##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hca.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings hca_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/hca.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'hca/DESCRIPTION' ... OK
* this is package 'hca' version '1.15.0'
* 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 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 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) )
Warning in open.connection(con, "rb") :
  cannot open URL 'https://service.azul.data.humancellatlas.org/openapi': HTTP status was '403 Forbidden'
Error in open.connection(con, "rb") : 
  cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Calls: filters ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
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.   └─hca::filters()
    3.     └─hca:::.filters_validate(filters_list)
    4.       └─hca::facet_options()
    5.         └─hca:::.hca_openapi()
    6.           └─jsonlite::read_json(api)
    7.             └─jsonlite::parse_json(...)
    8.               └─jsonlite:::parse_and_simplify(...)
    9.                 └─jsonlite:::parseJSON(txt, bigint_as_char)
   10.                   └─jsonlite:::parse_con(txt, bigint_as_char)
   11.                     ├─base::open(con, "rb")
   12.                     └─base::open.connection(con, "rb")
  
  [ FAIL 12 | WARN 12 | SKIP 1 | PASS 119 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/hca.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL hca
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'hca' ...
** this is package 'hca' version '1.15.0'
** 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) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 12 | WARN 12 | SKIP 1 | PASS 119 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_bundles.R:2:5'): 'bundles()' works with small size and default arguments ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. └─hca::bundles(size = 4) at test_bundles.R:2:5
  2.   └─hca::filters()
  3.     └─hca:::.filters_validate(filters_list)
  4.       └─hca::facet_options()
  5.         └─hca:::.hca_openapi()
  6.           └─jsonlite::read_json(api)
  7.             └─jsonlite::parse_json(...)
  8.               └─jsonlite:::parse_and_simplify(...)
  9.                 └─jsonlite:::parseJSON(txt, bigint_as_char)
 10.                   └─jsonlite:::parse_con(txt, bigint_as_char)
 11.                     ├─base::open(con, "rb")
 12.                     └─base::open.connection(con, "rb")
── Error ('test_files.R:2:5'): 'files()' works with small size and default arguments ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. └─hca::files(size = 4) at test_files.R:2:5
  2.   └─hca::filters()
  3.     └─hca:::.filters_validate(filters_list)
  4.       └─hca::facet_options()
  5.         └─hca:::.hca_openapi()
  6.           └─jsonlite::read_json(api)
  7.             └─jsonlite::parse_json(...)
  8.               └─jsonlite:::parse_and_simplify(...)
  9.                 └─jsonlite:::parseJSON(txt, bigint_as_char)
 10.                   └─jsonlite:::parse_con(txt, bigint_as_char)
 11.                     ├─base::open(con, "rb")
 12.                     └─base::open.connection(con, "rb")
── Error ('test_filters.R:2:5'): 'facet_options()' works ───────────────────────
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
    ▆
 1. └─hca::facet_options() at test_filters.R:2:5
 2.   └─hca:::.hca_openapi()
 3.     └─jsonlite::read_json(api)
 4.       └─jsonlite::parse_json(...)
 5.         └─jsonlite:::parse_and_simplify(...)
 6.           └─jsonlite:::parseJSON(txt, bigint_as_char)
 7.             └─jsonlite:::parse_con(txt, bigint_as_char)
 8.               ├─base::open(con, "rb")
 9.               └─base::open.connection(con, "rb")
── Error ('test_filters.R:10:5'): 'filters()' works ────────────────────────────
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. └─hca::filters() at test_filters.R:10:5
  2.   └─hca:::.filters_validate(filters_list)
  3.     └─hca::facet_options()
  4.       └─hca:::.hca_openapi()
  5.         └─jsonlite::read_json(api)
  6.           └─jsonlite::parse_json(...)
  7.             └─jsonlite:::parse_and_simplify(...)
  8.               └─jsonlite:::parseJSON(txt, bigint_as_char)
  9.                 └─jsonlite:::parse_con(txt, bigint_as_char)
 10.                   ├─base::open(con, "rb")
 11.                   └─base::open.connection(con, "rb")
── Error ('test_filters.R:73:5'): 'filters()' validates arguments ──────────────
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. ├─testthat::expect_s3_class(...) at test_filters.R:73:5
  2. │ └─testthat::quasi_label(enquo(object), arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─hca::filters(organ = list(is = "bar"))
  5.   └─hca:::.filters_validate(filters_list)
  6.     └─hca::facet_options()
  7.       └─hca:::.hca_openapi()
  8.         └─jsonlite::read_json(api)
  9.           └─jsonlite::parse_json(...)
 10.             └─jsonlite:::parse_and_simplify(...)
 11.               └─jsonlite:::parseJSON(txt, bigint_as_char)
 12.                 └─jsonlite:::parse_con(txt, bigint_as_char)
 13.                   ├─base::open(con, "rb")
 14.                   └─base::open.connection(con, "rb")
── Error ('test_hca.R:11:5'): '.hca_GET()' works ───────────────────────────────
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. └─hca::filters(organ = list(is = "pancreas")) at test_hca.R:11:5
  2.   └─hca:::.filters_validate(filters_list)
  3.     └─hca::facet_options()
  4.       └─hca:::.hca_openapi()
  5.         └─jsonlite::read_json(api)
  6.           └─jsonlite::parse_json(...)
