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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:iSEEhex.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings iSEEhex_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/iSEEhex.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘iSEEhex/DESCRIPTION’ ... OK
* this is package ‘iSEEhex’ version ‘1.5.0’
* 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 ‘iSEEhex’ 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
ReducedDimensionHexPlot-class 16.407   1.28   17.69
* 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:
   23. │                                         └─alabaster.se (local) meth(path, metadata = metadata, ...)
   24. │                                           └─alabaster.base::altReadObject(path, metadata = metadata, ...)
   25. │                                             └─scRNAseq (local) FUN(...)
   26. │                                               └─alabaster.base::readObject(...)
   27. │                                                 └─alabaster.se (local) meth(path, metadata = metadata, ...)
   28. │                                                   └─alabaster.base::altReadObject(...)
   29. │                                                     └─scRNAseq (local) FUN(...)
   30. │                                                       └─alabaster.base::readObject(...)
   31. │                                                         └─alabaster.matrix (local) meth(path, metadata = metadata, ...)
   32. │                                                           └─(function() {...
   33. │                                                             └─rhdf5::H5Fopen(fpath)
   34. └─base::.handleSimpleError(...)
   35.   └─testthat (local) h(simpleError(msg, call))
   36.     └─rlang::abort(...)
  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
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/iSEEhex.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL iSEEhex
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘iSEEhex’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (iSEEhex)

R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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(iSEEhex)
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

Loading required package: iSEE
Loading required package: SingleCellExperiment
> 
> test_check("iSEEhex")
Error in `FUN()`:
! In path: "/home/biocbuild/bbs-3.19-bioc/meat/iSEEhex.Rcheck/tests/testthat/setup-sce.R"
Caused by error in `H5Fopen()`:
! HDF5. File accessibility. Unable to open file.
Backtrace:
     ▆
  1. ├─testthat::test_check("iSEEhex")
  2. │ └─testthat::test_dir(...)
  3. │   └─testthat:::test_files(...)
  4. │     └─testthat:::test_files_serial(...)
  5. │       └─testthat:::test_files_setup_state(...)
  6. │         └─testthat::source_test_setup(".", env)
  7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
  8. │             └─base::lapply(...)
  9. │               └─testthat (local) FUN(X[[i]], ...)
 10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
 11. │                   ├─base::withCallingHandlers(...)
 12. │                   └─base::eval(exprs, env)
 13. │                     └─base::eval(exprs, env)
 14. │                       └─scRNAseq::ReprocessedAllenData(assays = "tophat_counts") at tests/testthat/setup-sce.R:4:1
 15. │                         └─scRNAseq::fetchDataset("legacy", "2023-12-18", "allen", realize.assays = TRUE)
 16. │                           └─alabaster.base::altReadObject(...)
 17. │                             └─scRNAseq (local) FUN(...)
 18. │                               └─alabaster.base::readObject(...)
 19. │                                 └─alabaster.sce (local) meth(path, metadata = metadata, ...)
 20. │                                   └─alabaster.base::altReadObject(path, metadata, ...)
 21. │                                     └─scRNAseq (local) FUN(...)
 22. │                                       └─alabaster.base::readObject(...)
 23. │                                         └─alabaster.se (local) meth(path, metadata = metadata, ...)
 24. │                                           └─alabaster.base::altReadObject(path, metadata = metadata, ...)
 25. │                                             └─scRNAseq (local) FUN(...)
 26. │                                               └─alabaster.base::readObject(...)
 27. │                                                 └─alabaster.se (local) meth(path, metadata = metadata, ...)
 28. │                                                   └─alabaster.base::altReadObject(...)
 29. │                                                     └─scRNAseq (local) FUN(...)
 30. │                                                       └─alabaster.base::readObject(...)
 31. │                                                         └─alabaster.matrix (local) meth(path, metadata = metadata, ...)
 32. │                                                           └─(function() {...
 33. │                                                             └─rhdf5::H5Fopen(fpath)
 34. └─base::.handleSimpleError(...)
 35.   └─testthat (local) h(simpleError(msg, call))
 36.     └─rlang::abort(...)
Execution halted