##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings hipathia_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/hipathia.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 ‘hipathia/DESCRIPTION’ ... OK
* this is package ‘hipathia’ version ‘3.4.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hipathia’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data      4.1Mb
    extdata   2.5Mb
* 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 ... NOTE
DAreport: no visible binding for global variable ‘ID’
DAreport: no visible binding for global variable ‘FDRp.value’
DAtop : <anonymous>: no visible binding for global variable
  ‘FDRp.value’
DAtop : <anonymous>: no visible binding for global variable ‘statistic’
DAtop : <anonymous>: no visible binding for global variable ‘p.value’
DAtop : <anonymous>: no visible binding for global variable ‘name’
DAtop : <anonymous>: no visible binding for global variable ‘logPV’
DAtop : <anonymous>: no visible binding for global variable ‘feature’
DAtop: no visible binding for global variable ‘name’
DAtop: no visible binding for global variable ‘logPV’
DAtop: no visible binding for global variable ‘direction’
get_edges_df: no visible binding for global variable ‘from’
get_edges_df: no visible binding for global variable ‘to’
nsig_plot: no visible binding for global variable ‘total’
nsig_plot: no visible binding for global variable ‘UPs’
nsig_plot: no visible binding for global variable ‘DOWNs’
nsig_plot: no visible binding for global variable ‘feature’
nsig_plot: no visible binding for global variable ‘UP’
nsig_plot: no visible binding for global variable ‘DOWN’
nsig_plot: no visible binding for global variable ‘Not’
nsig_plot: no visible binding for global variable ‘value’
nsig_plot: no visible binding for global variable ‘variable’
prepare_DAedges: no visible binding for global variable ‘to’
prepare_DAedges: no visible binding for global variable ‘functional’
prepare_DAedges: no visible binding for global variable ‘status’
prepare_DAedges: no visible binding for global variable ‘type’
prepare_DAnodes : <anonymous>: no visible binding for global variable
  ‘ID’
prepare_DAnodes : <anonymous>: no visible binding for global variable
  ‘FDRp.value’
prepare_DAnodes : <anonymous>: no visible binding for global variable
  ‘statistic’
prepare_DAnodes : <anonymous>: no visible binding for global variable
  ‘p.value’
prepare_edges: no visible binding for global variable ‘to’
prepare_edges: no visible binding for global variable ‘functional’
summary_plot: no visible binding for global variable ‘total’
summary_plot: no visible binding for global variable ‘UPs’
summary_plot: no visible binding for global variable ‘DOWNs’
summary_plot: no visible binding for global variable ‘name’
summary_plot: no visible binding for global variable ‘UP’
summary_plot: no visible binding for global variable ‘DOWN’
summary_plot: no visible binding for global variable ‘Not’
summary_plot: no visible binding for global variable ‘value’
summary_plot: no visible binding for global variable ‘variable’
summary_plot: no visible binding for global variable ‘UP.nodes’
summary_plot: no visible binding for global variable ‘DOWN.nodes’
summary_plot: no visible binding for global variable ‘nodes’
summary_plot: no visible binding for global variable ‘ratio.sigs’
summary_plot: no visible binding for global variable ‘ratio.UPs’
summary_plot: no visible binding for global variable ‘ratio.DOWNs’
Undefined global functions or variables:
  DOWN DOWN.nodes DOWNs FDRp.value ID Not UP UP.nodes UPs direction
  feature from functional logPV name nodes p.value ratio.DOWNs
  ratio.UPs ratio.sigs statistic status to total type value variable
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘hipathia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_report
> ### Title: Create visualization HTML
> ### Aliases: create_report
> 
> ### ** Examples
> 
> data(comp)
> pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
+ "hsa04012"))
Warning: file ‘1b41fe6c781c7f_75857’ has magic number 'SQLit'
  Use of save versions prior to 2 is deprecated
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
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:
    2.   └─hipathia:::load_mgi(species)
    3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
    4.     │ └─base::withCallingHandlers(...)
    5.     ├─hp[[names(hp)[hp$title == file]]]
    6.     └─hp[[names(hp)[hp$title == file]]]
    7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
    8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
    9.           └─base::tryCatch(...)
   10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12.                 └─value[[3L]](cond)
  
  [ FAIL 10 | WARN 10 | SKIP 0 | PASS 46 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘hipathia-vignette.Rmd’ using rmarkdown

Quitting from lines 327-328 [unnamed-chunk-14] (hipathia-vignette.Rmd)
Error: processing vignette 'hipathia-vignette.Rmd' failed with diagnostics:
failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
--- failed re-building ‘hipathia-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘hipathia-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/hipathia.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL hipathia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘hipathia’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (hipathia)

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(hipathia)
Loading required package: igraph

Attaching package: 'igraph'

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

    compare

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

    decompose, spectrum

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

    union

Loading required package: AnnotationHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    normalize, path, union

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: BiocFileCache
Loading required package: dbplyr
Loading required package: MultiAssayExperiment
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: 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

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

    cache

> 
> test_check("hipathia")
translated ids = 3184 (1) 
untranslated ids = 3 (0.00094) 
multihit ids = 0 (0) 
[ FAIL 10 | WARN 10 | SKIP 0 | PASS 46 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-color-node.R:10:1'): (code run outside of `test_that()`) ───────
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-color-node.R:10:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-hipathia.R:8:1'): (code run outside of `test_that()`) ──────────
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-hipathia.R:8:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-load-pathways.R:8:1'): (code run outside of `test_that()`) ─────
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways("hsa", pathways_list = pathways_list) at test-load-pathways.R:8:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-normalize-paths.R:8:1'): (code run outside of `test_that()`) ───
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-normalize-paths.R:8:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-path-annots.R:8:1'): (code run outside of `test_that()`) ───────
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-path-annots.R:8:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-path-list.R:8:1'): (code run outside of `test_that()`) ─────────
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-path-list.R:8:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-path-names.R:8:1'): (code run outside of `test_that()`) ────────
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-path-names.R:8:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-path-summary.R:9:1'): (code run outside of `test_that()`) ──────
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways("hsa", pathways_list = pathways_list) at test-path-summary.R:9:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-quantify.R:8:1'): (code run outside of `test_that()`) ──────────
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-quantify.R:8:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)
── Error ('test-translate-matrix.R:9:1'): (code run outside of `test_that()`) ──
Error: failed to load resource
  name: AH69111
  title: meta_graph_info_hsa_v2.rda
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
     ▆
  1. └─hipathia::load_pathways("hsa") at test-translate-matrix.R:9:1
  2.   └─hipathia:::load_mgi(species)
  3.     ├─base::suppressMessages(hp[[names(hp)[hp$title == file]]])
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─hp[[names(hp)[hp$title == file]]]
  6.     └─hp[[names(hp)[hp$title == file]]]
  7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
  9.           └─base::tryCatch(...)
 10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                 └─value[[3L]](cond)

[ FAIL 10 | WARN 10 | SKIP 0 | PASS 46 ]
Error: Test failures
Execution halted