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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocAzul.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocAzul_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BiocAzul.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-29 22:40:19 UTC
* using option ‘--no-vignettes’
* checking for file ‘BiocAzul/DESCRIPTION’ ... OK
* this is package ‘BiocAzul’ version ‘1.0.1’
* 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 ‘BiocAzul’ 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 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 ‘BiocAzul-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Azul-utils
> ### Title: Obtain a list of projects and their IDs from the specified
> ###   catalog
> ### Aliases: Azul-utils projectTable listCatalogs availableFacets
> ###   facetTable
> 
> ### ** Examples
> 
> hca <- Azul(provider = "hca")
> 
> listCatalogs(hca)
[1] "dcp58"    "dcp58-it" "dcp59"    "dcp59-it" "lm10"     "lm10-it" 
> projectTable(hca, catalog = "dcp58")
# A tibble: 530 × 3
   term                                               count projectId           
   <chr>                                              <int> <chr>               
 1 -Human-10x3pv2--21                                     1 888f1766-4c84-43bb-…
 2 1M Neurons                                             1 74b6d569-3b11-42ef-…
 3 AIDA                                                   1 f0f89c14-7460-4bab-…
 4 AIDA_DataFreeze_v2_JP                                  1 35d5b057-3daf-4ccd-…
 5 AIDA_DataFreeze_v2_TH                                  1 76bc0e97-8cae-43d4-…
 6 ASingle-CellAtlasOfHumanPediatricLiverRevealsAge-R     1 febdaddd-ad3c-4f4a-…
 7 Acellandtranscriptomeatlasofhumanarterialvasculatu     1 2245bca0-6563-4e88-…
 8 AcuteSkinInflammation                                  1 67a3de09-45b9-49c3-…
 9 AdaptiveNKCellsInMultipleMyeloma                       1 2eb4f5f8-42a5-4368-…
10 AdipocyteInsulinSpatial                                1 9f7aa401-70e3-4695-…
# ℹ 520 more rows
> 
> anvil <- Azul(provider = "anvil")
> 
> listCatalogs(anvil)
[1] "anvil13"    "anvil13-it"
> projectTable(anvil, catalog = "anvil13")
# A tibble: 375 × 2
   term                                     count
   <chr>                                    <int>
 1 ANVIL_1000G_PRIMED_data_model                1
 2 ANVIL_1000G_high_coverage_2019               1
 3 ANVIL_ALSCompute_Collection_GRU              1
 4 ANVIL_ALSCompute_Collection_HMB              1
 5 ANVIL_ALS_FTD_ALS_AssociatedGenes_GRU_v1     1
 6 ANVIL_ALS_FTD_DEMENTIA_SEQ_GRU_v1            1
 7 ANVIL_CCDG_Broad_AI_IBD_Brant_HMB_WGS        1
 8 ANVIL_CCDG_Broad_AI_IBD_Cho_WGS              1
 9 ANVIL_CCDG_Broad_AI_IBD_Kugathasan_WGS       1
10 ANVIL_CCDG_Broad_AI_IBD_McCauley_WGS         1
# ℹ 365 more rows
> availableFacets(hca, catalog = "dcp57")
Error in availableFacets(hca, catalog = "dcp57") : 
  Invalid catalog specified. Use 'listCatalogs()' for all catalogs.
Calls: availableFacets -> stopifnot
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/BiocAzul.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocAzul
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘BiocAzul’ ...
** this is package ‘BiocAzul’ version ‘1.0.1’
** 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 (BiocAzul)

R version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("BiocAzul")
Loading required package: AnVIL
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: AnVILBase

test_makeFilter.R.............    1 tests OK 
test_makeFilter.R.............    2 tests OK 
test_makeFilter.R.............    3 tests OK 
test_makeFilter.R.............    4 tests OK 
test_makeFilter.R.............    5 tests OK 
test_makeFilter.R.............    6 tests OK 
test_makeFilter.R.............    7 tests OK 
test_makeFilter.R.............    8 tests OK 
test_makeFilter.R.............    9 tests OK 
test_makeFilter.R.............   10 tests OK 
test_makeFilter.R.............   11 tests OK 
test_makeFilter.R.............   12 tests OK 
test_makeFilter.R.............   13 tests OK 
test_makeFilter.R.............   14 tests OK 
test_makeFilter.R.............   15 tests OK 
test_makeFilter.R.............   16 tests OK 
test_makeFilter.R.............   17 tests OK 
test_makeFilter.R.............   18 tests OK 25ms
All ok, 18 results (26ms)
> 
> proc.time()
   user  system elapsed 
  0.420   0.058   0.476