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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hca.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings hca_1.3.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/hca.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hca/DESCRIPTION' ... OK
* this is package 'hca' version '1.3.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'hca' 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 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 ... ERROR
Running examples in 'hca-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bundles
> ### Title: HCA Bundle Querying
> ### Aliases: bundles bundles_facets bundles_default_columns bundles_detail
> 
> ### ** Examples
> 
> title <- paste(
+     "Tabula Muris: Transcriptomic characterization of 20 organs and",
+     "tissues from Mus musculus at single cell resolution"
+ )
> filters <- filters( projectTitle = list(is = title) )
> bundles(filters = filters)
# A tibble: 0 x 6
# ... with 6 variables: projectTitle <chr>, genusSpecies <chr>, samples <chr>,
#   files <chr>, bundleUuid <chr>, bundleVersion <chr>
> 
> bundles_facets()
Error in .lol_valid_path(x, path) : 'path' not in 'x':
  path: 'organ.terms[*].term'
Calls: bundles_facets ... lapply -> FUN -> lol_lpull -> stopifnot -> .lol_valid_path
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:
  `expected`: TRUE 
  -- Failure (test_manifest.R:17:5): 'manifest()' works with specific filter criteria --
  nrow(test_manifest) > 0L is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  -- Failure (test_samples.R:4:5): 'samples()' works with small size and default arguments --
  nrow(test_samples) > 0L is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 4 | WARN 0 | SKIP 1 | PASS 151 ]
  Error: Test failures
  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: 2 ERRORs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/hca.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL hca
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'hca' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hca'
    finding HTML links ... done
    bundles                                 html  
    catalogs                                html  
    details                                 html  
    files                                   html  
    filters                                 html  
    hca                                     html  
    lol                                     html  
    manifest-internal                       html  
    manifest                                html  
    optimus_loom_annotation                 html  
    projects                                html  
    samples                                 html  
    summary                                 html  
    tbl_hca                                 html  
** 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 (hca)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(hca)

Attaching package: 'hca'

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

    summary

> 
> test_check("hca")
requesting manifest
waiting 1 more seconds (1 seconds total)...
waiting 1 more seconds (2 seconds total)...
waiting 1 more seconds (3 seconds total)...
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 151 ]

== Skipped tests ===============================================================
* manifest() generates an internal server 500 error, 7 February, 2022 (1)

== Failed tests ================================================================
-- Failure (test_bundles.R:4:5): 'bundles()' works with small size and default arguments --
nrow(test_bundles) > 0L is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test_files.R:4:5): 'files()' works with small size and default arguments --
nrow(test_files) > 0L is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test_manifest.R:17:5): 'manifest()' works with specific filter criteria --
nrow(test_manifest) > 0L is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test_samples.R:4:5): 'samples()' works with small size and default arguments --
nrow(test_samples) > 0L is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 4 | WARN 0 | SKIP 1 | PASS 151 ]
Error: Test failures
Execution halted