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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:iSEEfier.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings iSEEfier_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/iSEEfier.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘iSEEfier/DESCRIPTION’ ... OK
* this is package ‘iSEEfier’ version ‘1.1.0’
* 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 ‘iSEEfier’ 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
glue_initials        18.797  1.555  20.815
view_initial_tiles    8.848  0.732   9.865
iSEEinit              8.495  0.772   9.549
view_initial_network  7.625  0.764   8.659
iSEEnrich             4.518  0.572   5.462
* 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::readMetadata(...)
   29. │                                                     └─alabaster.base::altReadObject(metadata.path, ...)
   30. │                                                       └─scRNAseq (local) FUN(...)
   31. │                                                         └─alabaster.base::readObject(...)
   32. │                                                           └─alabaster.base (local) meth(path, metadata = metadata, ...)
   33. │                                                             └─alabaster.base:::load_list_json(lpath, all.children, simple_list.parallel)
   34. ├─base::stop(`<std::rn_>`)
   35. └─testthat (local) `<fn>`(`<std::rn_>`)
   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-3.20-bioc/meat/iSEEfier.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL iSEEfier
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘iSEEfier’ ...
** using staged installation
** R
** 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 (iSEEfier)

R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(iSEEfier)
> 
> test_check("iSEEfier")
--- Loading packages...
- Done!
--- Preparing datasets...
Error in `FUN()`:
! In path: "/home/biocbuild/bbs-3.20-bioc/meat/iSEEfier.Rcheck/tests/testthat/setuptests_iSEEfier.R"
Caused by error:
! failed to open file at '~/.cache/gypsum/bucket/scRNAseq/legacy/2023-12-18/allen/other_data/list_contents.json.gz'
Backtrace:
     ▆
  1. ├─testthat::test_check("iSEEfier")
  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/setuptests_iSEEfier.R:11:1
 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::readMetadata(...)
 29. │                                                     └─alabaster.base::altReadObject(metadata.path, ...)
 30. │                                                       └─scRNAseq (local) FUN(...)
 31. │                                                         └─alabaster.base::readObject(...)
 32. │                                                           └─alabaster.base (local) meth(path, metadata = metadata, ...)
 33. │                                                             └─alabaster.base:::load_list_json(lpath, all.children, simple_list.parallel)
 34. ├─base::stop(`<std::rn_>`)
 35. └─testthat (local) `<fn>`(`<std::rn_>`)
 36.   └─rlang::abort(...)
Execution halted