5
  3. │   └─testthat::quasi_label(enquo(object), label, arg = "object")
  4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
  5. └─scRNAseq::WuKidneyData(ensembl = TRUE)
  6.   └─scRNAseq:::.convert_to_ensembl(...)
  7.     └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id)
  8.       ├─AnnotationHub()[[ahub.id]]
  9.       └─AnnotationHub()[[ahub.id]]
 10.         └─AnnotationHub (local) .local(x, i, j = j, ...)
 11.           └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
 12.             └─base::tryCatch(...)
 13.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   └─value[[3L]](cond)

[ FAIL 28 | WARN 10 | SKIP 1 | PASS 67 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Execution halted