  7.             └─jsonlite:::parse_and_simplify(...)
  8.               └─jsonlite:::parseJSON(txt, bigint_as_char)
  9.                 └─jsonlite:::parse_con(txt, bigint_as_char)
 10.                   ├─base::open(con, "rb")
 11.                   └─base::open.connection(con, "rb")
── Error ('test_index.R:8:5'): testing .index_GET() with (almost) default parameters ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. └─hca:::.index_GET(size = 5) at test_index.R:8:5
  2.   ├─base::match.arg(sort, facet_options())
  3.   └─hca::facet_options()
  4.     └─hca:::.hca_openapi()
  5.       └─jsonlite::read_json(api)
  6.         └─jsonlite::parse_json(...)
  7.           └─jsonlite:::parse_and_simplify(...)
  8.             └─jsonlite:::parseJSON(txt, bigint_as_char)
  9.               └─jsonlite:::parse_con(txt, bigint_as_char)
 10.                 ├─base::open(con, "rb")
 11.                 └─base::open.connection(con, "rb")
── Error ('test_manifest.R:10:5'): 'manifest()' works with specific filter criteria ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. └─hca::filters(...) at test_manifest.R:10:5
  2.   └─hca:::.filters_validate(filters_list)
  3.     └─hca::facet_options()
  4.       └─hca:::.hca_openapi()
  5.         └─jsonlite::read_json(api)
  6.           └─jsonlite::parse_json(...)
  7.             └─jsonlite:::parse_and_simplify(...)
  8.               └─jsonlite:::parseJSON(txt, bigint_as_char)
  9.                 └─jsonlite:::parse_con(txt, bigint_as_char)
 10.                   ├─base::open(con, "rb")
 11.                   └─base::open.connection(con, "rb")
── Error ('test_projects.R:2:5'): 'projects()' works with small size and default arguments ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. └─hca::projects(size = 4) at test_projects.R:2:5
  2.   └─hca::filters()
  3.     └─hca:::.filters_validate(filters_list)
  4.       └─hca::facet_options()
  5.         └─hca:::.hca_openapi()
  6.           └─jsonlite::read_json(api)
  7.             └─jsonlite::parse_json(...)
  8.               └─jsonlite:::parse_and_simplify(...)
  9.                 └─jsonlite:::parseJSON(txt, bigint_as_char)
 10.                   └─jsonlite:::parse_con(txt, bigint_as_char)
 11.                     ├─base::open(con, "rb")
 12.                     └─base::open.connection(con, "rb")
── Error ('test_projects.R:10:5'): 'projects()' works for projectTitles with special characters ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. ├─hca::projects(filters = filters(projectTitle = list(is = "Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis"))) at test_projects.R:10:5
  2. └─hca::filters(projectTitle = list(is = "Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis"))
  3.   └─hca:::.filters_validate(filters_list)
  4.     └─hca::facet_options()
  5.       └─hca:::.hca_openapi()
  6.         └─jsonlite::read_json(api)
  7.           └─jsonlite::parse_json(...)
  8.             └─jsonlite:::parse_and_simplify(...)
  9.               └─jsonlite:::parseJSON(txt, bigint_as_char)
 10.                 └─jsonlite:::parse_con(txt, bigint_as_char)
 11.                   ├─base::open(con, "rb")
 12.                   └─base::open.connection(con, "rb")
── Error ('test_projects.R:28:5'): 'projects()' works for projectTitles that don't exist ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. ├─hca::projects(filters = filters(projectTitle = list(is = "blah blah blah"))) at test_projects.R:28:5
  2. └─hca::filters(projectTitle = list(is = "blah blah blah"))
  3.   └─hca:::.filters_validate(filters_list)
  4.     └─hca::facet_options()
  5.       └─hca:::.hca_openapi()
  6.         └─jsonlite::read_json(api)
  7.           └─jsonlite::parse_json(...)
  8.             └─jsonlite:::parse_and_simplify(...)
  9.               └─jsonlite:::parseJSON(txt, bigint_as_char)
 10.                 └─jsonlite:::parse_con(txt, bigint_as_char)
 11.                   ├─base::open(con, "rb")
 12.                   └─base::open.connection(con, "rb")
── Error ('test_samples.R:2:5'): 'samples()' works with small size and default arguments ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi'
Backtrace:
     ▆
  1. └─hca::samples(size = 4) at test_samples.R:2:5
  2.   └─hca::filters()
  3.     └─hca:::.filters_validate(filters_list)
  4.       └─hca::facet_options()
  5.         └─hca:::.hca_openapi()
  6.           └─jsonlite::read_json(api)
  7.             └─jsonlite::parse_json(...)
  8.               └─jsonlite:::parse_and_simplify(...)
  9.                 └─jsonlite:::parseJSON(txt, bigint_as_char)
 10.                   └─jsonlite:::parse_con(txt, bigint_as_char)
 11.                     ├─base::open(con, "rb")
 12.                     └─base::open.connection(con, "rb")

[ FAIL 12 | WARN 12 | SKIP 1 | PASS 119 ]
Error: Test failures
Execution halted