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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:hca.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings hca_1.11.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/hca.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hca/DESCRIPTION’ ... OK
* this is package ‘hca’ version ‘1.11.2’
* 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 for sufficient/correct file permissions ... 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 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 whether startup messages can be suppressed ... 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: 100 × 6
   projectTitle              genusSpecies samples files bundleUuid bundleVersion
   <chr>                     <chr>        <chr>   <lis> <chr>      <chr>        
 1 Tabula Muris: Transcript… Mus musculus 3_38_F… <chr> 00004ffa-… 2019-08-01T2…
 2 Tabula Muris: Transcript… Mus musculus 3_10_M… <chr> 00007f4c-… 2019-08-01T2…
 3 Tabula Muris: Transcript… Mus musculus 3_8_M_… <chr> 0000984f-… 2019-08-01T2…
 4 Tabula Muris: Transcript… Mus musculus 3_57_F… <chr> 00031982-… 2019-08-01T2…
 5 Tabula Muris: Transcript… Mus musculus 3_8_M_… <chr> 0004846a-… 2019-08-01T2…
 6 Tabula Muris: Transcript… Mus musculus 3_9_M_… <chr> 000598de-… 2019-08-01T2…
 7 Tabula Muris: Transcript… Mus musculus 3_10_M… <chr> 00071db7-… 2019-08-01T2…
 8 Tabula Muris: Transcript… Mus musculus 3_38_F… <chr> 00073cfb-… 2019-08-01T2…
 9 Tabula Muris: Transcript… Mus musculus 3_57_F… <chr> 00075c23-… 2019-08-01T2…
10 Tabula Muris: Transcript… Mus musculus 3_39_F… <chr> 0008b864-… 2019-08-01T2…
# ℹ 90 more rows
> 
> bundles_facets()
# A tibble: 38 × 3
   facet              n_terms n_values
   <chr>                <int>    <int>
 1 accessible               1   206132
 2 assayType                2   206132
 3 biologicalSex            5   212642
 4 bionetworkName           7   206144
 5 cellLineType             6   206677
 6 contactName              1   206132
 7 contentDescription      69   212704
 8 developmentStage       171   213677
 9 donorDisease           461   219595
10 effectiveOrgan         163   211412
# ℹ 28 more rows
> 
> bundle <- bundles(size = 1, as = "list")
Error in .hca_GET(index_path) : Service Unavailable (HTTP 503).
Calls: bundles -> .index_GET -> .hca_GET -> stop_for_status
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/hca.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL hca
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘hca’ ...
** 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 (hca)

R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(hca)

Attaching package: 'hca'

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

    summary

> 
> test_check("hca")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 160 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• manifest() generates an internal server 500 error, 7 February, 2022 (1):
  'test_manifest.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 160 ]
> 
> proc.time()
   user  system elapsed 
  5.575   0.784 177.869